Contacts of the helix formed by residues 480 - 499 (chain A) in PDB entry 3SRH


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with ALA 480 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    478A  GLN*     4.2     3.6    -      -       -      +
    479A  GLU*     1.3    77.6    -      -       -      +
    481A  TRP*     1.3    65.2    +      -       -      +
    482A  ALA*     4.6     2.9    -      -       +      +
    483A  GLU*     3.4    25.6    +      -       +      +
    484A  ASP*     3.2    21.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 481 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    430A  LEU*     6.4     0.9    -      -       +      -
    432A  LYS*     4.1    13.5    -      -       -      -
    478A  GLN      5.7     0.4    -      -       -      -
    479A  GLU      3.6     4.4    +      -       -      +
    480A  ALA*     1.3    73.1    -      -       -      +
    482A  ALA*     1.3    65.4    +      -       -      +
    484A  ASP*     3.3    13.4    +      -       +      +
    485A  VAL*     3.1    38.0    +      -       +      +
    488A  ARG*     3.4    28.7    -      -       -      -
    513A  GLY*     3.3    34.2    +      -       -      -
    514A  TRP*     3.4    19.2    +      -       -      +
    515A  ARG*     3.9    14.8    -      -       -      -
    516A  PRO*     3.5    42.0    -      -       +      -
    517A  GLY      4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 482 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    480A  ALA*     3.4     3.0    -      -       +      +
    481A  TRP*     1.3    82.7    -      -       +      +
    483A  GLU*     1.3    70.7    +      -       +      +
    485A  VAL*     3.6     5.9    +      -       -      +
    486A  ASP*     2.9    35.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 483 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    478A  GLN*     3.0    25.6    -      -       +      +
    480A  ALA*     3.4    24.6    +      -       +      +
    481A  TRP      3.2     0.6    -      -       -      -
    482A  ALA*     1.3    87.1    -      -       -      +
    484A  ASP*     1.3    59.8    +      -       -      +
    485A  VAL      3.2     0.4    -      -       -      -
    486A  ASP*     3.5    14.7    +      -       -      +
    487A  LEU*     3.0    24.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 484 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454A  ARG*     2.6    37.1    +      -       -      -
    476A  PRO      4.1     0.7    -      -       -      +
    477A  VAL*     3.7    10.3    -      -       -      +
    478A  GLN*     3.0    38.6    +      -       +      +
    480A  ALA      3.2    11.9    +      -       -      +
    481A  TRP*     3.3    17.9    +      -       +      +
    483A  GLU*     1.3    74.5    -      -       -      +
    485A  VAL*     1.3    65.6    +      -       -      +
    487A  LEU*     3.6     3.0    -      -       -      +
    488A  ARG*     3.1    48.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 485 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    430A  LEU*     4.6     4.0    -      -       +      -
    481A  TRP*     3.1    47.1    +      -       +      +
    482A  ALA*     3.6     9.9    -      -       -      +
    483A  GLU      3.2     0.2    -      -       -      -
    484A  ASP*     1.3    74.0    -      -       -      +
    486A  ASP*     1.3    69.0    +      -       -      +
    488A  ARG*     2.9    18.9    +      -       -      +
    489A  VAL*     2.8    38.5    +      -       +      +
    512A  THR*     3.8    32.3    -      -       +      +
    513A  GLY      5.0     0.4    -      -       -      +
    525A  ARG*     4.8     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 486 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    482A  ALA*     2.9    20.0    +      -       -      +
    483A  GLU*     3.5    17.3    +      -       -      +
    485A  VAL*     1.3    82.6    -      -       -      +
    487A  LEU*     1.3    56.2    +      -       -      +
    489A  VAL*     4.3     7.2    -      -       -      -
    490A  ASN*     2.8    48.2    +      -       -      +
    525A  ARG*     5.2     5.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 487 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454A  ARG*     4.4     9.9    -      -       -      +
