Contacts of the strand formed by residues 259 - 266 (chain A) in PDB entry 2ABJ


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 MET 259 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  VAL*     5.5     0.7    -      -       +      -
    242A  GLN*     4.1     8.3    -      -       +      +
    255A  GLU*     3.2    12.8    -      -       -      +
    256A  VAL*     2.8    48.2    +      -       +      +
    257A  GLY      3.4     0.8    +      -       -      -
    258A  THR*     1.3    77.1    -      -       -      +
    260A  ASN*     1.3    61.0    +      -       -      +
    328A  SER*     3.3    36.6    -      -       -      +
    329A  SER      3.2    14.1    -      -       -      +
    333A  CYS*     3.6    17.5    -      -       -      -
    336A  CYS*     3.8    10.3    -      -       +      -
    420A  PLP      3.8     0.7    -      -       -      -
   1401A  CBC      3.4    65.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254A  THR      5.4     0.2    -      -       -      +
    255A  GLU*     3.8     9.6    -      -       -      +
    256A  VAL      4.7     0.4    -      -       -      -
    259A  MET*     1.3    73.8    -      -       -      +
    261A  LEU*     1.3    60.5    +      -       -      +
    262A  PHE*     3.9     2.2    +      -       +      -
    276A  THR*     5.0     1.6    -      -       -      +
    283A  ILE*     3.5    16.6    -      -       -      +
    284A  LEU      2.9    18.1    +      -       -      +
    286A  GLY*     3.3    30.7    -      -       -      +
    289A  ARG*     3.4    28.2    -      -       +      +
    327A  PHE      3.8     0.2    -      -       -      +
    328A  SER*     3.1     9.2    -      -       -      -
    329A  SER*     2.8    45.3    +      -       -      +
    420A  PLP      3.4    16.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 261 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  LEU*     4.6     5.6    -      -       +      -
    253A  ILE*     3.8    32.1    -      -       +      -
    254A  THR      3.5    27.0    +      -       -      +
    255A  GLU*     4.2     3.6    -      -       -      -
    256A  VAL*     3.2    28.5    -      -       +      -
    259A  MET      3.9     0.4    +      -       -      -
    260A  ASN*     1.3    74.7    -      -       -      +
    262A  PHE*     1.3    70.6    +      -       -      +
    263A  LEU*     4.6     1.1    -      -       +      -
    276A  THR*     2.5    31.3    +      -       -      -
    277A  PRO*     3.3     9.6    -      -       +      +
    309A  LEU*     4.2    12.6    -      -       +      -
    326A  MET*     3.6    31.9    -      -       +      -
    327A  PHE      4.0     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 262 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    260A  ASN*     4.4     3.8    -      -       +      -
    261A  LEU*     1.3    78.8    -      -       -      +
    263A  LEU*     1.3    59.8    +      -       -      +
    274A  LEU*     3.9    23.1    -      -       +      -
    275A  ALA      3.5     2.0    -      -       -      -
    276A  THR*     3.7    21.8    -      -       -      -
    289A  ARG*     3.7    38.6    -      -       +      -
    292A  ILE*     3.7    26.0    -      -       +      -
    293A  LEU*     3.8    16.8    -      -       +      -
    325A  GLU      4.8     0.2    -      -       -      -
    326A  MET*     3.4     9.0    -      -       -      +
    327A  PHE*     2.9    67.5    +      +       +      +
    329A  SER*     3.3    28.7    -      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
    253A  ILE*     4.9     1.8    -      -       +      -
    261A  LEU*     4.4     2.2    -      -       +      +
    262A  PHE*     1.3    74.4    -      -       -      +
    264A  TYR*     1.3    63.0    +      -       -      +
    265A  TRP*     3.6    42.2    +      -       +      -
    273A  GLU      3.6     2.6    -      -       -      +
    274A  LEU*     3.6     2.8    -      -       -      -
    275A  ALA*     2.8    41.7    +      -       +      +
    309A  LEU*     4.2    26.2    -      -       +      -
    313A  ASP*     6.4     0.2    -      -       +      -
    314A  LEU*     4.4    19.7    -      -       +      -
    323A  VAL*     3.8    26.5    -      -       +      -
    325A  GLU      3.5    15.7    -      -       -      +
    326A  MET*     4.3    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 264 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262A  PHE      4.3     0.2    -      -       -      -
    263A  LEU*     1.3    70.9    -      -       -      +
    265A  TRP*     1.3    61.6    +      -       -      +
    272A  GLU*     2.3    45.5    +      -       +      -
    273A  GLU      3.4    15.9    -      -       -      -
    274A  LEU*     4.2     5.8    -      -       +      -
    302A  PHE*     4.2    16.0    -      +       -      -
    323A  VAL*     4.3     0.3    -      -       -      -
    324A  ARG*     2.9    74.1    +      -       +      +
    325A  GLU*     2.8    45.5    +      -       +      +
    327A  PHE*     4.7     2.9    -      -       +      -
    358A  LYS*     4.4     7.6    -      -       -      -
    359A  LEU*     3.7    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 265 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263A  LEU*     3.6    35.7    -      -       +      -
    264A  TYR*     1.3    78.8    -      -       -      +
    266A  ILE*     1.3    63.5    +      -       -      +
    267A  ASN*     3.8    10.9    -      -       +      +
    268A  GLU*     3.7    18.2    -      -       -      -
    272A  GLU*     3.5     3.4    -      -       -      +
    273A  GLU*     2.7    74.6    +      -       +      +
    275A  ALA*     4.1     5.1    -      -       -      +
    307A  ARG*     3.7    27.4    -      -       -      -
    309A  LEU*     4.2     9.6    -      -       +      -
    313A  ASP*     3.7    21.5    -      -       +      -
    314A  LEU*     5.1     0.2    -      -       -      -
    317A  ALA*     3.6    26.2    -      -       +      -
    322A  ARG*     3.4    32.1    -      -       -      +
    323A  VAL*     4.0     7.6    -      -       +      -
    324A  ARG*     4.2     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 266 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265A  TRP*     1.3    78.2    -      -       -      +
    267A  ASN*     1.3    58.0    +      -       -      +
    270A  GLY*     3.5    37.7    -      -       -      +
    271A  GLU      3.4     1.8    -      -       -      -
    272A  GLU*     3.8    30.3    -      -       +      +
    321A  ASN      5.5     1.1    -      -       -      +
    322A  ARG*     2.8    66.6    +      -       +      +
    324A  ARG*     5.5     9.4    -      -       +      -
----------------------------------------------------------
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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