Contacts of the strand formed by residues 483 - 495 (chain A) in PDB entry 4Z2A


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 ARG 483 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    481A  ILE*     3.6     2.7    -      -       -      -
    482A  THR*     1.3    91.8    -      -       -      +
    484A  LEU*     1.3    66.6    +      -       -      +
    485A  GLU*     4.6     1.7    -      -       -      +
    540A  ASP*     4.6    17.3    -      -       -      +
    541A  GLU      3.6     2.5    -      -       -      -
    572A  GLY*     3.3     2.1    -      -       -      -
    573A  THR*     3.0    45.5    +      -       -      +
    574A  ALA      4.6     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 484 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    395A  HIS*     5.5     0.2    -      -       -      -
    481A  ILE*     4.0     3.6    -      -       +      +
    483A  ARG*     1.3    74.5    -      -       -      +
    485A  GLU*     1.3    70.9    +      -       -      +
    486A  HIS      3.6     9.6    -      -       -      +
    487A  ALA*     4.1    15.5    -      -       +      -
    538A  SER*     3.7    36.8    -      -       -      +
    539A  TRP*     4.3     0.7    -      -       -      -
    540A  ASP*     2.7    29.8    +      -       -      +
    541A  GLU*     2.8    22.6    +      -       +      +
    543A  PRO*     4.1    13.5    -      -       +      -
    547A  TRP*     4.1    14.6    -      -       +      -
    570A  LEU*     3.7    31.4    -      -       +      -
    571A  TYR      3.3    15.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 485 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391A  ARG*     2.8    49.2    +      -       -      +
    395A  HIS*     2.8    36.9    +      -       +      +
    447A  GLN*     4.4     4.9    +      -       -      +
    483A  ARG      4.6     1.6    -      -       -      +
    484A  LEU*     1.3    86.2    -      -       -      +
    486A  HIS*     1.3    71.9    +      -       -      +
    487A  ALA      3.9     0.2    +      -       -      -
    535A  THR      4.4     3.5    -      -       -      +
    536A  THR*     4.9     0.2    -      -       -      -
    539A  TRP*     3.5    48.5    +      -       +      -
    571A  TYR*     2.7    14.0    +      -       -      +
    572A  GLY*     3.9    13.3    +      -       -      -
    573A  THR*     4.0     8.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 486 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    312A  ILE*     3.5    55.9    +      -       +      +
    390A  TRP*     4.6    10.5    -      +       -      -
    391A  ARG*     5.2     1.8    -      -       +      -
    394A  GLN*     2.8    30.2    +      -       -      -
    447A  GLN*     5.1     1.0    +      -       -      -
    484A  LEU*     3.6     4.0    -      -       -      +
    485A  GLU*     1.3    89.5    +      -       +      +
    487A  ALA*     1.3    60.8    +      -       -      +
    534A  MET*     4.0    21.1    -      -       +      -
    535A  THR      3.8     5.4    -      -       -      -
    536A  THR*     4.7     3.4    -      -       +      -
    539A  TRP*     3.5    22.8    -      +       -      -
    571A  TYR*     3.0    41.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 487 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    484A  LEU*     4.1    19.7    -      -       +      -
    486A  HIS*     1.3    73.9    -      -       -      +
    488A  GLN*     1.3    65.9    +      -       -      +
    505A  LEU*     5.1     1.3    -      -       +      -
    534A  MET*     3.4     4.5    -      -       -      +
    535A  THR*     2.9    49.9    +      -       +      +
    538A  SER*     5.8     0.4    -      -       -      -
    547A  TRP*     4.4    10.5    -      -       +      -
    568A  LEU*     5.0     1.6    -      -       +      -
    569A  VAL      3.3     9.6    -      -       -      +
    570A  LEU*     4.3    10.8    -      -       +      -
    571A  TYR*     4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 488 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310A  ASN      5.3     1.6    +      -       -      -
    311A  SER*     5.9     1.2    -      -       -      +
    312A  ILE*     4.2    15.9    -      -       -      +
    487A  ALA*     1.3    78.4    -      -       -      +
    489A  ALA*     1.3    61.4    +      -       -      +
    490A  ARG*     3.9     9.8    +      -       +      +
    505A  LEU*     5.3     1.8    -      -       -      -
    532A  ALA*     3.9    27.2    +      -       +      +
    533A  PHE      3.2     6.7    -      -       -      +
    534A  MET*     4.1    18.7    -      -       +      +
    568A  LEU*     3.5    10.7    -      -       -      +
    569A  VAL*     2.8    50.2    +      -       +      +
    571A  TYR*     3.0    35.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 489 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488A  GLN*     1.3    73.8    -      -       -      +
    490A  ARG*     1.3    61.9    +      -       -      +
    491A  LEU*     3.5     7.1    +      -       +      -
    505A  LEU*     4.4    10.2    -      -       +      +
    515A  LEU*     3.7    27.6    -      -       +      -