    473A  CYS*     5.5     1.6    -      -       -      -
    475A  ASP*     3.6    40.6    -      -       +      +
    476A  PRO*     4.1    10.5    -      -       +      +
    478A  GLN*     3.4    29.6    -      -       +      +
    483A  GLU      3.0    16.4    +      -       -      +
    484A  ASP      3.6     5.8    -      -       -      +
    485A  VAL      3.2     0.2    -      -       -      -
    486A  ASP*     1.3    75.6    -      -       -      +
    488A  ARG*     1.3    58.5    +      -       +      +
    490A  ASN*     4.1     4.5    -      -       -      +
    491A  PHE*     3.2    25.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 488 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    430A  LEU*     3.6    37.6    -      -       +      +
    431A  THR      5.1     4.2    +      -       -      +
    432A  LYS*     4.0    19.0    -      -       -      +
    452A  VAL*     3.8    29.9    +      -       +      +
    453A  THR*     6.0     1.6    -      -       -      +
    454A  ARG*     3.6    37.6    -      -       -      +
    473A  CYS*     4.2    12.1    -      -       -      -
    481A  TRP*     3.4    35.6    -      -       -      -
    484A  ASP*     3.1    32.9    +      -       -      +
    485A  VAL*     2.9    16.3    +      -       -      +
    487A  LEU*     1.3    79.5    -      -       +      +
    489A  VAL*     1.3    64.3    +      -       -      +
    491A  PHE*     3.4     8.5    +      -       -      +
    492A  ALA      3.2    15.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 489 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    428A  ILE*     4.9     7.4    -      -       +      -
    430A  LEU*     3.7    25.6    -      -       +      -
    485A  VAL*     2.8    31.3    +      -       +      +
    486A  ASP*     3.9     7.0    -      -       -      +
    488A  ARG*     1.3    75.4    -      -       -      +
    490A  ASN*     1.3    67.1    +      -       -      +
    492A  ALA*     3.0    18.5    +      -       -      +
    493A  MET*     3.0    26.6    +      -       +      +
    510A  VAL*     4.0    32.3    -      -       +      -
    525A  ARG*     4.5     9.4    -      -       -      +
    527A  VAL*     5.7     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 490 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    486A  ASP*     2.8    34.2    +      -       -      +
    487A  LEU*     4.1     3.9    -      -       -      +
    489A  VAL*     1.3    74.8    -      -       -      +
    491A  PHE*     1.3    63.3    +      -       -      +
    493A  MET*     3.2    10.8    +      -       -      +
    494A  ASN*     3.0    31.6    +      -       -      +
    530A  PRO*     4.2    22.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 491 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  PRO*     3.5    32.8    -      -       +      -
    102A  ILE*     3.7    23.3    -      -       +      -
    452A  VAL*     4.1    18.2    -      -       +      -
    471A  VAL*     3.8    31.9    -      -       +      -
    472A  LEU      3.6    25.8    -      -       -      -
    473A  CYS*     4.2    11.0    -      -       +      -
    475A  ASP*     4.9    13.5    -      -       -      +
    487A  LEU*     3.2    19.5    +      -       +      +
    488A  ARG*     3.5     4.7    -      -       -      +
    489A  VAL      3.2     0.2    -      -       -      -
    490A  ASN*     1.3    76.4    -      -       -      +
    492A  ALA*     1.3    57.0    +      -       -      +
    494A  ASN*     3.1    11.0    +      -       -      +
    495A  VAL*     3.1    34.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 492 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    428A  ILE*     3.8    22.7    -      -       +      -
    450A  ILE*     4.0    14.8    -      -       +      +
    452A  VAL*     3.6    27.8    -      -       +      -
    488A  ARG      3.2     2.9    +      -       -      +
    489A  VAL      3.0    10.4    +      -       -      +
    491A  PHE*     1.3    76.8    -      -       -      +
    493A  MET*     1.3    65.8    +      -       -      +
    495A  VAL*     3.1    11.6    +      -       -      +
    496A  GLY      3.1    18.9    +      -       -      -
    502A  PHE*     3.9     6.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 493 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    428A  ILE*     3.5    22.0    -      -       +      -
