Contacts of the strand formed by residues 1334 - 1339 (chain A) in PDB entry 5IYB


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 TRP1334 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1143A  LEU*     4.1    34.0    +      -       +      +
   1147A  SER      4.5     2.5    -      -       -      +
   1148A  ALA*     3.7     3.2    +      -       -      +
   1149A  ARG*     3.8    36.5    +      -       -      -
   1150A  ASP      4.1     9.2    -      -       -      -
   1151A  ALA*     3.9    24.4    -      -       +      +
   1154A  ALA*     4.9     0.7    -      -       +      -
   1310A  HIS*     3.2    36.3    -      +       +      +
   1311A  LEU      3.5     2.9    -      -       -      -
   1312A  PRO*     3.4    52.7    -      -       +      -
   1333A  GLU*     1.3    83.4    -      -       -      +
   1335A  ILE*     1.3    65.0    +      -       -      +
    249U  GLN      5.0     1.3    -      -       -      -
    250U  MET*     4.2    18.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE1335 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1140A  THR*     4.1    15.0    -      -       +      -
   1141A  VAL      3.5     9.6    -      -       -      +
   1142A  PHE*     3.4    32.3    -      -       +      +
   1143A  LEU*     4.9     2.2    -      -       -      -
   1310A  HIS*     4.5     1.2    +      -       -      -
   1311A  LEU*     3.0    43.2    +      -       +      +
   1313A  GLN*     3.6    37.2    -      -       +      +
   1318A  LYS*     5.6     0.4    -      -       +      -
   1333A  GLU*     4.6     4.7    -      -       +      +
   1334A  TRP*     1.3    80.5    -      -       -      +
   1336A  LEU*     1.3    68.9    +      -       -      +
   1337A  GLU*     3.5    21.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU1336 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1139A  LEU      3.4     1.9    -      -       -      +
   1140A  THR*     3.7     0.8    -      -       -      -
   1141A  VAL*     2.8    49.9    +      -       +      +
   1143A  LEU*     4.0    31.2    -      -       +      +
   1154A  ALA      4.9     1.3    -      -       -      +
   1157A  ILE*     5.3     2.2    -      -       +      -
   1158A  LEU*     4.0    42.4    -      -       +      +
   1161A  LEU*     4.6    12.3    -      -       +      -
   1309A  MET      3.8    12.8    -      -       -      +
   1310A  HIS*     3.7    29.2    -      -       +      +
   1335A  ILE*     1.3    78.7    -      -       -      +
   1337A  GLU*     1.3    65.9    +      -       -      +
   1338A  THR*     4.3     6.9    -      -       +      +
   1352A  VAL*     6.0     0.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU1337 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1113A  SER*     3.7    12.4    +      -       -      +
   1116A  ASN*     4.3    19.2    +      -       -      +
   1138A  SER*     5.6     4.9    -      -       -      +
   1139A  LEU      3.8     4.7    -      -       -      +
   1140A  THR*     4.5    16.2    -      -       +      +
   1309A  MET*     3.1    38.9    +      -       +      +
   1311A  LEU*     3.0    37.5    -      -       +      +
   1335A  ILE*     3.5    25.7    +      -       -      +
   1336A  LEU*     1.3    72.8    -      -       -      +
   1338A  THR*     1.3    64.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR1338 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1138A  SER*     3.0    26.5    -      -       -      -
   1139A  LEU*     3.2    34.0    +      -       -      +
   1141A  VAL*     4.5     4.4    -      -       +      +
   1158A  LEU*     5.7     2.0    -      -       +      -
   1161A  LEU*     4.0    26.2    -      -       +      -
   1304A  ILE*     4.6    16.2    -      -       +      +
   1307A  VAL      4.6     7.2    -      -       -      -
   1308A  TYR*     5.1     7.6    -      -       +      -
   1309A  MET      4.8     1.6    -      -       -      +
   1336A  LEU*     4.3    11.7    -      -       +      +
   1337A  GLU*     1.3    81.5    -      -       -      +
   1339A  ASP*     1.3    61.6    +      -       -      +
   1340A  GLY*     3.2     2.1    +      -       -      -
   1346A  VAL*     5.8     0.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP1339 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1136A  THR*     5.0    10.8    -      -       +      +
   1137A  PRO*     3.1    30.7    -      -       -      +
   1138A  SER*     4.3     2.5    -      -       -      +
   1304A  ILE*     2.8    27.9    -      -       -      +
   1305A  SER*     4.4     6.2    +      -       -      -
   1307A  VAL*     2.9    46.0    +      -       +      +
   1308A  TYR      5.8     0.2    -      -       -      -
   1338A  THR*     1.3    71.0    -      -       -      +
   1340A  GLY*     1.3    57.2    +      -       -      +
----------------------------------------------------------
 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