Contacts of the strand formed by residues 356 - 367 (chain A) in PDB entry 4H3T


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 LEU 356 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  GLY*     5.8     1.7    -      -       -      -
    205A  GLN*     5.7     0.7    -      -       -      +
    354A  ILE*     3.6     9.0    -      -       -      +
    355A  ALA*     1.4    86.5    -      -       +      +
    357A  VAL*     1.3    71.9    +      -       -      +
    382A  ASP*     4.7     4.9    -      -       +      +
    383A  THR      3.5    11.7    -      -       -      +
    384A  PRO*     3.8    24.5    -      -       +      -
    385A  LEU*     4.2     2.2    -      -       -      -
    469A  THR*     3.9    44.4    -      -       +      +
    472A  ALA*     4.3     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 357 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  PRO*     4.1    10.3    -      -       +      -
    203A  VAL      3.8     7.2    -      -       -      +
    204A  GLY*     5.4     1.3    -      -       -      -
    213A  LEU*     3.9    27.1    -      -       +      -
    346A  VAL*     4.3    15.7    -      -       +      -
    354A  ILE*     4.1     7.0    -      -       +      -
    356A  LEU*     1.3    80.2    -      -       -      +
    358A  SER*     1.3    60.1    +      -       -      +
    359A  LEU*     3.8    25.7    +      -       +      -
    381A  LEU      3.7     0.3    -      -       -      +
    382A  ASP*     3.7     3.2    -      -       -      -
    383A  THR*     2.8    36.7    +      -       -      +
    385A  LEU*     4.1    18.2    -      -       +      -
    388A  LEU*     4.9     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 358 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  VAL*     2.7    47.2    +      -       -      +
    204A  GLY      5.7     0.4    -      -       -      -
    357A  VAL*     1.3    72.3    -      -       -      +
    359A  LEU*     1.3    60.3    +      -       -      +
    360A  LEU      3.5     0.5    +      -       -      -
    380A  ARG*     2.3    52.6    +      -       -      +
    381A  LEU      3.6     6.0    +      -       -      -
    382A  ASP*     3.4    19.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 359 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  VAL*     4.3    10.3    -      -       +      -
    201A  ALA      3.5     2.2    -      -       -      +
    202A  PRO*     3.9    14.8    -      -       +      -
    327A  LEU*     6.3     0.2    -      -       +      -
    330A  VAL*     3.8    28.7    -      -       +      -
    343A  LEU*     3.6    30.3    -      -       +      -
    357A  VAL*     3.8    21.8    -      -       +      -
    358A  SER*     1.3    70.8    +      -       -      +
    360A  LEU*     1.3    61.0    +      -       -      +
    361A  VAL*     3.7     8.6    +      -       +      +
    379A  ASP      3.7     0.3    -      -       -      +
    380A  ARG*     3.2     5.3    -      -       -      -
    381A  LEU*     2.9    40.0    +      -       +      +
    383A  THR*     3.6    33.2    -      -       +      +
    388A  LEU*     5.0     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 360 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  GLU*     3.7    41.7    -      -       +      +
     51A  PRO*     4.8     4.3    -      -       +      -
     54A  LEU*     5.4     5.4    -      -       +      -
    199A  PHE*     3.8    24.1    -      -       +      +
    200A  VAL*     3.3     5.7    -      -       -      -
    201A  ALA*     2.8    34.6    +      -       +      +
    203A  VAL*     4.2     8.3    -      -       +      -
    358A  SER      3.5     1.6    +      -       -      -
    359A  LEU*     1.3    71.6    -      -       -      +
    361A  VAL*     1.3    59.0    +      -       -      +
    362A  THR*     4.4     7.6    -      -       +      -
    378A  TYR*     3.8    28.0    -      -       +      -
    379A  ASP      3.5    15.9    -      -       -      +
    380A  ARG*     3.6    21.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 361 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199A  PHE      3.3     8.1    -      -       -      +
    200A  VAL*     4.1    19.1    -      -       +      -
    317A  ALA*     3.2    36.3    -      -       +      -
    323A  VAL*     4.1    24.5    -      -       +      -
    330A  VAL*     4.8    12.1    -      -       +      -
    359A  LEU*     4.1    12.3    -      -       +      +
