Contacts of the strand formed by residues 386 - 392 (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 SER 386 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    378A  CYS*     3.5     1.2    -      -       -      -
    379A  SER*     2.8    38.1    +      -       -      -
    384A  GLU      3.7     7.1    +      -       -      -
    385A  GLY*     1.3    77.9    -      -       -      -
    387A  LEU*     1.3    74.0    +      -       -      +
    388A  ARG*     2.9    26.5    +      -       -      +
    714A  THR*     4.6     2.2    -      -       -      -
    715A  VAL      3.4    11.2    -      -       -      -
    716A  PRO*     4.3     6.1    -      -       -      -
    717A  LEU*     3.8    11.2    -      -       -      -
    721A  PRO*     3.3    10.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 387 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    376A  VAL*     4.5     4.5    -      -       +      -
    377A  THR      3.2    11.4    -      -       -      +
    378A  CYS*     4.0    14.4    -      -       -      -
    386A  SER*     1.3    94.0    +      -       -      +
    388A  ARG*     1.3    64.1    +      -       -      +
    389A  ILE*     4.8     4.9    -      -       +      -
    715A  VAL*     2.9    43.3    +      -       +      -
    717A  LEU*     4.0    17.0    -      -       +      +
    724A  ILE*     4.1    29.2    -      -       +      -
    733A  PHE*     5.0     0.7    -      -       +      -
    735A  VAL*     4.3    13.7    -      -       +      -
    794A  ILE*     4.5    15.7    -      -       +      -
    799A  PHE*     4.2    26.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 388 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329A  GLY*     5.6     0.6    -      -       -      -
    330A  ASP*     2.3    45.0    +      -       -      +
    354A  THR*     3.3    27.1    -      -       -      +
    355A  ASN      3.4    12.9    +      -       -      -
    356A  LEU*     4.1    10.5    -      -       +      +
    375A  LEU      3.3     5.9    -      -       -      +
    376A  VAL*     3.4     0.3    -      -       -      -
    377A  THR*     3.0    34.3    +      -       -      +
    379A  SER*     3.5    20.9    -      -       -      +
    384A  GLU      5.1     4.6    +      -       -      -
    386A  SER*     2.9    19.7    +      -       -      +
    387A  LEU*     1.3    81.2    -      -       -      +
    389A  ILE*     1.3    62.4    +      -       -      +
    390A  ILE*     3.8    16.8    -      -       +      +
    712A  ILE*     4.3     7.2    -      -       +      +
    713A  ARG      3.1     8.3    -      -       -      +
    714A  THR*     3.4    28.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 389 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367A  LEU*     3.8    15.7    -      -       +      -
    374A  GLN*     3.4    35.2    -      -       +      +
    375A  LEU      3.4     1.8    -      -       -      -
    376A  VAL*     3.8    16.6    -      -       +      -
    387A  LEU*     4.8     2.2    -      -       +      -
    388A  ARG*     1.3    78.6    -      -       -      +
    390A  ILE*     1.3    61.1    +      -       -      +
    391A  ARG      4.1     0.2    -      -       -      -
    711A  HIS*     3.8     0.7    -      -       -      +
    712A  ILE*     3.3     5.2    -      -       -      +
    713A  ARG*     2.7    69.6    +      -       +      +
    715A  VAL*     4.2    14.4    -      -       +      -
    799A  PHE*     3.8    32.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 390 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  LEU*     3.8    37.9    -      -       +      -
    374A  GLN*     3.2     5.3    -      -       -      -
    375A  LEU*     2.7    67.8    +      -       +      +
    377A  THR*     4.4     6.5    -      -       +      -
    388A  ARG*     3.8    18.4    -      -       +      +
    389A  ILE*     1.3    76.0    -      -       -      +
    391A  ARG*     1.3    59.8    +      -       -      +
    392A  ASN      4.2     0.2    -      -       -      -
    710A  LEU*     4.4    22.2    -      -       +      -
    711A  HIS      3.3    13.7    -      -       -      +
    712A  ILE*     3.8    15.9    -      -       +      -
   1012A  LEU*     4.1    11.0    -      -       +      +
   1037A  ILE*     4.5     4.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 391 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372A  GLN*     4.3     8.1    -      -       +      +
    373A  GLY      4.9     0.2    -      -       -      -
    374A  GLN*     2.7    50.8    +      -       -      +
    389A  ILE      4.1     0.4    -      -       -      -
    390A  ILE*     1.3    73.3    -      -       -      +
    392A  ASN*     1.3    76.0    +      -       -      +
    393A  GLY      3.3    13.6    +      -       -      -
    395A  GLY*     4.7     3.4    -      -       -      -
    397A  HIS*     6.2     0.8    -      -       -      -
    672A  ASN*     3.2    28.6    -      -       -      +
    705A  ASP*     2.3    32.5    +      -       -      -
    710A  LEU*     3.8     2.8    -      -       -      -
    711A  HIS*     2.9    65.6    +      -       +      +
   1012A  LEU*     5.5     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 392 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372A  GLN*     5.9     2.9    -      -       -      +
    373A  GLY      4.9     1.8    +      -       -      -
    390A  ILE      4.2     0.8    +      -       -      -
    391A  ARG*     1.3    80.9    -      -       -      +
    393A  GLY*     1.3    69.9    +      -       -      +
    670A  ASN*     5.7     5.2    -      -       -      +
    672A  ASN*     3.2    14.7    +      -       -      +
    709A  LYS*     3.9    24.0    -      -       -      +
    710A  LEU*     3.1    31.6    -      -       +      +
   1012A  LEU*     3.3    45.6    +      -       +      +
   1013A  VAL*     4.3     4.2    -      -       +      +
   1140A  HIS      3.8    19.9    -      -       -      -
----------------------------------------------------------
 Back to top of page


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