Contacts of the strand formed by residues 13 - 20 (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 GLY 13 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7C  ARG      3.9     0.2    -      -       -      +
      8C  GLY*     3.2    23.0    -      -       -      -
      9C  LYS      3.3     6.1    +      -       -      -
     12C  GLN*     1.3    81.2    -      -       -      +
     14C  TYR*     1.3    64.3    +      -       -      -
     15C  TYR*     4.0     7.6    -      -       -      -
     30C  LEU*     3.7    18.2    -      -       -      -
    113C  SER      5.2     0.7    -      -       -      +
    115C  TRP*     4.8     1.2    -      -       -      -
   1386C  BSD      3.2    20.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 14 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  LEU*     4.6     6.7    -      -       +      -
      7C  ARG      3.3    10.5    -      -       -      +
      8C  GLY      4.1     5.6    -      -       -      -
      9C  LYS      3.9    17.7    -      -       -      -
     10C  SER      3.6     4.7    +      -       -      -
     13C  GLY*     1.3    71.6    -      -       -      -
     15C  TYR*     1.3    61.7    +      -       -      +
     30C  LEU*     3.5     6.9    -      -       -      +
     31C  VAL*     2.9    31.1    +      -       +      +
    154C  LEU*     3.7    45.1    -      -       +      -
    155C  CYS      3.2    24.4    +      -       -      -
    156C  GLY*     3.5     3.5    -      -       -      -
    171C  GLY      3.4    27.8    -      -       -      -
    229C  SER      5.2     1.9    +      -       -      +
    335C  ALA*     4.5     0.9    -      -       +      -
    339C  GLU*     2.6    34.2    +      -       +      -
   1386C  BSD      3.8    25.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with TYR 15 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  ASN      3.9     0.5    -      -       -      +
      6C  LEU*     3.3    11.6    -      -       -      +
      7C  ARG*     2.9    79.9    +      -       +      +
      8C  GLY*     3.9     6.9    +      -       -      -
     13C  GLY      4.0     8.7    -      -       -      -
     14C  TYR*     1.3    73.3    -      -       -      +
     16C  VAL*     1.3    60.4    +      -       -      +
     28C  ASN*     3.5    36.8    -      -       +      -
     29C  ILE      3.1    22.4    -      -       -      +
     30C  LEU*     3.8     3.8    -      -       -      +
     31C  VAL      4.3     0.4    -      -       -      +
    113C  SER      3.6    20.0    -      -       -      -
    114C  ASN*     2.6    27.5    +      -       +      +
    115C  TRP*     4.0    19.7    -      +       +      -
    166C  VAL*     4.8     6.8    +      -       +      +
    167C  LEU*     4.3     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 16 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  ASN*     3.8    31.4    -      -       +      +
      6C  LEU*     3.6    12.3    -      -       +      +
     15C  TYR*     1.3    75.0    -      -       -      +
     17C  GLU*     1.3    72.8    +      -       -      +
     18C  MET*     3.6    19.9    +      -       +      -
     28C  ASN*     4.6     3.1    -      -       -      -
     29C  ILE*     2.8    38.7    +      -       +      +
     31C  VAL*     3.8    14.1    -      -       +      +
     87C  ILE*     4.0    17.5    -      -       +      -
     89C  HIS*     5.5     2.2    -      -       +      +
    119C  LEU*     4.8     7.2    -      -       +      -
    174C  MET*     5.0     7.2    -      -       +      -
    176C  ILE*     5.7     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 17 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  ASN      4.5     2.8    +      -       -      -
      7C  ARG*     5.5     2.9    +      -       -      -
     15C  TYR*     5.2     0.4    -      -       -      -
     16C  VAL*     1.3    77.7    -      -       -      +
     18C  MET*     1.3    67.6    +      -       -      +
     26C  THR*     3.6    31.1    +      -       +      +
     27C  LEU      3.6     5.2    -      -       -      +
     28C  ASN*     3.9    16.3    +      -       -      +
     50C  ARG*     5.4     0.5    +      -       -      -
     87C  ILE*     3.6    11.6    -      -       -      +
     88C  PRO*     3.2    40.1    -      -       +      +
     89C  HIS*     4.5    21.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with MET 18 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16C  VAL*     3.6    11.2    +      -       +      +
     17C  GLU*     1.3    80.8    -      -       -      +
     19C  THR*     1.3    67.4    +      -       -      +
     20C  VAL*     5.4     2.0    -      -       +      -
     26C  THR*     3.5     3.8    -      -       -      +
     27C  LEU*     2.8    32.9    +      -       +      +
     29C  ILE*     3.6    38.4    -      -       +      -
     38C  PHE*     4.0    17.3    -      -       +      -
     85C  VAL*     3.5    26.7    -      -       +      -
     86C  SER      3.4     7.2    -      -       -      +
     87C  ILE*     3.8    23.3    -      -       +      -
     88C  PRO*     3.8     1.1    -      -       -      -
    119C  LEU*     4.1    19.5    -      -       +      -
    136C  PHE*     4.0    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 19 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18C  MET*     1.3    79.0    -      -       -      +
     20C  VAL*     1.3    65.0    +      -       -      +
     21C  GLY      5.4     0.7    +      -       -      -
     24C  PRO*     3.8    28.2    -      -       +      +
     25C  GLN      3.1     8.7    -      -       -      -
     26C  THR*     3.9    18.2    -      -       -      +
     85C  VAL*     3.3     6.4    -      -       -      +
     86C  SER*     2.8    46.0    +      -       -      +
     88C  PRO*     3.7    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 20 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18C  MET*     5.4     3.1    -      -       +      -
     19C  THR*     1.3    80.6    -      -       -      +
     21C  GLY*     1.3    61.8    +      -       -      +
     25C  GLN*     2.9    40.5    +      -       +      +
     27C  LEU*     3.9    22.2    -      -       +      -
     29C  ILE*     6.2     0.7    -      -       +      -
     38C  PHE*     4.1    17.3    -      -       +      -
     40C  VAL*     5.1     4.0    -      -       +      -
     52C  TYR*     3.7    28.3    -      -       +      -
     83C  ASP*     4.7     0.2    -      -       -      -
     84C  LEU      3.4     5.2    -      -       -      +
     85C  VAL*     4.1     9.9    -      -       +      -
     99C  ILE*     4.0    26.0    -      -       +      -
----------------------------------------------------------
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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