Contacts of the strand formed by residues 260 - 266 (chain D) in PDB entry 2C11


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 THR 260 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182D  MET*     3.4    13.8    -      -       -      +
    187D  GLU*     5.8     0.2    -      -       -      -
    249D  VAL*     3.4     5.0    -      -       -      +
    250D  ASN*     2.7    52.8    +      -       -      +
    258D  ARG      3.6    12.1    -      -       -      +
    259D  TRP*     1.3    81.9    -      -       -      +
    261D  ILE*     1.3    63.6    +      -       -      +
    262D  GLN*     4.4     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 261 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182D  MET*     3.7    15.7    -      -       +      -
    183D  ILE*     5.0     2.0    -      -       +      -
    187D  GLU*     3.4    41.0    +      -       +      +
    247D  LEU*     4.2    19.5    -      -       +      -
    248D  LEU      3.4     3.8    -      -       -      +
    249D  VAL*     3.9    20.9    -      -       +      -
    260D  THR*     1.3    77.5    +      -       -      +
    262D  GLN*     1.3    63.0    +      -       -      +
    263D  LYS*     3.7    11.9    -      -       -      +
    264D  VAL*     3.7    30.1    -      -       +      -
    272D  ASP      4.2    11.0    -      -       -      +
    273D  SER*     5.3     3.4    -      -       -      -
    274D  LEU*     5.1     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 262 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224D  ALA*     3.5    26.9    -      -       -      +
    248D  LEU*     2.8    30.3    +      -       +      +
    250D  ASN*     2.7    42.0    +      -       +      +
    260D  THR*     4.4     3.6    -      -       -      +
    261D  ILE*     1.3    74.7    -      -       -      +
    263D  LYS*     1.3    71.1    +      -       +      +
    272D  ASP*     4.2     6.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 263 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    553C  TRP*     4.5    21.3    +      -       +      +
    226D  TRP*     4.1    15.3    -      -       +      -
    247D  LEU*     3.8     0.2    -      -       -      -
    248D  LEU*     3.0    33.5    +      -       +      +
    261D  ILE*     3.4     3.4    -      -       -      +
    262D  GLN*     1.3    82.8    -      -       -      +
    264D  VAL*     1.3    70.8    +      -       -      +
    270D  TYR*     3.8    42.0    -      -       +      -
    271D  TYR      3.4    11.7    -      -       -      +
    272D  ASP*     3.4    28.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 264 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226D  TRP*     4.4     2.7    -      -       -      -
    245D  LEU*     3.4    27.8    -      -       +      -
    246D  GLU      3.7     2.7    -      -       -      -
    247D  LEU*     3.6    17.9    -      -       +      -
    261D  ILE*     3.7    16.2    -      -       +      -
    263D  LYS*     1.3    80.0    -      -       -      +
    265D  PHE*     1.3    68.5    +      -       -      +
    266D  TYR      4.5     0.4    -      -       -      +
    270D  TYR*     3.3     6.4    -      -       -      +
    271D  TYR*     2.7    44.4    +      -       +      +
    273D  SER*     4.2     3.6    -      -       -      +
    274D  LEU*     3.7    22.9    -      -       +      +
    277D  LEU*     4.1    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 265 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226D  TRP*     3.8    20.2    -      -       +      -
    244D  GLY      4.4     3.8    -      -       -      -
    245D  LEU*     3.2     6.2    -      -       -      +
    246D  GLU*     2.8    41.7    +      -       +      +
    264D  VAL*     1.3    76.5    -      -       -      +
    266D  TYR*     1.3    62.7    +      -       -      +
    267D  GLN*     4.2     2.0    -      -       -      -
    268D  GLY*     3.3    50.3    -      -       -      -
    269D  ARG      3.5     3.4    -      -       -      -
    270D  TYR*     3.5    29.2    -      +       +      -
    375D  ASN      5.3     1.1    -      -       -      -
    376D  SER*     4.1     5.6    -      -       -      -
    377D  PRO*     3.3    35.0    -      -       +      -
    499D  PHE*     6.2     1.6    -      +       +      -
    501D  PHE*     3.7    24.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with TYR 266 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194D  LEU*     4.2    14.6    -      -       +      -
    195D  LEU*     6.2     1.6    -      -       +      -
    198D  CYS*     3.5    17.2    -      -       -      +
    199D  CYS*     5.0     2.2    -      -       -      -
    243D  VAL      4.2     8.3    -      -       -      -
    244D  GLY      3.1    13.9    -      -       -      -
    245D  LEU*     3.8    19.7    -      -       +      -
    264D  VAL      4.2     0.2    -      -       -      -
    265D  PHE*     1.3    76.9    -      -       -      +
    267D  GLN*     1.3   113.6    +      -       +      +
    268D  GLY      2.6     5.8    +      -       -      -
    269D  ARG*     2.9    19.7    +      -       -      +
    271D  TYR*     4.2    11.0    +      +       +      -
    277D  LEU*     3.7    23.8    -      -       +      -
    286D  VAL*     4.2    19.3    -      -       +      -
    287D  ASN      4.8     0.7    -      -       -      -
    288D  VAL*     3.3    32.9    -      -       +      +
----------------------------------------------------------
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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