Contacts of the strand formed by residues 317 - 323 (chain A) in PDB entry 1J71


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 THR 317 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  ALA*     4.2    22.0    -      -       +      +
    187A  LEU      3.1    16.6    -      -       -      +
    188A  PRO*     4.5     4.0    -      -       +      -
    189A  VAL*     3.8     1.8    -      -       -      +
    195A  LEU*     6.0     0.2    -      -       -      +
    312A  ASP*     2.9    47.8    +      -       -      +
    315A  ASP*     3.5    16.0    -      -       +      +
    316A  LYS*     1.3    84.1    -      -       -      +
    318A  ILE*     1.3    67.8    +      -       -      +
    319A  SER*     4.9     0.9    +      -       -      -
    573A  EOH      4.7     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 318 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  THR      3.8     0.7    -      -       -      +
    187A  LEU*     2.8    33.7    +      -       -      +
    189A  VAL*     3.9    13.2    -      -       +      -
    195A  LEU*     3.9    39.3    -      -       +      +
    197A  VAL*     3.7    26.5    -      -       +      -
    217A  LEU*     3.9    15.0    -      -       +      -
    309A  ILE*     3.7    28.3    -      -       +      -
    310A  VAL      3.4     4.0    -      -       -      +
    311A  TYR*     4.1    18.6    -      -       +      -
    317A  THR*     1.3    80.1    -      -       -      +
    319A  SER*     1.3    64.1    +      -       -      +
    320A  LEU*     4.0     5.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 319 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184A  LEU*     4.2    13.9    -      -       -      +
    185A  THR      3.2    11.7    -      -       -      -
    186A  ALA*     3.3    23.6    +      -       -      +
    308A  TYR      3.6     0.5    -      -       -      +
    309A  ILE*     3.4     6.4    -      -       -      +
    310A  VAL*     2.9    47.3    +      -       -      -
    317A  THR*     4.2     1.8    +      -       -      -
    318A  ILE*     1.3    72.2    -      -       -      +
    320A  LEU*     1.3    62.9    -      -       -      +
    573A  EOH      3.6    23.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 320 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  THR      3.9     2.4    -      -       -      +
    184A  LEU*     3.8     2.2    -      -       -      -
    185A  THR*     3.2    27.9    +      -       -      +
    187A  LEU*     4.1    17.5    -      -       +      -
    197A  VAL*     5.1     1.8    -      -       +      -
    217A  LEU*     4.0    15.5    -      -       +      -
    264A  PHE*     3.9    40.6    -      -       +      -
    268A  VAL*     4.1    17.8    -      -       +      +
    270A  ILE*     4.5     9.4    -      -       +      -
    303A  PHE*     5.0     2.2    -      -       +      -
    307A  ALA*     4.4     7.0    -      -       +      -
    308A  TYR      3.6     2.5    -      -       -      +
    309A  ILE*     3.4    39.3    -      -       +      -
    318A  ILE*     4.3     5.4    -      -       +      -
    319A  SER*     1.3    79.6    -      -       -      +
    321A  ALA*     1.3    65.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 321 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  TYR*     3.8    26.7    -      -       +      -
    181A  THR      4.0     6.1    -      -       -      +
    183A  THR      4.3     4.3    -      -       -      +
    184A  LEU*     3.5    24.9    -      -       +      -
    270A  ILE*     3.6    12.1    -      -       -      +
    308A  TYR      2.9    26.0    +      -       -      +
    320A  LEU*     1.3    78.9    -      -       -      +
    322A  GLN*     1.3    67.0    +      -       -      +
    323A  VAL      3.3     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 322 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  TYR*     3.3     4.3    -      -       -      +
    181A  THR*     3.0    47.1    +      -       -      +
    269A  LYS      4.1     5.8    +      -       -      +
    270A  ILE*     3.5    14.0    -      -       +      +
    271A  THR*     2.8    53.9    +      -       -      +
    306A  ARG*     3.4    28.9    +      -       -      +
    321A  ALA*     1.3    70.8    -      -       -      +
    323A  VAL*     1.3    70.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 323 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  TYR*     3.5    31.6    -      -       +      -
    179A  LYS      3.5    13.5    -      -       -      +
    180A  TYR*     4.3     0.4    -      -       -      +
    181A  THR*     4.8     2.4    +      -       -      +
    305A  ARG      3.7     7.9    -      -       -      +
    306A  ARG*     3.1    47.6    +      -       -      +
    307A  ALA      4.0    12.3    -      -       -      +
    308A  TYR*     4.3     2.9    -      -       +      +
    321A  ALA      3.3     3.5    +      -       -      -
    322A  GLN*     1.3    84.2    +      -       -      +
    324A  LYS*     1.3    64.8    +      -       -      +
    325A  TYR*     3.7    24.3    -      -       +      -
----------------------------------------------------------
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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