    489A  VAL*     3.0    23.0    +      -       +      +
    490A  ASN*     3.2    17.0    +      -       -      +
    492A  ALA*     1.3    75.7    -      -       -      +
    494A  ASN*     1.3    59.8    +      -       -      +
    497A  LYS*     3.2    41.8    +      -       -      +
    502A  PHE*     3.4    36.7    -      -       +      -
    508A  VAL*     3.6    18.8    -      -       +      -
    527A  VAL*     5.0     4.3    -      -       -      -
    528A  PRO      4.7     1.6    -      -       -      +
    529A  VAL*     3.7     8.1    -      -       +      -
    530A  PRO*     3.4    37.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 494 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  ILE*     3.8    25.1    -      -       +      +
    490A  ASN*     3.0    21.5    +      -       -      +
    491A  PHE*     3.1    12.1    +      -       -      +
    493A  MET*     1.3    77.1    -      -       -      +
    495A  VAL*     1.3    62.6    +      -       -      +
    497A  LYS*     3.8    23.0    +      -       -      +
    498A  ALA*     3.3    24.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 495 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  ILE*     4.1    20.0    -      -       +      +
    450A  ILE*     4.9     5.8    -      -       +      -
    469A  PHE*     4.2    12.6    -      -       +      -
    471A  VAL*     3.8    33.4    -      -       +      -
    491A  PHE*     3.1    32.1    +      -       +      +
    492A  ALA*     3.1    10.9    +      -       -      +
    494A  ASN*     1.3    76.1    -      -       -      +
    496A  GLY*     1.3    67.1    +      -       -      +
    498A  ALA*     3.2     4.2    +      -       -      -
    499A  ARG*     2.9    44.2    +      -       +      +
    501A  PHE*     5.3     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 496 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    450A  ILE*     4.4     1.9    -      -       -      +
    492A  ALA      3.1    10.5    +      -       -      -
    493A  MET      3.6     0.2    +      -       -      -
    495A  VAL*     1.3    77.3    -      -       -      +
    497A  LYS*     1.3    56.1    +      -       -      +
    499A  ARG      3.6     0.2    -      -       -      -
    500A  GLY*     2.9     8.5    +      -       -      -
    501A  PHE*     2.8    43.6    +      -       -      -
    502A  PHE*     3.4    32.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 497 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    493A  MET*     3.2    25.3    +      -       -      +
    494A  ASN*     3.8    22.1    +      -       -      +
    496A  GLY*     1.3    74.2    -      -       -      +
    498A  ALA*     1.3    63.6    +      -       -      +
    500A  GLY*     3.2    11.8    +      -       -      -
    502A  PHE*     3.4    24.0    -      -       +      +
    503A  LYS*     4.5     5.2    -      -       -      -
    504A  LYS*     4.7     8.1    -      -       +      +
    529A  VAL*     4.1     9.9    -      -       +      -
    530A  PRO*     2.9    32.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 498 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  ILE*     3.7    20.4    -      -       +      -
    103A  LEU*     4.2    17.1    -      -       +      +
    494A  ASN      3.3    18.8    +      -       -      +
    495A  VAL      3.2     4.5    +      -       -      +
    497A  LYS*     1.3    79.5    -      -       -      +
    499A  ARG*     1.3    60.8    +      -       +      +
    500A  GLY      3.3     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 499 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  THR*     3.7    11.3    +      -       -      -
    102A  ILE      3.6     8.5    +      -       -      +
    103A  LEU*     3.1    58.7    +      -       +      +
    104A  TYR      4.5     2.8    +      -       -      -
    105A  ARG*     3.4    45.4    -      -       -      +
    469A  PHE*     3.5    31.7    -      -       -      -
    495A  VAL*     2.9    26.9    +      -       +      +
    496A  GLY      4.3     0.4    -      -       -      +
    498A  ALA*     1.3    81.2    -      -       +      +
    500A  GLY*     1.3    62.1    +      -       -      +
    501A  PHE*     3.3    27.6    +      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il