    531A  TRP      3.2     3.3    -      -       -      +
    532A  ALA*     4.4     0.2    -      -       -      -
    533A  PHE*     2.9    34.9    +      -       -      -
    549A  LEU*     4.8     1.6    -      -       +      -
    566A  PHE*     3.8    22.2    -      -       +      -
    567A  THR      3.5     5.4    -      -       -      -
    568A  LEU*     5.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 490 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488A  GLN*     4.6    11.1    +      -       +      +
    489A  ALA*     1.3    69.6    -      -       -      +
    491A  LEU*     1.3    61.1    +      -       -      +
    530A  ASP*     3.0    54.1    +      -       -      +
    531A  TRP      3.3     7.0    -      -       -      +
    532A  ALA*     3.7    29.0    -      -       +      +
    565A  LYS*     3.5     3.6    -      -       -      +
    566A  PHE*     3.5     3.6    -      -       -      -
    567A  THR*     2.8    46.8    +      -       -      +
    569A  VAL*     4.1    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 491 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    489A  ALA*     3.8    14.4    -      -       +      +
    490A  ARG*     1.3    76.0    -      -       -      +
    492A  THR*     1.3    62.8    +      -       -      +
    493A  LEU*     4.1    11.9    -      -       +      -
    503A  ILE*     4.0    31.4    -      -       +      -
    515A  LEU*     4.9     0.2    -      -       +      -
    528A  PHE*     3.7     9.1    -      -       +      +
    530A  ASP      3.2     2.4    +      -       -      -
    531A  TRP      3.0    28.7    +      -       -      +
    533A  PHE*     3.7    27.8    -      -       +      -
    549A  LEU*     3.9    19.1    -      -       +      -
    551A  ILE*     4.9     2.0    -      -       +      -
    563A  LEU*     4.3     7.6    -      -       +      -
    565A  LYS      3.4     2.0    -      -       -      +
    566A  PHE*     3.6    39.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 492 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    490A  ARG      5.2     0.2    +      -       -      -
    491A  LEU*     1.3    70.9    -      -       -      +
    493A  LEU*     1.3    67.1    +      -       -      +
    528A  PHE      3.3     9.9    -      -       -      +
    529A  ASN*     4.3    10.0    +      -       -      +
    530A  ASP*     3.0    27.3    +      -       -      +
    563A  LEU*     3.4     3.7    -      -       -      +
    564A  THR*     2.8    42.1    +      -       -      +
    565A  LYS*     2.9    33.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 493 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461A  ILE*     4.2     6.1    -      -       +      -
    491A  LEU*     4.6     9.2    -      -       +      -
    492A  THR*     1.3    78.1    -      -       -      +
    494A  SER*     1.3    73.9    +      -       -      +
    495A  TYR*     4.0     2.5    -      -       +      +
    501A  LEU*     3.9    24.7    -      -       +      -
    503A  ILE*     4.3    14.8    -      -       +      -
    526A  ASP      4.5     1.4    -      -       -      +
    527A  GLY*     3.4     4.5    -      -       -      -
    528A  PHE*     3.0    59.4    +      -       +      +
    551A  ILE*     4.2    22.9    -      -       +      -
    562A  THR      3.1    14.1    -      -       -      +
    563A  LEU*     3.9    13.0    -      -       +      -
    564A  THR*     4.4     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 494 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461A  ILE*     3.9     1.0    -      -       -      +
    493A  LEU*     1.3    80.4    -      -       -      +
    495A  TYR*     1.3    65.4    +      -       -      +
    525A  ALA      5.8     1.1    -      -       -      -
    526A  ASP      5.6     0.9    -      -       -      -
    527A  GLY*     4.5     2.9    -      -       -      +
    561A  GLY*     3.2     5.6    -      -       -      -
    562A  THR*     2.9    47.7    +      -       -      +
    564A  THR*     5.6     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 495 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461A  ILE*     3.7    22.6    -      -       +      +
    462A  GLY      2.8    19.9    +      -       -      -
    493A  LEU*     4.0     4.4    -      -       +      +
    494A  SER*     1.3    78.4    -      -       -      +
    496A  ASN*     1.3    67.9    +      -       -      +
    497A  ARG      3.4    26.6    +      -       -      +
    498A  ARG*     4.8     2.6    +      -       -      -
    500A  ASP*     4.8     2.9    -      -       +      -
    501A  LEU*     3.5    41.2    -      -       +      +
    524A  SER      4.3     1.6    -      -       -      +
    525A  ALA*     3.6    23.3    +      -       -      +
    527A  GLY*     4.4     7.5    +      -       -      -
    553A  ASN*     3.3    12.0    -      -       -      +
    559A  ASN*     3.0    37.7    -      -       +      +
    560A  TYR*     3.3    28.9    -      -       -      -
    561A  GLY*     3.7     4.0    -      -       -      -
----------------------------------------------------------
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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