Contacts of the strand formed by residues 318 - 322 (chain C) in PDB entry 2VKM


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 ASP 318 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159C  PHE*     6.0     2.4    -      -       -      +
    160C  PRO*     5.9     3.1    -      -       -      +
    269C  CYS*     3.5     1.2    -      -       -      -
    270C  TRP*     2.9    29.7    +      -       -      +
    271C  GLN      5.2     0.2    -      -       -      +
    272C  ALA*     4.2     2.1    -      -       -      +
    273C  GLY*     2.8    33.8    +      -       -      +
    275C  THR*     3.8     9.4    +      -       -      +
    316C  GLN      3.9     3.7    +      -       -      +
    317C  ASP*     1.3    77.8    -      -       -      +
    319C  CYS*     1.3    60.8    +      -       -      +
    320C  TYR*     3.5    30.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 319 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160C  PRO*     5.5     3.2    -      -       -      +
    267C  LEU*     3.9    11.2    -      -       +      -
    268C  VAL      3.2     3.8    -      -       -      +
    269C  CYS*     2.5    44.2    -      -       -      -
    308C  PRO*     3.4     3.5    -      -       -      +
    309C  VAL*     2.9    37.9    +      -       -      +
    311C  ASP*     3.5    35.2    -      -       -      +
    317C  ASP*     3.8     3.9    +      -       -      -
    318C  ASP*     1.3    75.1    -      -       -      +
    320C  TYR*     1.3    71.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 320 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158C  GLY*     4.0    19.6    +      -       -      -
    159C  PHE*     5.8     0.2    -      -       -      -
    261C  PHE*     4.5     3.3    -      -       +      -
    267C  LEU*     3.1     6.2    -      -       -      +
    268C  VAL*     2.8    32.7    +      -       +      +
    270C  TRP*     3.8    19.1    -      +       +      -
    275C  THR*     2.9    34.6    +      -       +      -
    277C  TRP*     3.3    30.3    -      +       -      -
    306C  LEU*     3.5    36.6    -      -       +      -
    307C  ARG      3.0    10.8    -      -       -      +
    308C  PRO*     3.7    11.7    -      -       +      -
    309C  VAL*     4.1     2.5    -      -       -      -
    318C  ASP*     3.5    30.8    +      -       +      +
    319C  CYS*     1.3    81.1    -      -       -      +
    321C  LYS*     1.3    63.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 321 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261C  PHE*     4.4     3.4    -      -       -      -
    264C  GLY*     4.0    21.4    +      -       -      +
    265C  GLU      4.4    13.8    +      -       -      -
    266C  GLN*     4.7     2.9    -      -       -      +
    267C  LEU*     3.9    28.3    -      -       +      +
    306C  LEU*     3.4     4.2    -      -       -      -
    307C  ARG*     2.9    37.7    +      -       +      +
    309C  VAL*     4.1    20.0    -      -       +      +
    320C  TYR*     1.3    77.4    -      -       -      +
    322C  PHE*     1.3    66.3    +      -       -      +
    323C  ALA*     3.3     1.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 322 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233C  ASN*     4.7     3.6    +      -       -      -
    245C  VAL*     4.1    15.5    -      -       +      -
    248C  ILE*     4.1    14.1    -      -       +      -
    261C  PHE*     3.4    41.5    +      +       +      +
    262C  TRP*     3.4    55.0    -      +       -      -
    264C  GLY*     3.8    16.5    -      -       -      -
    280C  PHE*     6.2     0.4    -      +       -      -
    305C  TYR*     3.9    24.7    -      +       -      -
    306C  LEU*     4.1    17.0    -      -       +      -
    321C  LYS*     1.3    73.0    -      -       -      +
    323C  ALA*     1.3    59.7    +      -       -      +
    324C  ILE*     3.4    48.0    +      -       +      +
    325C  SER*     5.8     0.3    -      -       -      -
----------------------------------------------------------
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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