Contacts of the strand formed by residues 1247 - 1252 (chain A) in PDB entry 6Q6Q


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 GLU1247 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    562A  CYS*     3.4    21.3    -      -       +      -
   1183A  ILE      3.1    11.8    +      -       -      +
   1184A  ARG*     3.1    32.9    +      -       +      +
   1185A  THR      2.9    25.6    +      -       -      -
   1245A  PRO*     4.0     3.3    -      -       -      +
   1246A  THR*     1.3    78.7    -      -       -      +
   1248A  LEU*     1.3    61.9    +      -       -      +
   1249A  HIS*     2.8    35.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU1248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  ARG*     4.4    13.0    -      -       +      -
    562A  CYS      3.0    11.0    +      -       -      +
    563A  SER*     3.2     8.8    -      -       -      -
    564A  THR      3.1    23.7    +      -       -      +
    565A  LEU*     5.3     1.5    -      -       +      +
   1185A  THR*     3.4    27.4    -      -       +      +
   1187A  ILE*     4.5     6.7    -      -       +      -
   1205A  GLU*     3.7    36.8    -      -       +      +
   1208A  PHE*     5.2     7.0    -      -       +      -
   1209A  ILE*     6.3     3.4    -      -       +      -
   1244A  MET*     5.6     7.0    -      -       +      -
   1245A  PRO*     4.6    18.2    -      -       +      +
   1247A  GLU*     1.3    74.7    -      -       -      +
   1249A  HIS*     1.3    72.3    +      -       -      +
   1250A  ILE*     4.1    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS1249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    562A  CYS*     5.1     3.4    -      -       -      -
    564A  THR*     2.3    46.9    +      -       +      +
    983A  MET*     4.0    15.9    -      -       +      +
   1184A  ARG*     3.3    22.6    +      -       +      -
   1185A  THR      2.9     7.2    +      -       -      +
   1186A  ASP*     3.1    28.2    -      -       -      +
   1187A  ILE*     2.7    32.8    +      -       -      +
   1247A  GLU*     2.8    37.4    +      -       +      +
   1248A  LEU*     1.3    77.9    +      -       -      +
   1250A  ILE*     1.3    58.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    564A  THR      3.1     7.0    +      -       -      +
    565A  LEU*     3.3    18.6    -      -       +      +
    566A  LYS*     2.9    23.7    +      -       -      +
    983A  MET*     4.9     1.1    -      -       -      -
   1187A  ILE*     3.2    22.7    -      -       +      +
   1201A  ILE*     4.5    20.2    -      -       +      +
   1204A  ILE*     3.7    38.4    -      -       +      -
   1205A  GLU*     3.5    35.4    -      -       +      +
   1248A  LEU*     4.1    13.0    -      -       +      -
   1249A  HIS*     1.3    78.4    -      -       -      +
   1251A  ALA*     1.3    69.1    +      -       -      +
   1252A  LEU*     5.0     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA1251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    566A  LYS*     3.5    21.5    -      -       +      -
    979A  GLU*     4.2    16.2    -      -       -      +
    983A  MET*     3.6    24.9    -      -       -      -
   1187A  ILE      2.9     6.5    +      -       -      +
   1188A  VAL*     3.2    10.3    -      -       +      +
   1189A  MET      3.1    22.9    +      -       -      -
   1250A  ILE*     1.3    77.6    -      -       -      +
   1252A  LEU*     1.3    67.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    566A  LYS*     2.9    18.6    +      -       -      +
    567A  TYR*     4.0    27.0    -      -       +      -
    568A  GLN*     5.4     3.3    +      -       -      +
    979A  GLU*     5.6     1.1    -      -       -      +
   1189A  MET*     3.6     9.6    -      -       +      +
   1191A  VAL*     4.2    28.3    -      -       +      -
   1194A  SER*     4.6    14.1    -      -       -      +
   1197A  PRO*     4.7     4.7    -      -       +      -
   1200A  ASP*     5.4     3.1    -      -       +      -
   1201A  ILE*     4.0    22.0    -      -       +      -
   1204A  ILE*     3.8    29.8    -      -       +      -
   1250A  ILE*     5.0     1.6    -      -       +      -
   1251A  ALA*     1.3    79.4    -      -       -      +
   1253A  LEU*     1.3    68.7    +      -       -      +
   1254A  PRO*     3.4     6.8    -      -       -      +
   1268A  LEU*     5.4     0.4    -      -       +      -
----------------------------------------------------------
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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