Contacts of the strand formed by residues 312 - 317 (chain R) in PDB entry 5A31


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 VAL 312 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272R  ALA*     4.2     4.3    -      -       -      +
    273R  CYS*     3.6    19.6    -      -       -      -
    284R  GLY*     4.1     6.4    -      -       -      +
    285R  SER      3.1    20.2    +      -       -      +
    288R  HIS      3.7    25.4    -      -       -      +
    289R  ARG      4.2     0.9    -      -       -      +
    290R  ILE*     3.8    30.7    -      -       +      -
    308R  HIS*     3.6    29.6    -      -       +      -
    311R  GLU*     1.3    79.9    -      -       -      +
    313R  CYS*     1.3    59.6    +      -       -      +
    314R  GLY      3.9    18.2    -      -       -      +
    315R  LEU*     4.1     1.8    -      -       +      -
    326R  SER*     4.6     0.9    -      -       -      -
    327R  GLY      4.0     6.1    -      -       -      +
    328R  GLY*     4.2     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 313 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189R  TYR*     4.2    38.5    -      -       +      +
    272R  ALA*     4.8     3.8    -      -       +      +
    273R  CYS*     3.9    14.9    -      -       -      +
    311R  GLU*     4.2     6.5    -      -       +      +
    312R  VAL*     1.3    75.2    -      -       -      +
    314R  GLY*     1.3    58.0    +      -       -      +
    327R  GLY      3.0    14.3    +      -       -      -
    328R  GLY      3.8    20.0    -      -       -      -
    329R  ASN*     3.9     6.1    -      -       -      -
    353R  ALA*     4.5     5.6    -      -       -      -
    354R  VAL      3.8    10.8    -      -       -      -
    355R  LYS*     3.4    31.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 314 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273R  CYS*     4.1     2.7    -      -       -      -
    312R  VAL*     3.8     2.5    -      -       -      +
    313R  CYS*     1.3    75.9    -      -       -      +
    315R  LEU*     1.3    66.8    +      -       -      +
    326R  SER*     3.3     5.6    -      -       -      -
    327R  GLY*     2.8    42.1    +      -       -      +
    354R  VAL      4.0     2.0    +      -       -      -
    355R  LYS      3.6    19.1    -      -       -      -
    357R  MET*     4.3     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 315 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273R  CYS*     3.9    20.1    -      -       +      +
    274R  LEU      3.9     6.6    -      -       -      +
    275R  SER*     3.6    17.8    -      -       -      -
    282R  THR*     3.7    22.4    -      -       +      +
    283R  SER      3.7     8.3    -      -       -      +
    284R  GLY*     3.5    30.7    -      -       -      +
    290R  ILE*     3.9    17.0    -      -       +      -
    312R  VAL*     4.1     2.2    -      -       +      -
    314R  GLY*     1.3    80.0    -      -       -      +
    316R  LYS*     1.3    74.0    +      -       -      +
    324R  LEU*     4.2    15.5    -      -       +      -
    325R  ALA      3.5     5.8    -      -       -      +
    326R  SER*     3.5    24.0    -      -       -      -
    357R  MET*     4.5     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 316 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274R  LEU      6.1     0.4    -      -       -      -
    275R  SER*     3.6     4.0    -      -       -      +
    315R  LEU*     1.3    81.0    -      -       -      +
    317R  TRP*     1.3    63.2    +      -       -      +
    324R  LEU*     3.8     4.4    -      -       -      +
    325R  ALA*     2.9    34.7    +      -       +      +
    357R  MET*     3.1    47.8    +      -       +      +
    358R  ALA*     4.9     5.4    -      -       -      +
    359R  TRP*     3.1    24.4    +      -       +      +
    400R  ASN*     5.1     5.1    +      -       -      -
    401R  MET      4.1    14.5    +      -       -      -
    402R  VAL*     5.6     3.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 317 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275R  SER*     3.0    41.2    +      -       -      +
    276R  TRP      3.4    24.5    -      -       -      +
    277R  ASN*     3.1    37.5    -      -       +      +
    280R  VAL*     4.5     7.3    -      -       +      +
    282R  THR*     2.9    21.9    +      -       -      -
    292R  HIS*     3.5    25.4    -      +       -      -
    316R  LYS*     1.3    78.1    -      -       -      +
    318R  ASN*     1.3    62.4    +      -       -      +
    319R  VAL*     4.2     8.4    -      -       +      +
    322R  ASN*     4.0     8.5    -      -       -      -
    323R  LYS      3.3    34.8    -      -       -      -
    324R  LEU*     3.8    15.1    -      -       +      +
    338R  GLY*     3.4    31.4    -      -       -      -
    339R  THR*     4.3     2.9    -      -       -      -
    359R  TRP*     3.7     9.5    -      -       -      +
----------------------------------------------------------
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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