Contacts of the strand formed by residues 257 - 263 (chain D) in PDB entry 4OIN


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 GLY 257 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255D  GLU      4.4     0.2    +      -       -      -
    256D  GLU*     1.3    76.0    -      -       -      +
    258D  VAL*     1.3    61.8    +      -       -      -
    272D  LEU*     4.8     2.0    -      -       -      -
    273D  ARG      3.8    11.4    -      -       -      -
    274D  ARG*     4.0    10.5    -      -       -      -
    297D  ILE*     3.8     8.5    -      -       -      +
    298D  VAL*     3.0    40.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 258 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257D  GLY*     1.3    72.0    -      -       -      -
    259D  VAL*     1.3    65.1    +      -       -      +
    271D  VAL      3.1     5.9    -      -       -      +
    272D  LEU*     3.3     1.3    -      -       -      -
    273D  ARG*     2.9    61.3    +      -       +      +
    274D  ARG      5.7     0.2    -      -       -      +
    276D  ASP*     6.0     1.3    -      -       -      +
    295D  GLY*     3.3    33.7    -      -       -      +
    296D  GLU      3.6     1.8    -      -       -      -
    297D  ILE*     3.8    20.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 259 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258D  VAL*     1.3    74.0    -      -       -      +
    260D  GLU*     1.3    63.9    +      -       -      +
    261D  LEU*     4.1     1.1    -      -       +      +
    270D  LEU*     3.6    30.1    -      -       +      -
    271D  VAL      3.7     2.9    -      -       -      -
    272D  LEU*     3.8    14.4    -      -       +      -
    292D  VAL*     4.0     7.9    -      -       +      -
    293D  VAL      3.6    19.3    -      -       -      +
    294D  HIS*     3.7     0.7    +      -       -      -
    295D  GLY*     2.6    34.3    +      -       -      -
    296D  GLU*     2.9    22.7    +      -       +      +
    298D  VAL*     3.7    32.5    -      -       +      -
    304D  LEU*     4.5     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 260 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259D  VAL*     1.3    74.1    -      -       -      +
    261D  LEU*     1.3    61.9    +      -       -      +
    262D  LYS*     3.7    21.0    +      -       +      +
    269D  PHE      3.4     6.4    -      -       -      +
    270D  LEU*     3.4     0.7    -      -       -      -
    271D  VAL*     2.9    56.3    +      -       +      +
    273D  ARG*     2.3    42.6    +      -       -      +
    294D  HIS*     3.6    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 261 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259D  VAL      3.9     1.8    -      -       -      -
    260D  GLU*     1.3    72.0    -      -       -      +
    262D  LYS*     1.3    59.8    +      -       -      +
    263D  GLU*     3.9    37.4    +      -       +      +
    268D  ALA*     4.1    15.0    -      -       +      -
    269D  PHE      3.5     8.1    -      -       -      +
    270D  LEU*     3.6    24.5    -      -       +      -
    290D  PRO*     4.7    13.9    -      -       +      -
    292D  VAL      3.4    25.6    -      -       -      +
    293D  VAL*     4.3    10.8    -      -       -      +
    294D  HIS*     3.1    34.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 262 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217D  LYS*     4.3    11.3    -      -       -      +
    260D  GLU*     3.7    20.7    +      -       +      +
    261D  LEU*     1.3    72.0    -      -       -      +
    263D  GLU*     1.3    65.7    +      -       -      +
    264D  LEU*     3.8     5.7    +      -       +      +
    268D  ALA*     3.6     1.6    -      -       -      -
    269D  PHE*     2.9    53.4    +      -       +      +
    271D  VAL*     6.3     1.1    -      -       +      -
    339D  TRP*     5.7     3.6    -      -       +      -
    341D  GLU*     3.2    40.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 263 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261D  LEU*     3.9    37.3    +      -       +      +
    262D  LYS*     1.3    76.1    -      -       -      +
    264D  LEU*     1.3    72.3    +      -       -      +
    267D  GLY      4.1     4.9    -      -       -      +
    268D  ALA*     4.5     4.9    -      -       +      +
    290D  PRO*     5.6     5.1    -      -       +      +
----------------------------------------------------------
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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