    360A  LEU*     1.3    78.4    -      -       -      +
    362A  THR*     1.3    68.5    +      -       -      +
    377A  ALA*     5.9     0.4    -      -       +      -
    378A  TYR*     3.3     4.9    +      -       -      -
    379A  ASP*     2.8    39.3    +      -       +      +
    381A  LEU*     5.9     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 362 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  PRO*     4.6     6.1    -      -       +      +
     48A  THR*     6.3     0.7    -      -       -      -
     51A  PRO*     3.8    28.5    -      -       +      +
    167A  PHE*     4.6    13.2    -      -       +      -
    194A  LEU      5.4     1.7    +      -       -      -
    197A  ILE      4.2     0.6    -      -       -      +
    198A  GLY*     3.7     1.2    -      -       -      -
    199A  PHE*     2.9    53.4    +      -       +      +
    317A  ALA*     5.1     0.3    -      -       -      +
    360A  LEU*     4.4     7.9    -      -       +      -
    361A  VAL*     1.3    84.8    -      -       -      +
    363A  SER*     1.4    63.7    +      -       -      +
    376A  LEU*     5.6     4.3    -      -       -      -
    377A  ALA      3.2    11.7    -      -       -      +
    378A  TYR*     4.3    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 363 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  PHE*     6.2     2.2    -      -       -      -
    194A  LEU      5.8     0.9    -      -       -      -
    197A  ILE      4.5     7.0    -      -       -      -
    198A  GLY*     4.5     5.6    -      -       -      -
    316A  ARG*     4.4    16.3    -      -       -      +
    317A  ALA      2.6    37.5    +      -       -      -
    319A  PRO*     4.3     5.2    -      -       -      +
    362A  THR*     1.4    76.9    -      -       -      +
    364A  ALA*     1.3    60.1    +      -       -      +
    376A  LEU*     3.5     8.0    -      -       -      +
    377A  ALA*     2.8    40.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 364 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  PHE*     5.4     4.9    -      -       +      -
    195A  ALA*     3.8    24.8    +      -       +      +
    197A  ILE      5.1     0.6    +      -       -      -
    316A  ARG*     4.8    12.2    +      -       -      +
    319A  PRO*     5.5     2.2    -      -       -      -
    363A  SER*     1.3    79.4    -      -       -      +
    365A  LYS*     1.3    62.0    +      -       -      +
    366A  PHE*     3.8    17.5    -      -       +      -
    373A  LEU*     3.7    21.5    -      -       +      -
    375A  ASP      3.5     5.8    -      -       -      +
    376A  LEU*     4.1     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 365 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  PRO*     4.8    21.2    -      -       +      +
    364A  ALA*     1.3    73.9    -      -       -      +
    366A  PHE*     1.3    64.0    +      -       -      +
    373A  LEU*     3.6     3.8    -      -       -      +
    374A  ASP*     2.7    37.0    +      -       +      +
    375A  ASP*     2.9    33.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 366 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  PHE*     4.5     8.7    -      +       -      -
    168A  GLY      4.6     0.7    -      -       -      -
    169A  SER*     3.9    20.2    -      -       -      -
    191A  ILE*     4.0    23.3    -      -       +      -
    195A  ALA*     3.6    35.7    -      -       +      -
    364A  ALA*     3.8    17.0    -      -       +      -
    365A  LYS*     1.3    83.5    -      -       -      +
    367A  GLY*     1.3    58.0    +      -       -      +
    370A  SER*     3.8    33.6    +      -       -      +
    372A  THR      3.1    20.6    -      -       -      +
    373A  LEU*     3.8    26.0    -      -       +      -
    374A  ASP*     4.2     4.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 367 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366A  PHE*     1.3    73.8    -      -       -      +
    368A  ASN*     1.3    70.4    +      -       -      -
    369A  MSE      3.4     2.0    -      -       -      -
    370A  SER      3.2     3.0    +      -       -      -
    371A  THR      3.1     5.9    +      -       -      -
    372A  THR*     2.7    35.2    +      -       -      -
    374A  ASP*     3.5    18.5    -      -       -      -
----------------------------------------------------------
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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