Contacts of the strand formed by residues 277 - 284 (chain A) in PDB entry 2J25


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 ARG 277 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  TRP*     2.8    27.2    +      -       +      +
    229A  ALA*     3.0    12.7    -      -       +      +
    230A  VAL*     2.9    26.8    +      -       -      +
    268A  LEU*     6.0     0.4    -      -       -      -
    275A  ASN      3.8    12.4    +      -       -      +
    276A  VAL*     1.3    74.6    -      -       -      +
    278A  LEU*     1.3    61.3    +      -       -      +
    279A  LEU*     4.7     0.7    -      -       +      -
    306A  HIS*     3.4    52.4    +      -       +      +
   1502A  SO4      2.6    38.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 278 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  VAL*     3.6    13.9    -      -       +      +
    232A  ALA*     3.7    25.6    -      -       +      +
    260A  ILE*     3.6    37.5    -      -       +      -
    264A  LEU*     3.7    32.5    -      -       +      -
    265A  GLY*     4.9     2.9    -      -       -      -
    268A  LEU*     4.8    11.7    -      -       +      -
    276A  VAL      3.9     2.0    +      -       -      +
    277A  ARG*     1.3    74.1    -      -       -      +
    279A  LEU*     1.3    67.9    +      -       -      +
    304A  TYR*     3.5    24.6    +      -       +      +
    305A  VAL*     3.8     4.1    -      -       +      -
    306A  HIS*     3.0    28.3    +      -       -      +
    307A  GLY      3.6     4.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 279 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175A  LEU*     3.8    25.4    -      -       +      -
    228A  TRP*     4.0    16.8    -      -       +      -
    229A  ALA*     4.1    10.1    -      -       +      -
    230A  VAL      2.8    13.0    +      -       -      +
    231A  THR*     3.3    17.7    -      -       +      -
    232A  ALA      2.9    25.3    +      -       -      -
    278A  LEU*     1.3    83.8    -      -       -      +
    280A  MET*     1.3    61.7    +      -       -      +
    306A  HIS*     4.1    10.3    -      -       +      -
    307A  GLY*     3.2    18.8    -      -       -      +
    309A  ALA*     4.2    10.8    -      -       +      +
    335A  MET*     3.8    22.9    -      -       +      -
    337A  PHE*     4.2    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 280 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  ALA*     4.5     5.4    -      -       -      -
    256A  GLN*     3.6    10.1    -      -       -      +
    260A  ILE*     4.3    12.6    -      -       +      -
    279A  LEU*     1.3    72.4    -      -       -      +
    281A  LEU*     1.3    70.4    +      -       +      +
    282A  ASP*     2.8     9.0    +      -       -      -
    288A  LEU*     5.2     0.2    -      -       +      -
    291A  TRP*     3.6    42.4    -      -       +      +
    292A  ALA*     3.9     5.6    -      -       +      +
    295A  VAL*     3.7    31.2    -      -       +      -
    296A  LEU*     4.1    16.4    -      -       -      -
    305A  VAL*     3.8    11.5    -      -       +      +
    307A  GLY      2.9    19.1    +      -       -      +
    308A  ILE*     3.8    20.0    -      -       +      -
    309A  ALA*     2.6    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 281 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  ALA      6.3     0.2    -      -       -      -
    233A  GLU      3.3     2.5    -      -       -      +
    236A  PRO*     2.9    25.5    -      -       -      +
    256A  GLN*     3.0    15.1    +      -       -      +
    280A  MET*     1.3    78.7    -      -       +      +
    282A  ASP*     1.3    70.2    +      -       -      +
    283A  ASP*     3.1    38.6    -      -       +      +
    284A  GLN      3.7     7.0    -      -       -      +
    287A  LEU*     3.9    11.0    -      -       +      -
    288A  LEU*     3.6    41.5    -      -       +      -
    291A  TRP*     3.7    34.3    -      -       +      -
    308A  ILE*     3.9     7.2    -      -       +      -
    309A  ALA      3.2    14.6    -      -       -      +
    310A  VAL*     4.0     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 282 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  ARG*     3.0    11.7    +      -       -      -
    231A  THR*     2.8    33.0    +      -       -      -
    232A  ALA      5.5     0.2    -      -       -      +
    233A  GLU      3.4     8.1    -      -       -      +
    234A  ASN*     3.0    18.5    -      -       -      -
    235A  GLU*     2.7    32.6    +      -       -      -
    280A  MET      2.8     7.6    +      -       -      +
    281A  LEU*     1.3    76.6    -      -       -      +
    283A  ASP*     1.3    54.1    +      -       -      +
    309A  ALA*     2.8    19.1    +      -       +      -
    311A  HIS*     2.7    22.4    +      -       -      -
    339A  SER*     2.5    29.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 283 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  GLU*     3.1    24.9    -      -       -      +
    236A  PRO*     3.3     5.9    -      -       +      +
    237A  SER*     2.7    48.2    +      -       -      -
    281A  LEU*     3.1    27.8    -      -       +      +
    282A  ASP*     1.3    77.1    -      -       -      +
    284A  GLN*     1.3    84.1    +      -       -      +
    287A  LEU*     3.6     5.0    -      -       +      +
    309A  ALA      3.6     1.6    +      -       -      -
    310A  VAL*     3.3     6.1    -      -       -      -
    311A  HIS*     2.8    32.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  GLU*     3.6    20.6    -      -       -      +
    237A  SER*     5.6     0.7    -      -       -      +
    281A  LEU*     3.7     9.5    -      -       -      +
    283A  ASP*     1.3    89.6    +      -       -      +
    285A  ARG*     1.3    64.3    +      -       -      +
    286A  LEU*     3.2    21.1    +      -       +      -
    287A  LEU*     3.3    14.4    +      -       +      +
    311A  HIS*     3.9     9.4    +      -       -      +
    312A  TRP      3.9     1.8    -      -       -      -
    313A  TYR*     3.1    20.9    -      -       -      +
    314A  LEU*     2.4    71.1    +      -       +      +
----------------------------------------------------------
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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