Contacts of the strand formed by residues 256 - 264 (chain A) in PDB entry 3RJD


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 256 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  MET*     4.9     6.1    -      -       -      -
    254A  ASP      3.4     3.7    +      -       -      -
    255A  SER*     1.3    74.9    -      -       -      +
    257A  LEU*     1.3    64.0    +      -       -      -
    258A  TYR*     3.5    10.2    -      -       -      -
    277A  GLU*     3.6     5.9    -      -       -      +
    278A  LEU      3.1    31.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 257 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  MET*     3.4     4.5    -      -       -      +
    232A  GLY*     2.9    35.6    +      -       -      +
    256A  GLY*     1.3    72.7    -      -       -      -
    258A  TYR*     1.3    61.3    +      -       -      +
    259A  TRP*     4.1     1.9    -      -       -      -
    275A  GLU*     4.0    43.3    -      -       +      +
    276A  LEU      3.9     1.1    -      -       -      -
    277A  GLU*     3.9    30.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 258 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  LEU*     3.6    18.2    -      -       +      +
    210A  LEU*     3.6    17.0    -      -       +      -
    230A  TYR      3.5     5.6    -      -       -      +
    231A  MET*     3.8    17.9    -      -       +      -
    236A  LEU*     3.5    29.6    -      -       +      -
    247A  ILE*     4.0    21.7    -      -       +      +
    254A  ASP*     2.5    46.3    +      -       -      +
    256A  GLY      3.5    18.6    -      -       -      -
    257A  LEU*     1.3    73.7    -      -       -      +
    259A  TRP*     1.3    62.5    +      -       -      +
    274A  PRO      4.2     0.2    -      -       -      +
    275A  GLU*     3.4     0.7    -      -       -      -
    276A  LEU*     2.6    44.0    +      -       +      +
    278A  LEU*     3.7    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 259 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  LEU*     3.6     8.1    -      -       -      +
    229A  PHE*     4.0     1.4    -      -       -      +
    230A  TYR*     3.0    82.4    +      +       +      +
    232A  GLY      3.2    28.2    +      -       -      +
    233A  SER*     5.7     1.8    -      -       -      -
    257A  LEU      4.1     7.6    -      -       -      -
    258A  TYR*     1.3    78.7    -      -       -      +
    260A  CYS*     1.3    76.5    +      -       -      +
    261A  GLU*     4.0     6.5    -      -       -      -
    272A  ARG*     3.6    55.4    -      -       +      -
    273A  SER*     3.6    20.9    -      -       -      +
    274A  PRO      4.6     0.4    -      -       -      -
    275A  GLU*     3.8    30.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192A  PRO*     4.0     3.1    -      -       -      -
    194A  LEU*     4.2    11.2    -      -       +      +
    212A  CYS*     2.0    55.9    -      -       +      -
    228A  SER      3.4    11.7    -      -       -      +
    229A  PHE*     4.0    14.6    -      -       +      -
    259A  TRP*     1.3    81.6    -      -       -      +
    261A  GLU*     1.3    58.6    +      -       -      +
    272A  ARG*     3.5     2.8    -      -       -      -
    273A  SER*     2.8    49.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 261 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  CYS*     4.4     2.8    -      -       -      -
    226A  TYR      3.8     1.4    -      -       -      +
    227A  PHE*     3.3     7.8    -      -       -      +
    228A  SER*     3.0    40.5    +      -       -      +
    230A  TYR*     2.9    35.2    +      -       +      -
    259A  TRP*     4.0     3.3    -      -       -      -
    260A  CYS*     1.3    74.4    -      -       -      +
    262A  ALA*     1.3    60.1    +      -       -      +
    263A  ALA*     5.5     1.3    -      -       +      -
    270A  LEU*     4.3    30.1    -      -       +      +
    271A  LYS      3.5    12.8    -      -       -      +
    272A  ARG*     3.3    34.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 262 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  PHE*     3.4    26.0    -      -       +      -
    192A  PRO*     3.9    19.2    -      -       +      +
    214A  THR*     4.2     6.5    -      -       +      -
    225A  LEU*     5.2     2.2    -      -       +      -
    226A  TYR      3.8     3.4    -      -       -      -
    227A  PHE*     4.1    24.9    -      -       +      -
    261A  GLU*     1.3    72.5    -      -       -      +
    263A  ALA*     1.3    60.2    +      -       -      +
    270A  LEU*     3.2     1.8    -      -       -      -
    271A  LYS      2.8    36.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 263 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  PHE*     4.1     1.5    -      -       -      -
    225A  LEU*     3.4    11.5    -      -       -      +
    226A  TYR*     2.7    47.8    +      -       +      +
    239A  ARG*     5.9     5.4    -      -       +      -
    261A  GLU*     5.5     2.0    -      -       +      -
    262A  ALA*     1.3    74.6    -      -       -      +
    264A  THR*     1.3    67.8    +      -       -      +
    267A  GLY*     5.0     4.9    -      -       -      -
    269A  VAL      3.3     7.0    -      -       -      +
    270A  LEU*     3.5    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 264 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188A  LEU*     4.3    20.4    -      -       +      -
    189A  PHE*     4.0    20.9    -      -       +      -
    216A  LEU*     5.9     2.2    -      -       +      -
    224A  GLN      3.8     7.6    -      -       -      +
    225A  LEU*     4.2     5.4    -      -       +      -
    226A  TYR*     4.6     3.2    -      -       -      +
    239A  ARG*     4.8     2.1    +      -       -      -
    263A  ALA*     1.3    78.2    -      -       -      +
    265A  GLU*     1.4    57.5    +      -       -      +
    266A  ASP*     3.1    12.8    +      -       -      -
    267A  GLY*     2.8    24.8    +      -       -      -
    268A  ASN*     3.6     8.0    +      -       -      +
    269A  VAL*     3.3    27.9    +      -       +      +
----------------------------------------------------------
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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