Contacts of the strand formed by residues 313 - 320 (chain A) in PDB entry 3STJ


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 LYS 313 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291A  ASN*     4.6     2.3    +      -       -      +
    311A  GLY      3.7     5.6    +      -       -      +
    312A  THR*     1.3    82.0    -      -       -      +
    314A  VAL*     1.3    64.8    +      -       -      +
    328A  GLU*     3.6    38.0    +      -       +      +
    329A  VAL      3.3     4.7    -      -       -      +
    330A  THR*     3.4    29.6    -      -       -      +
    120K  ASN*     5.4     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 314 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242A  LEU*     4.2     4.0    -      -       +      -
    290A  LEU*     3.8    17.5    -      -       +      -
    291A  ASN*     3.5    17.5    -      -       -      +
    305A  ILE*     4.1     6.1    -      -       +      -
    308A  THR*     4.6    13.0    -      -       +      +
    312A  THR*     4.7     2.0    -      -       +      -
    313A  LYS*     1.3    77.3    -      -       -      +
    315A  LYS*     1.3    61.8    +      -       -      +
    316A  LEU*     3.9    21.3    -      -       +      -
    327A  VAL      3.6     0.7    -      -       -      +
    328A  GLU*     3.3     4.9    -      -       -      -
    329A  VAL*     2.8    42.4    +      -       +      +
    331A  LEU*     4.0    35.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 315 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289A  SER      3.9     0.2    -      -       -      +
    290A  LEU*     3.5     6.6    -      -       -      +
    291A  ASN*     2.7    47.1    +      -       -      +
    314A  VAL*     1.3    75.1    -      -       -      +
    316A  LEU*     1.3    60.5    +      -       -      +
    317A  GLY      4.0     0.5    +      -       -      -
    326A  GLU*     3.4    31.7    -      -       -      +
    327A  VAL      3.4     4.0    -      -       -      +
    328A  GLU*     3.5    32.7    +      -       +      +
     73K  SER*     4.9    10.5    +      -       -      +
    121K  PRO*     3.0    29.1    +      -       -      +
    122K  SER*     4.7     5.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242A  LEU*     4.1    19.5    -      -       +      -
    244A  ILE*     5.7     0.2    -      -       +      -
    276A  SER*     5.0     1.3    -      -       -      +
    281A  VAL*     4.3    14.8    -      -       +      -
    287A  ILE*     3.9    38.1    -      -       +      -
    289A  SER      3.6     2.5    -      -       -      +
    290A  LEU*     3.9    25.4    -      -       +      -
    301A  LEU*     5.2     1.1    -      -       +      -
    314A  VAL*     3.9    17.5    -      -       +      -
    315A  LYS*     1.3    72.4    -      -       -      +
    317A  GLY*     1.3    62.6    +      -       -      +
    318A  LEU*     3.3     9.7    +      -       +      +
    325A  LEU      3.6     0.3    -      -       -      +
    326A  GLU*     3.4     6.7    -      -       -      -
    327A  VAL*     2.7    40.0    +      -       +      +
    329A  VAL*     3.8    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287A  ILE*     3.3     7.3    -      -       -      +
    288A  THR*     2.6    35.7    +      -       -      -
    289A  SER*     2.9    31.9    +      -       -      -
    316A  LEU*     1.3    68.2    -      -       -      +
    318A  LEU*     1.3    56.1    +      -       -      -
    325A  LEU      3.9     4.0    -      -       -      -
    326A  GLU*     3.9    11.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 318 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281A  VAL*     4.2    18.8    -      -       +      -
    285A  ASP*     3.3    42.2    -      -       +      +
    286A  ILE      3.5     8.3    -      -       -      +
    287A  ILE*     4.5     6.1    -      -       +      +
    288A  THR*     4.9     2.4    +      -       -      -
    316A  LEU*     3.9    11.7    -      -       +      +
    317A  GLY*     1.3    72.9    -      -       -      -
    319A  LEU*     1.3    76.2    +      -       -      +
    320A  ARG*     4.1     7.0    -      -       -      +
    324A  PRO*     3.6     5.7    -      -       -      +
    325A  LEU*     2.8    63.4    +      -       +      +
    327A  VAL*     4.1    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 319 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259A  LEU*     4.1    29.2    -      -       +      -
    260A  ASP      5.7     1.1    -      -       -      +
    261A  VAL*     3.8    28.0    -      -       +      -
    284A  GLY      4.4     1.0    -      -       -      +
    285A  ASP*     3.8     2.1    -      -       -      -
    286A  ILE*     3.0    44.3    +      -       +      +
    288A  THR*     4.5     7.9    -      -       +      +
    318A  LEU*     1.3    84.8    -      -       -      +
    320A  ARG*     1.4    61.0    +      -       -      +
    321A  ASN      4.2     0.5    +      -       -      -
    322A  GLY*     4.2    14.0    +      -       -      +
    323A  LYS      3.5     5.2    -      -       -      +
    324A  PRO*     3.8    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 320 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280A  GLY      2.6    29.1    +      -       -      -
    281A  VAL*     4.0     1.0    -      -       -      +
    282A  LYS*     3.6    34.2    -      -       -      +
    284A  GLY      5.3     1.8    -      -       -      +
    285A  ASP*     3.0    43.5    +      -       -      +
    318A  LEU*     4.1     8.2    -      -       +      +
    319A  LEU*     1.4    70.9    -      -       -      +
    321A  ASN*     1.3    72.3    +      -       +      +
    322A  GLY      3.1     0.9    -      -       -      -
    323A  LYS*     3.0    31.6    +      -       +      +
    325A  LEU*     3.7    32.1    -      -       +      +
    327A  VAL*     5.3     2.4    -      -       -      +
----------------------------------------------------------
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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