Contacts of the strand formed by residues 209 - 214 (chain C) in PDB entry 6PSI


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 209 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277A  TYR*     2.7    64.7    +      -       -      +
    235B  GLU      3.3    29.5    -      -       -      +
    236B  THR*     3.4    18.6    -      -       -      +
    249B  GLU*     5.3    15.7    -      -       -      +
    278B  LEU*     5.4     1.5    -      -       -      +
    203C  ILE*     3.6     8.4    -      -       -      +
    208C  GLY*     1.4    78.4    -      -       -      +
    210C  VAL*     1.4    66.0    +      -       -      +
    220C  GLU*     3.0    36.6    +      -       +      +
    221C  VAL      3.0    13.0    -      -       -      +
    222C  ALA*     3.8     7.6    -      -       +      -
    223C  VAL*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 210 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    278B  LEU*     6.4     0.2    -      -       -      -
    283B  ASP*     6.0     3.1    -      -       -      +
    197C  LEU*     3.9    25.5    -      -       +      +
    198C  ASP      3.2    24.7    -      -       -      +
    199C  VAL*     3.9    14.1    -      -       +      -
    200C  PRO*     3.7    26.0    -      -       +      -
    203C  ILE*     3.7    13.5    -      -       +      -
    209C  LYS*     1.4    79.0    -      -       -      +
    211C  ARG*     1.3    65.7    +      -       -      +
    220C  GLU*     4.6     2.0    -      -       -      -
    221C  VAL*     2.9    36.0    +      -       -      +
    223C  VAL*     4.3     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 211 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233B  PHE*     3.5    44.6    -      -       +      -
    278B  LEU*     5.5     3.6    -      -       +      +
    283B  ASP*     3.0    60.0    +      -       +      +
    286B  MET*     4.9     4.6    -      -       -      +
    197C  LEU*     4.0     8.4    -      -       -      +
    210C  VAL*     1.3    75.8    -      -       -      +
    212C  ALA*     1.3    69.8    +      -       -      +
    213C  MET*     3.2    29.4    -      -       -      +
    218C  PRO*     3.6    21.7    -      -       +      +
    219C  VAL      3.3    13.5    -      -       -      +
    220C  GLU*     4.3     3.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 212 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283B  ASP*     5.4     0.2    -      -       -      -
    186C  PHE*     5.7     2.7    -      -       +      -
    197C  LEU*     3.7    20.4    -      -       +      -
    210C  VAL      3.6     2.0    +      -       -      -
    211C  ARG*     1.3    73.5    -      -       -      +
    213C  MET*     1.3    59.9    +      -       -      +
    214C  THR*     3.2     2.3    +      -       -      -
    219C  VAL*     2.9    50.0    +      -       +      +
    221C  VAL*     4.2     2.2    -      -       +      +
    235C  LEU*     4.6     0.4    -      -       +      -
    249C  LEU*     4.7     5.2    -      -       +      -
    251C  LEU*     3.8    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 213 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170B  THR*     5.6    11.2    -      -       +      -
    171B  ALA*     5.1    10.1    -      -       +      -
    283B  ASP*     5.3     0.9    -      -       -      +
    128C  GLU*     3.8    26.5    -      -       +      +
    183C  HIS*     4.1    20.4    -      -       +      -
    186C  PHE*     3.0    23.2    -      -       +      -
    211C  ARG*     3.2    33.1    -      -       -      +
    212C  ALA*     1.3    67.0    -      -       -      +
    214C  THR*     1.3    74.0    +      -       -      +
    217C  GLY*     5.0     4.3    -      -       -      +
    218C  PRO*     4.2    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 214 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  ALA*     4.7     0.9    -      -       -      +
    186C  PHE*     4.3     7.0    -      -       +      -
    193C  LEU*     5.2     0.4    -      -       +      -
    212C  ALA      3.2     1.4    +      -       -      -
    213C  MET*     1.3    90.8    -      -       -      +
    215C  LEU*     1.3    77.3    +      -       +      +
    216C  GLU*     3.3     9.4    -      -       -      +
    217C  GLY      3.1    27.9    +      -       -      +
    219C  VAL*     3.2    30.1    +      -       -      +
    238C  LYS*     3.6    36.9    -      -       +      +
    249C  LEU*     4.0    17.5    -      -       +      +
----------------------------------------------------------
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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