Contacts of the strand formed by residues 312 - 317 (chain A) in PDB entry 4HXG


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 312 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275A  TYR*     3.7    40.4    -      -       +      +
    286A  LEU*     3.9    17.3    -      -       +      -
    296A  ILE*     3.6    36.6    -      -       +      -
    306A  PHE*     4.7     6.1    -      -       +      -
    307A  ASP      3.7    11.7    -      -       -      +
    308A  ALA*     3.7     8.3    -      -       +      -
    311A  ARG*     1.3    75.2    -      -       -      +
    313A  ILE*     1.3    70.2    +      -       -      +
    314A  TYR*     4.3     3.3    -      -       +      -
    327A  LEU*     3.1    21.6    -      -       -      +
    328A  TRP*     3.1    31.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 313 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PRO*     3.5    30.3    -      -       +      -
     21A  ARG      3.9    12.8    -      -       -      +
     22A  THR*     4.3     8.3    -      -       -      +
     27A  VAL*     3.4    48.5    -      -       +      -
     50A  LEU*     5.0     0.7    -      -       +      -
    306A  PHE*     3.2     4.9    -      -       -      +
    307A  ASP      3.0    39.1    +      -       -      +
    311A  ARG*     4.8     2.7    -      -       +      -
    312A  LEU*     1.3    81.5    -      -       -      +
    314A  TYR*     1.3    63.4    +      -       -      +
    325A  LEU*     4.1     7.9    -      -       +      -
    326A  TYR      3.2    11.9    -      -       -      +
    327A  LEU*     4.2    11.7    -      -       +      -
    335A  LEU*     4.6     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 314 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PRO*     5.1     0.7    -      -       -      -
    286A  LEU*     3.5    22.4    -      -       +      -
    296A  ILE*     4.7     0.7    -      -       +      -
    297A  ALA*     4.0    18.2    -      -       +      +
    303A  ILE*     3.8    27.8    -      -       +      -
    305A  GLY      3.1    14.6    -      -       -      +
    306A  PHE*     3.6    10.3    -      -       +      +
    312A  LEU*     4.3     2.9    -      -       +      -
    313A  ILE*     1.3    82.9    -      -       -      +
    315A  LEU*     1.3    62.3    +      -       -      +
    316A  LYS*     4.6     1.6    -      -       +      -
    325A  LEU*     3.4     7.8    -      -       -      +
    326A  TYR*     2.7    60.5    +      +       +      +
    327A  LEU      4.3     2.1    +      -       -      -
    328A  TRP*     4.2    25.4    -      -       +      +
    332A  GLU*     2.7    42.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 315 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  LEU*     3.7    37.0    -      -       +      +
     18A  SER*     3.8    10.1    -      -       -      -
     19A  ASP      4.3     0.2    -      -       -      +
     20A  PRO*     3.7    31.9    -      -       +      -
     29A  TYR*     5.4     4.0    -      -       +      -
    303A  ILE*     3.4     8.5    -      -       -      +
    304A  MET*     2.9    35.0    +      -       +      -
    305A  GLY*     2.8    16.7    +      -       -      +
    314A  TYR*     1.3    73.5    -      -       -      +
    316A  LYS*     1.3    59.3    +      -       -      +
    317A  GLU      4.2     0.2    -      -       -      -
    323A  ALA*     4.1    12.3    -      -       +      -
    324A  GLU      3.3     7.4    -      -       -      +
    325A  LEU*     3.3    36.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  HIS*     3.5    41.2    +      -       +      +
    302A  TRP      3.6     2.5    -      -       -      +
    303A  ILE*     4.0    10.3    -      -       +      -
    314A  TYR*     4.5     3.4    -      -       +      -
    315A  LEU*     1.3    73.0    -      -       -      +
    317A  GLU*     1.3    62.5    +      -       -      +
    318A  THR*     4.1    17.9    -      -       +      +
    322A  PRO      4.3     1.2    -      -       -      +
    323A  ALA*     3.2     2.7    -      -       -      -
    324A  GLU*     2.9    30.5    +      -       -      +
    326A  TYR*     3.4    38.4    +      -       +      +
    332A  GLU*     2.9    39.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  HIS*     3.3     6.2    -      -       -      +
    302A  TRP*     2.8    34.6    +      -       +      +
    304A  MET*     3.7    37.6    -      -       +      +
    315A  LEU      4.2     0.4    -      -       -      -
    316A  LYS*     1.3    73.0    -      -       -      +
    318A  THR*     1.3    67.3    +      -       -      +
    321A  ARG      3.3    17.0    -      -       -      +
    322A  PRO*     4.6     1.5    -      -       -      +
    323A  ALA*     3.9    20.0    +      -       -      +
    394A  TYR      4.4     0.4    -      -       -      -
    395A  TYR*     3.6    10.0    -      -       -      +
    396A  PHE*     2.8    35.0    +      -       +      +
----------------------------------------------------------
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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