Contacts of the strand formed by residues 1279 - 1285 (chain D) in PDB entry 6M6C


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 GLY1279 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1278D  ASP*     1.3    78.7    -      -       -      +
   1280D  VAL*     1.3    63.8    +      -       -      -
   1294D  VAL*     3.8     9.7    -      -       -      +
   1295D  GLU      3.4    13.0    -      -       -      -
   1296D  SER*     4.3     4.9    -      -       -      -
   1317D  ASP      3.7     0.5    -      -       -      +
   1318D  TYR*     3.1    34.1    -      -       -      -
   1319D  VAL*     3.3    10.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1280 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1279D  GLY*     1.3    77.6    -      -       -      +
   1281D  VAL*     1.3    72.6    +      -       -      +
   1293D  PHE      3.1     5.7    -      -       -      +
   1294D  VAL*     3.5     2.3    -      -       -      -
   1295D  GLU*     2.9    44.0    +      -       +      +
   1316D  GLY*     3.9     9.2    -      -       -      -
   1317D  ASP      3.3    22.4    -      -       -      +
   1318D  TYR*     4.9     8.7    -      -       +      -
   1319D  VAL*     6.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1281 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1280D  VAL*     1.3    79.1    -      -       -      +
   1282D  ARG*     1.3    63.5    +      -       -      +
   1283D  ILE*     3.8    15.5    -      -       +      -
   1292D  VAL*     3.6    26.7    -      -       +      -
   1293D  PHE      3.5     3.8    -      -       -      -
   1294D  VAL*     4.9     3.8    -      -       +      +
   1313D  VAL*     3.7    25.1    -      -       +      -
   1314D  LYS      3.1    27.4    -      -       -      +
   1315D  ASP*     3.6     4.7    -      -       -      +
   1316D  GLY*     3.2    18.0    +      -       -      +
   1317D  ASP      2.9    26.2    +      -       -      +
   1319D  VAL*     5.1     6.3    -      -       +      +
   1325D  LEU*     5.6     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1282 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1281D  VAL*     1.3    77.0    -      -       -      +
   1283D  ILE*     1.3    78.9    +      -       -      +
   1284D  GLU*     4.8     4.3    -      -       -      +
   1292D  VAL*     3.7     0.3    -      -       -      -
   1293D  PHE*     2.9    83.4    +      -       -      +
   1295D  GLU*     2.9    48.9    +      -       -      +
   1315D  ASP*     3.2     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1283 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1281D  VAL*     3.8    17.7    -      -       +      -
   1282D  ARG*     1.3    81.9    -      -       -      +
   1284D  GLU*     1.3    62.2    +      -       -      +
   1285D  GLU*     3.3    24.4    -      -       +      +
   1290D  LEU*     3.8    21.8    -      -       +      -
   1291D  SER      3.7     5.2    -      -       -      +
   1292D  VAL*     4.7     7.6    -      -       +      +
   1311D  LEU*     4.4    20.6    -      -       +      -
   1313D  VAL*     4.4     7.9    -      -       +      +
   1314D  LYS*     4.4     4.9    -      -       +      +
   1315D  ASP*     2.7    56.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU1284 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1282D  ARG*     3.8     6.0    +      -       -      +
   1283D  ILE*     1.3    72.6    -      -       -      +
   1285D  GLU*     1.3    62.9    +      -       -      +
   1286D  THR*     3.1    26.0    +      -       -      -
   1289D  LYS*     6.2     0.2    -      -       -      +
   1290D  LEU*     3.3     3.9    +      -       -      +
   1291D  SER*     2.3    66.0    +      -       -      +
   1293D  PHE*     3.9    16.2    -      -       +      -
   1302D  GLU*     5.1     0.5    -      -       -      +
   1304D  LYS*     4.2     6.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU1285 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1283D  ILE*     3.3    25.9    -      -       +      +
   1284D  GLU*     1.3    79.7    -      -       -      +
   1286D  THR*     1.3    64.6    +      -       -      +
   1287D  GLU*     4.1     8.6    +      -       -      +
   1289D  LYS      3.8     4.0    -      -       -      +
   1290D  LEU*     3.9    13.9    -      -       +      -
   1307D  LYS*     4.8     2.7    -      -       -      +
----------------------------------------------------------
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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