Contacts of the strand formed by residues 325 - 331 (chain A) in PDB entry 1J07


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 GLN 325 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  HIS      4.5     4.2    +      -       -      +
    224A  ARG*     3.3    38.9    +      -       +      +
    225A  ALA      3.2    22.3    +      -       -      -
    323A  ASP*     4.2     9.1    +      -       -      +
    324A  LEU*     1.3    88.3    -      -       -      +
    326A  VAL*     1.3    62.2    +      -       -      +
    424A  ARG*     3.3    38.5    -      -       +      +
    483A  PHE*     3.4    21.4    -      -       +      -
    486A  THR      4.6     2.1    -      -       -      +
    487A  GLY*     3.8    12.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 326 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  ILE*     4.2    12.1    -      -       +      -
    225A  ALA*     3.1    12.6    -      -       +      +
    227A  LEU*     3.6    13.0    -      -       +      -
    324A  LEU*     3.6    30.7    -      -       +      +
    325A  GLN*     1.3    81.2    -      -       -      +
    327A  LEU*     1.3    63.0    +      -       -      +
    328A  VAL*     3.4    27.1    -      -       +      -
    418A  LEU*     4.3    17.7    -      -       +      -
    423A  ALA*     5.3     1.3    -      -       +      -
    424A  ARG      2.8    12.3    +      -       -      +
    425A  VAL*     3.3    10.2    -      -       +      +
    426A  TYR*     2.9    25.1    +      -       -      +
    483A  PHE*     3.7     6.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 327 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  ALA      2.9     6.1    +      -       -      +
    226A  VAL*     3.1    25.7    -      -       +      +
    227A  LEU      2.9    25.1    +      -       -      -
    326A  VAL*     1.3    73.1    -      -       -      +
    328A  VAL*     1.3    63.4    +      -       -      +
    426A  TYR*     3.4    18.4    -      -       +      +
    428A  TYR*     4.0    10.3    -      -       +      -
    480A  TRP*     4.0    39.7    -      -       +      -
    483A  PHE*     3.7    26.4    -      -       +      -
    489A  PRO*     5.3     3.4    -      -       +      -
    500A  TRP*     3.3    37.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 328 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227A  LEU*     3.4    22.0    -      -       +      +
    326A  VAL*     3.4    22.4    -      -       +      -
    327A  LEU*     1.3    79.2    -      -       -      +
    329A  GLY*     1.3    59.2    +      -       -      +
    411A  VAL*     4.3    16.4    -      -       +      +
    414A  LEU*     4.6    14.6    -      -       +      -
    415A  ALA*     4.3    13.7    -      -       +      -
    418A  LEU*     5.4     1.3    -      -       +      -
    425A  VAL*     4.2    13.5    -      -       +      -
    426A  TYR      2.8    18.0    +      -       -      +
    427A  ALA*     3.0    20.4    -      -       +      -
    428A  TYR*     3.0    28.7    +      -       -      -
    524A  LEU*     6.3     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 329 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227A  LEU      3.3     7.1    +      -       -      +
    228A  GLN      3.8     0.3    -      -       -      -
    229A  SER      2.8    25.1    +      -       -      -
    328A  VAL*     1.3    78.9    -      -       -      +
    330A  VAL*     1.3    71.2    +      -       -      +
    411A  VAL*     4.5     6.9    -      -       -      +
    427A  ALA*     5.6     0.2    -      -       -      -
    428A  TYR*     3.1    30.6    -      -       -      -
    524A  LEU*     6.2     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 330 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  SER*     3.9     2.7    -      -       -      -
    329A  GLY*     1.3    81.1    -      -       -      +
    331A  VAL*     1.3    64.1    +      -       -      +
    334A  GLU*     3.3    13.9    -      -       +      +
    407A  VAL*     3.8    20.6    -      -       +      -
    408A  VAL*     4.1    23.8    -      -       +      -
    411A  VAL*     3.9    21.3    -      -       +      -
    428A  TYR*     3.2    11.9    +      -       -      +
    429A  ILE*     3.2    18.8    -      -       +      -
    430A  PHE      2.8    30.3    +      -       -      -
    524A  LEU*     4.9    10.5    -      -       +      -
    525A  ARG*     6.2     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 331 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  SER*     4.1     5.2    -      -       -      +
    330A  VAL*     1.3    83.6    -      -       -      +
    332A  LYS*     1.3    65.5    +      -       -      +
    333A  ASP      3.3     0.2    +      -       -      -
    334A  GLU*     2.6    45.8    +      -       -      +
    408A  VAL*     5.3     1.6    -      -       -      +
    429A  ILE*     4.4     2.5    -      -       -      +
    430A  PHE*     3.4    15.0    -      -       +      +
    445A  VAL*     3.4    25.1    -      -       +      +
    446A  PRO      3.8    17.7    -      -       -      +
    447A  HIS*     4.0     1.6    -      -       -      +
    448A  GLY      4.8     1.6    -      -       -      +
    450A  GLU*     3.7    40.4    -      -       +      +
----------------------------------------------------------
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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