Contacts of the strand formed by residues 425 - 430 (chain A) in PDB entry 1HNY


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 GLY 425 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397A  PHE*     4.0     7.4    -      -       -      -
    401A  VAL*     3.8    13.9    -      -       -      +
    420A  GLY*     3.2     3.1    -      -       -      -
    421A  ARG      2.9    29.3    +      -       -      -
    424A  ARG*     1.3    80.8    -      -       -      +
    426A  PHE*     1.3    61.9    -      -       -      +
    444A  LEU*     3.6    12.5    -      -       -      +
    490A  ILE      3.2    13.0    -      -       -      -
    491A  HIS*     4.0     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 426 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397A  PHE*     3.7     5.2    -      -       -      -
    408A  ASN*     3.9    11.4    -      -       +      -
    410A  TYR*     6.0     0.7    -      -       +      -
    418A  ALA*     3.7    18.2    -      -       +      -
    419A  PHE      3.4    22.9    -      -       -      -
    420A  GLY*     3.6     8.5    -      -       -      -
    425A  GLY*     1.3    73.6    -      -       -      +
    427A  ILE*     1.3    61.6    +      -       -      +
    428A  VAL*     3.5    28.9    -      -       +      -
    440A  LEU*     4.1     8.5    -      -       +      -
    441A  GLN      3.4    25.8    -      -       -      -
    442A  THR*     3.3    35.7    -      -       +      -
    444A  LEU*     3.9    20.6    -      -       +      +
    477A  PHE*     3.8    13.9    -      +       -      -
    488A  ILE      4.8     0.2    -      -       -      -
    489A  ALA*     3.5     2.3    -      -       -      -
    490A  ILE*     3.0    33.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 427 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326A  GLY      4.0     4.7    -      -       -      +
    330A  ALA*     4.0     5.4    -      -       +      -
    394A  MET*     3.6    32.8    -      -       +      -
    397A  PHE*     4.5     4.9    -      -       +      -
    418A  ALA*     3.1     6.2    -      -       -      +
    419A  PHE*     3.0    74.3    +      -       +      +
    426A  PHE*     1.3    77.2    -      -       -      +
    428A  VAL*     1.3    70.0    +      -       -      +
    429A  PHE*     3.4    33.2    -      -       +      -
    487A  PHE*     4.2     7.6    -      -       +      -
    488A  ILE      3.3    13.9    -      -       -      +
    489A  ALA*     3.9    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 428 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    417A  VAL      3.6     7.9    -      -       -      +
    418A  ALA*     4.0     4.9    -      -       +      -
    426A  PHE*     3.5    26.5    -      -       +      -
    427A  ILE*     1.3    82.1    -      -       -      +
    429A  PHE*     1.3    66.0    +      -       -      +
    436A  PHE*     3.7    35.4    -      -       +      -
    440A  LEU*     4.4     0.4    -      -       +      -
    477A  PHE*     3.7    28.3    -      -       +      -
    479A  ILE*     3.7    17.0    -      -       +      +
    487A  PHE*     3.1     7.8    -      -       -      +
    488A  ILE      2.8    34.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 429 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266A  ILE*     6.3     0.4    -      -       +      -
    274A  MET*     3.7    32.1    -      -       +      -
    323A  MET*     3.6    35.2    -      -       +      -
    327A  PHE*     3.8    34.5    -      +       +      -
    415A  ASN      4.2     0.2    -      -       -      -
    416A  GLN*     3.2     5.7    -      -       -      +
    417A  VAL*     2.7    45.9    +      -       +      +
    418A  ALA*     5.2     0.2    -      -       -      -
    419A  PHE*     4.2     3.4    -      +       -      -
    427A  ILE*     3.4    44.6    -      -       +      -
    428A  VAL*     1.3    79.7    -      -       -      +
    430A  ASN*     1.3    62.6    +      -       -      +
    431A  ASN      4.0     0.4    -      -       -      -
    436A  PHE*     5.1     2.1    -      -       -      -
    479A  ILE*     4.9     0.4    -      -       -      -
    486A  PRO      3.7     2.7    -      -       -      +
    487A  PHE*     3.6    28.0    -      +       +      -
----------------------------------------------------------
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Residues in contact with ASN 430 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  MET*     5.0     1.1    -      -       -      -
    415A  ASN      3.9     0.9    -      -       -      -
    416A  GLN*     3.1    22.1    +      -       -      +
    429A  PHE*     1.3    76.2    -      -       -      +
    431A  ASN*     1.3    58.0    +      -       -      +
    432A  ASP      3.0    18.9    +      -       -      +
    434A  TRP      2.9    23.1    +      -       -      +
    435A  SER*     3.7     0.8    -      -       -      +
    436A  PHE*     3.4    15.8    -      -       +      +
    479A  ILE*     3.1    41.5    +      -       +      +
    481A  ASN*     3.9    11.8    -      -       -      +
    486A  PRO*     2.9    35.2    +      -       -      +
----------------------------------------------------------
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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