Contacts of the strand formed by residues 313 - 316 (chain A) in PDB entry 3I7O


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 CYS 313 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  VAL*     4.1     7.6    -      -       +      -
     17A  GLY*     3.6     6.5    -      -       -      -
     18A  CYS*     2.0    72.0    -      -       +      +
    260A  CYS*     5.1     0.2    -      -       -      -
    311A  ALA*     3.9     0.4    -      -       -      +
    312A  GLU*     1.3    75.0    -      -       +      +
    314A  LEU*     1.3    68.8    -      -       -      +
    315A  THR*     4.1     1.1    -      -       -      -
    325A  GLY*     2.5    48.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 314 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    260A  CYS*     3.7    31.9    -      -       +      +
    261A  HIS      4.4     2.6    +      -       -      +
    262A  ASN*     3.1    31.1    -      -       +      +
    272A  LEU*     4.9     6.3    -      -       +      -
    273A  LEU*     4.2     2.5    -      -       -      -
    274A  GLY*     3.8    19.5    -      -       -      +
    280A  LEU*     3.8    24.7    -      -       +      -
    308A  THR*     5.4     0.4    -      -       -      +
    311A  ALA*     3.6    11.7    -      -       +      -
    312A  GLU      4.1     0.8    +      -       -      -
    313A  CYS*     1.3    85.5    -      -       -      +
    315A  THR*     1.3    69.2    +      -       -      +
    322A  VAL*     4.6     5.8    -      -       +      -
    323A  PHE      3.7     2.9    -      -       -      +
    324A  VAL*     3.3    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 315 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  CYS*     3.1    30.3    +      -       -      -
     19A  VAL*     4.5     3.5    -      -       -      -
     20A  THR*     3.3    43.0    -      -       +      +
     31A  LEU*     4.5     6.5    -      -       +      -
    262A  ASN*     3.4     6.5    +      -       -      +
    314A  LEU*     1.3    82.1    +      -       -      +
    316A  TYR*     1.3    71.1    +      -       -      +
    317A  LEU*     3.2    14.2    -      -       +      +
    322A  VAL*     4.0     3.7    -      -       -      +
    323A  PHE      2.9    36.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  THR*     4.3     8.7    +      -       -      +
    262A  ASN*     3.0    23.8    -      -       -      +
    263A  ARG      4.1     1.7    -      -       -      +
    264A  VAL*     3.5    55.4    -      -       +      -
    265A  ASP*     5.6     0.9    -      -       -      -
    270A  ARG*     4.9     6.9    +      -       -      -
    272A  LEU*     4.2     3.4    -      -       +      +
    315A  THR*     1.3    83.3    -      -       -      +
    317A  LEU*     1.3    80.3    +      -       -      +
    318A  ASP      2.8    20.1    +      -       -      -
    319A  ASN*     3.4     7.4    +      -       -      -
    320A  GLY*     3.0    28.9    +      -       -      -
    321A  VAL      3.4    10.5    -      -       -      -
    322A  VAL*     3.8    14.6    -      -       +      -
    336A  LEU*     4.7     6.3    -      -       +      -
----------------------------------------------------------
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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