Contacts of the strand formed by residues 261 - 267 (chain A) in PDB entry 2V90


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 PHE 261 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252A  LEU*     4.2     0.9    -      -       +      -
    259A  PHE*     3.9    24.4    -      +       +      +
    260A  GLY*     1.3    79.8    -      -       -      +
    262A  LEU*     1.3    60.9    +      -       -      +
    263A  LEU*     4.0    34.2    +      -       +      -
    277A  LEU*     3.9    28.0    -      -       +      -
    279A  GLU      3.3    13.2    -      -       -      +
    280A  VAL*     4.4     2.2    -      -       -      -
    281A  ASP*     3.8     4.4    +      -       -      -
    286A  ALA*     3.8    21.1    -      -       +      -
    291A  MET*     3.8    15.5    -      -       +      -
    297A  LEU*     5.5     1.6    -      -       +      -
    317A  ILE*     4.3    24.9    -      -       +      -
    326A  LEU*     3.8    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 262 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261A  PHE*     1.3    73.4    -      -       -      +
    263A  LEU*     1.3    67.1    -      -       -      +
    264A  ARG*     4.4    21.3    -      -       +      +
    277A  LEU*     3.6     2.9    -      -       -      -
    278A  TRP*     2.7    44.9    +      -       +      +
    279A  GLU*     2.9    49.9    +      -       +      +
    281A  ASP*     5.7     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 263 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261A  PHE*     4.0    22.8    +      -       +      -
    262A  LEU*     1.3    79.1    -      -       -      +
    264A  ARG*     1.3    61.3    +      -       -      +
    275A  GLN*     3.9    20.6    -      -       +      +
    276A  PHE      3.3    20.6    -      -       -      +
    277A  LEU*     4.3     2.9    -      -       +      +
    297A  LEU*     4.0    17.7    -      -       +      -
    310A  HIS*     3.1    32.4    +      -       +      -
    313A  THR*     3.9    25.4    -      -       +      -
    314A  VAL*     4.1    17.0    -      -       +      -
    317A  ILE*     4.1    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 264 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262A  LEU*     3.8    19.4    +      -       +      +
    263A  LEU*     1.3    75.2    -      -       -      +
    265A  GLU*     1.3    74.7    +      -       -      +
    266A  GLU*     3.7     5.2    +      -       -      -
    275A  GLN*     4.0     4.3    -      -       -      -
    276A  PHE*     2.8    41.0    +      -       -      +
    278A  TRP*     3.5    60.2    -      -       +      +
    310A  HIS*     4.3     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 265 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264A  ARG*     1.3    88.9    -      -       -      +
    266A  GLU*     1.3    74.0    +      -       -      +
    267A  LYS*     3.5    27.3    -      -       +      +
    273A  PRO*     3.6    19.6    -      -       +      +
    274A  GLY      3.3     8.7    -      -       -      +
    275A  GLN*     3.0    30.8    +      -       -      +
    309A  GLY*     3.8     1.9    -      -       -      -
    310A  HIS*     3.1    30.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 266 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264A  ARG*     3.7     6.4    +      -       -      -
    265A  GLU*     1.3    80.2    -      -       -      +
    267A  LYS*     1.3    70.7    +      -       -      +
    268A  GLY      4.0     0.2    +      -       -      -
    272A  ARG      3.9     0.2    -      -       -      +
    274A  GLY*     2.8    35.2    +      -       -      +
    276A  PHE*     3.7    19.4    -      -       +      -
    278A  TRP*     3.1    40.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 267 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265A  GLU*     3.5    26.2    -      -       +      +
    266A  GLU*     1.3    82.6    +      -       -      +
    268A  GLY*     1.3    70.7    +      -       -      +
    271A  GLY*     3.4    29.1    +      -       -      +
    272A  ARG      3.4     4.0    -      -       -      -
    273A  PRO*     4.2    10.1    -      -       +      -
----------------------------------------------------------
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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