Contacts of the strand formed by residues 315 - 321 (chain A) in PDB entry 2HVI


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 LYS 315 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313A  ALA*     3.1     7.5    +      -       +      +
    314A  ASP*     1.3    86.3    -      -       -      +
    316A  ALA*     1.3    68.7    +      -       -      +
    339A  ASN*     3.3    16.5    -      -       -      +
    340A  GLU*     4.6     1.0    +      -       -      +
    367A  LYS*     3.3    17.8    +      -       +      +
    369A  SER*     3.7     8.9    +      -       -      +
    391A  SER*     4.0    10.7    +      -       -      -
    455A  TRP*     3.8    25.5    -      -       +      -
    458A  GLU*     3.1    38.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313A  ALA      5.0     0.9    -      -       -      +
    315A  LYS*     1.3    80.4    -      -       -      +
    317A  ALA*     1.3    56.2    +      -       -      +
    337A  VAL*     4.1    17.5    -      -       +      -
    338A  VAL      3.4    13.2    -      -       -      +
    339A  ASN*     3.8    10.3    -      -       +      +
    360A  TRP*     4.1    20.0    -      -       +      -
    367A  LYS      2.9     7.7    +      -       -      +
    368A  LYS*     3.2     5.9    -      -       -      -
    369A  SER*     2.7    33.8    +      -       -      -
    455A  TRP*     3.6     8.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316A  ALA*     1.3    73.4    -      -       -      +
    318A  LEU*     1.3    58.8    +      -       -      +
    319A  VAL      4.3     0.2    -      -       -      -
    336A  ALA      3.8     0.5    -      -       -      +
    337A  VAL*     3.5     6.1    -      -       -      +
    338A  VAL*     2.9    33.6    +      -       +      +
    369A  SER*     3.2    12.8    -      -       -      +
    451A  ALA*     3.2    34.4    -      -       -      +
    454A  ILE*     4.2     6.3    -      -       +      -
    455A  TRP*     3.7    22.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 318 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316A  ALA      3.8     0.6    +      -       -      -
    317A  ALA*     1.3    73.5    -      -       -      +
    319A  VAL*     1.3    74.2    +      -       -      +
    320A  VAL*     3.9    20.2    -      -       +      -
    335A  ILE*     4.2     7.4    -      -       +      -
    336A  ALA      3.6    10.1    -      -       -      +
    337A  VAL*     4.0    15.5    -      -       +      -
    357A  PHE*     4.7     3.6    -      -       +      -
    360A  TRP*     4.3    12.8    -      -       +      -
    361A  LEU*     3.7    24.2    -      -       +      -
    368A  LYS*     4.0    26.0    -      -       +      -
    369A  SER      2.7    11.6    +      -       -      +
    370A  MET*     3.4    48.4    -      -       +      +
    371A  PHE      4.8     0.3    +      -       -      -
    387A  LEU*     4.1     4.9    -      -       +      -
    454A  ILE*     4.5     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 319 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318A  LEU*     1.3    78.7    -      -       -      +
    320A  VAL*     1.3    64.1    +      -       -      +
    321A  GLU*     3.8    25.6    -      -       +      +
    335A  ILE*     3.3    10.2    -      -       -      +
    336A  ALA*     2.9    40.7    +      -       +      +
    370A  MET*     4.8     0.4    -      -       -      -
    447A  LEU*     3.8    24.0    -      -       +      +
    450A  LYS*     4.2     9.9    -      -       +      +
    451A  ALA*     3.7    35.4    -      -       +      +
    454A  ILE*     4.1    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 320 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318A  LEU*     3.9    29.8    +      -       +      -
    319A  VAL*     1.3    76.6    -      -       -      +
    321A  GLU*     1.3    61.0    +      -       -      +
    322A  VAL*     3.5     9.2    +      -       +      +
    332A  ILE*     3.7    38.8    -      -       +      -
    334A  GLY      3.9     3.1    -      -       -      -
    335A  ILE*     4.8     9.6    -      -       +      -
    352A  LEU*     6.4     0.2    -      -       +      -
    357A  PHE*     6.3     0.7    -      -       +      -
    361A  LEU*     5.2     2.9    -      -       +      -
    370A  MET*     4.3     8.7    -      -       +      +
    375A  ARG*     5.4     3.1    -      -       -      +
    376A  ALA*     3.9    23.3    +      -       +      +
    380A  LEU*     4.3    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 321 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  VAL*     3.8     8.0    -      -       +      +
    320A  VAL*     1.3    70.2    -      -       -      +
    322A  VAL*     1.3    63.6    +      -       -      +
    323A  VAL*     4.0     6.7    -      -       +      -
    332A  ILE*     3.3     5.7    -      -       -      -
    333A  VAL*     3.0    45.1    +      -       +      +
    334A  GLY      3.0    19.0    +      -       -      +
    425A  ASP*     4.8     0.3    -      -       -      -
    429A  TYR*     2.4    40.2    +      -       -      +
    447A  LEU*     3.3    22.3    -      -       +      +
    450A  LYS*     2.9    35.7    +      -       -      -
----------------------------------------------------------
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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