Contacts of the strand formed by residues 261 - 267 (chain D) 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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252D  LEU*     4.3     1.6    -      -       +      -
    259D  PHE*     3.8    17.3    -      +       +      -
    260D  GLY*     1.3    78.7    -      -       -      +
    262D  LEU*     1.3    64.3    +      -       -      +
    263D  LEU*     4.2    11.4    -      -       +      -
    277D  LEU*     3.3    28.0    -      -       +      -
    279D  GLU      3.4    12.1    -      -       -      +
    280D  VAL*     4.4     5.6    -      -       +      -
    281D  ASP*     3.6     7.4    +      -       -      -
    286D  ALA*     3.8    11.4    -      -       +      -
    291D  MET*     3.5    20.4    -      -       +      -
    297D  LEU*     5.7     0.4    -      -       +      -
    317D  ILE*     4.1    19.3    -      -       +      -
    326D  LEU*     3.7    31.6    -      -       +      -
    338F  SER*     3.4     4.0    +      -       -      -
    339F  VAL*     2.9    59.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 262 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261D  PHE*     1.3    73.4    -      -       -      +
    263D  LEU*     1.3    58.6    +      -       -      +
    264D  ARG*     5.0     7.6    -      -       +      +
    277D  LEU*     3.5     4.0    -      -       -      -
    278D  TRP*     2.8    48.8    +      -       +      +
    279D  GLU*     3.0    53.8    +      -       +      +
    281D  ASP*     5.0     1.5    +      -       -      +
    336F  GLU*     4.4    22.9    -      -       +      +
    337F  THR      3.6    27.8    -      -       -      +
    338F  SER*     3.9    12.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 263 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261D  PHE*     4.0    11.3    -      -       +      -
    262D  LEU*     1.3    72.1    -      -       -      +
    264D  ARG*     1.3    60.2    +      -       -      +
    275D  GLN*     3.9    21.1    -      -       +      +
    276D  PHE      3.3    17.3    -      -       -      +
    277D  LEU*     3.6    22.7    -      -       +      -
    297D  LEU*     4.1    10.1    -      -       +      -
    310D  HIS*     3.2    22.4    -      -       +      +
    313D  THR*     3.9    26.2    -      -       +      -
    314D  VAL*     4.1    14.4    -      -       +      -
    317D  ILE*     4.2     9.4    -      -       +      -
    336F  GLU*     3.2     2.9    -      -       -      +
    337F  THR      2.7    44.0    +      -       -      +
    339F  VAL*     5.5     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 264 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262D  LEU*     4.0     8.9    +      -       +      +
    263D  LEU*     1.3    74.7    -      -       -      +
    265D  GLU*     1.3    72.2    +      -       -      +
    266D  GLU*     3.7    13.5    -      -       -      -
    275D  GLN*     4.1     2.2    -      -       -      -
    276D  PHE*     2.9    35.9    +      -       -      +
    278D  TRP*     3.6    52.5    -      -       +      +
    310D  HIS*     4.4     0.2    -      -       -      -
    293F  ALA*     3.7    30.6    +      -       -      +
    294F  GLY*     4.1     0.9    -      -       -      -
    331F  PRO*     3.9    19.3    -      -       +      +
    332F  GLU      4.6     5.5    +      -       -      -
    333F  ALA*     6.0     0.2    -      -       -      +
    335F  ARG      3.5    10.5    +      -       -      +
    336F  GLU*     2.8    46.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 265 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264D  ARG*     1.3    77.9    -      -       -      +
    266D  GLU*     1.3    80.9    +      -       -      +
    267D  LYS*     3.9    14.3    -      -       +      +
    273D  PRO*     3.8    13.6    -      -       +      +
    274D  GLY      3.3     9.0    -      -       -      +
    275D  GLN*     2.8    35.8    +      -       -      +
    309D  GLY*     3.8     3.7    -      -       -      -
    310D  HIS*     3.1    19.2    +      -       +      +
    331F  PRO*     5.3     4.2    -      -       -      +
    335F  ARG*     2.8    62.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 266 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264D  ARG*     3.7     6.7    +      -       -      -
    265D  GLU*     1.3    81.2    -      -       -      +
    267D  LYS*     1.3    66.1    +      -       -      +
    268D  GLY      3.8     0.7    +      -       -      -
    274D  GLY*     2.9    30.4    +      -       -      +
    276D  PHE*     3.8    15.0    -      -       +      -
    278D  TRP*     3.4    27.2    -      -       +      -
    276F  PHE*     3.4    38.4    -      -       +      -
    294F  GLY*     2.7    40.8    -      -       -      +
    296F  ARG*     4.9     6.6    +      -       -      +
    331F  PRO*     4.5     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 267 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265D  GLU*     3.9    21.5    -      -       +      +
    266D  GLU*     1.3    81.2    +      -       -      +
    268D  GLY*     1.3    66.4    +      -       -      +
    271D  GLY*     3.4    29.2    -      -       -      +
    272D  ARG      3.4     3.1    -      -       -      -
    273D  PRO*     4.0    16.8    -      -       +      -
    276F  PHE*     4.5     9.0    -      -       -      -
    296F  ARG*     4.4    19.4    +      -       -      +
    335F  ARG*     3.8    16.4    -      -       -      +
----------------------------------------------------------
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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