Contacts of the strand formed by residues 17 - 23 (chain A) in PDB entry 2O2V


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 LEU 17 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  VAL*     1.3    73.3    -      -       -      +
     18A  VAL*     1.3    70.7    +      -       -      +
     19A  ILE*     4.1    17.9    -      -       +      -
     32A  THR*     3.7     1.7    -      -       -      -
     33A  VAL*     2.8    47.3    +      -       +      +
     39A  LEU*     4.1    20.4    -      -       +      -
     82A  LEU*     3.8    23.6    -      -       +      -
     85A  TYR*     3.5    38.8    -      -       +      -
     86A  TYR*     3.8    21.3    -      -       +      +
    102A  LEU*     4.5     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 18 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  VAL*     4.2    12.9    +      -       +      +
     17A  LEU*     1.3    78.9    -      -       -      +
     19A  ILE*     1.3    64.2    +      -       -      +
     30A  ASP*     3.9    30.1    -      -       +      +
     31A  TRP      3.3     7.4    -      -       -      +
     32A  THR*     3.9    17.5    -      -       +      +
     85A  TYR*     4.3     3.4    +      -       -      +
    101A  PRO*     3.3    22.5    -      -       +      +
    102A  LEU*     3.0    27.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  LEU*     4.1    17.9    -      -       +      -
     18A  VAL*     1.3    76.6    -      -       -      +
     20A  ARG*     1.3    59.6    +      -       -      +
     21A  ILE*     3.7     9.4    +      -       +      +
     29A  VAL      3.5     3.3    -      -       -      +
     30A  ASP*     3.4     0.7    -      -       -      -
     31A  TRP*     2.8    58.4    +      -       +      +
     33A  VAL*     4.0    18.2    -      -       +      -
     39A  LEU*     4.0    20.9    -      -       +      -
     44A  VAL*     4.5     9.2    -      -       +      -
     78A  MET*     6.3     0.2    -      -       -      -
     81A  MET*     5.7     5.2    -      -       +      -
     82A  LEU*     5.5     1.8    -      -       +      -
    102A  LEU*     3.5    18.6    -      -       +      +
    104A  ILE*     3.6    35.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  VAL      4.0     1.2    -      -       -      -
     19A  ILE*     1.3    70.0    -      -       -      +
     21A  ILE*     1.3    59.0    +      -       -      +
     22A  LYS      3.6     0.2    +      -       -      -
     28A  ALA*     3.4    28.0    +      -       +      +
     29A  VAL      3.6     0.2    -      -       -      -
     30A  ASP*     2.6    42.5    +      -       -      +
    101A  PRO*     3.7    33.6    -      -       +      +
    102A  LEU      2.8    13.3    +      -       -      +
    103A  GLN*     3.3    26.3    -      -       -      +
    104A  ILE*     2.8    31.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  ILE*     4.0    17.0    -      -       +      +
     20A  ARG*     1.3    73.2    -      -       -      +
     22A  LYS*     1.3    67.2    +      -       -      +
     23A  ILE*     3.4     3.2    +      -       +      +
     28A  ALA*     3.2     1.9    -      -       -      -
     29A  VAL*     2.7    48.2    +      -       +      +
     31A  TRP*     4.4    14.1    -      -       +      -
     44A  VAL*     5.9     0.7    -      -       +      -
     47A  VAL*     4.0    27.6    -      -       +      -
     48A  ILE*     4.2    21.8    -      -       +      -
     51A  VAL*     4.6    21.1    -      -       +      -
     52A  LEU*     5.0     0.2    -      -       +      -
    104A  ILE*     3.8    11.4    -      -       +      -
    106A  PRO*     3.6    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  ARG*     3.6     2.2    +      -       -      +
     21A  ILE*     1.3    73.2    -      -       -      +
     23A  ILE*     1.3    80.2    +      -       -      +
     25A  ASN      4.8     0.6    -      -       -      +
     26A  SER*     3.6    14.9    -      -       -      +
     27A  GLY      2.8    36.2    +      -       -      +
     28A  ALA*     4.1     4.2    -      -       +      +
     52A  LEU*     4.1     2.6    -      -       -      +
    103A  GLN*     4.1    17.9    -      -       -      +
    104A  ILE      3.0    12.1    +      -       -      +
    105A  PHE*     3.4    39.7    -      -       +      -
    106A  PRO*     3.3    22.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  ILE      3.4     8.0    +      -       -      +
     22A  LYS*     1.3   107.5    +      -       -      +
     24A  PRO*     1.4    81.5    -      -       +      +
     27A  GLY*     3.2    33.0    +      -       -      +
     28A  ALA      3.9     1.3    -      -       -      +
     29A  VAL*     4.1    17.3    -      -       +      -
     51A  VAL*     3.6    30.5    -      -       +      +
     52A  LEU*     3.9    11.2    -      -       +      -
----------------------------------------------------------
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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