Contacts of the strand formed by residues 1116 - 1120 (chain v) in PDB entry 6FF7


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 SER1116 (chain v).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1106v  LYS*     4.9     1.8    -      -       -      -
   1107v  THR*     2.9    27.8    +      -       -      +
   1108v  THR*     6.1     0.2    -      -       -      -
   1114v  SER      3.7     2.6    +      -       -      -
   1115v  GLU*     1.3    77.2    -      -       -      +
   1117v  LEU*     1.3    63.9    +      -       -      +
   1118v  VAL*     3.5     5.2    +      -       -      +
   1128v  ILE*     4.7    11.9    -      -       -      -
   1129v  LEU      3.6    15.5    -      -       -      -
   1130v  VAL*     4.6     9.2    -      -       -      +
   1131v  PRO      5.8     0.2    -      -       -      -
   1215v  TYR*     4.5    19.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU1117 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1104v  LEU*     6.5     1.1    -      -       +      -
   1105v  GLN      3.7     8.5    -      -       -      +
   1106v  LYS*     4.5     8.5    -      -       +      +
   1116v  SER*     1.3    70.4    -      -       -      +
   1118v  VAL*     1.3    60.7    +      -       -      +
   1119v  TYR*     3.9     0.7    +      -       -      +
   1128v  ILE*     3.0     7.8    -      -       -      +
   1129v  LEU*     2.8    50.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1118 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1103v  SER      3.5     1.7    -      -       -      +
   1104v  LEU*     3.4     3.5    -      -       -      -
   1105v  GLN*     2.9    45.6    +      -       +      +
   1107v  THR*     6.0     3.4    -      -       -      +
   1116v  SER      3.5     3.5    +      -       -      +
   1117v  LEU*     1.3    72.7    -      -       -      +
   1119v  TYR*     1.3    60.8    +      -       -      +
   1127v  GLY      3.6     7.0    -      -       -      +
   1128v  ILE*     4.4     4.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR1119 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1101v  VAL*     4.6    17.0    -      -       +      -
   1103v  SER      3.4     6.5    -      -       -      +
   1104v  LEU*     4.6     6.5    -      -       +      +
   1117v  LEU      3.9     1.8    +      -       -      +
   1118v  VAL*     1.3    75.3    -      -       -      +
   1120v  THR*     1.3    59.9    +      -       -      +
   1121v  THR      4.1     1.0    +      -       -      -
   1126v  ILE*     3.7     1.9    -      -       -      +
   1127v  GLY*     2.9    37.9    +      -       -      +
   1128v  ILE*     5.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR1120 (chain v). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407v  ILE*     4.7    12.0    -      -       -      +
    410v  CYS*     4.1    25.6    -      -       -      -
   1101v  VAL*     3.6     2.4    -      -       -      +
   1102v  LEU*     3.1    25.1    +      -       -      +
   1103v  SER*     3.0    16.1    +      -       -      -
   1119v  TYR*     1.3    74.5    -      -       -      +
   1121v  THR*     1.3    64.1    +      -       -      +
   1125v  GLY      3.8     5.4    -      -       -      -
   1126v  ILE*     4.5     7.2    -      -       -      +
----------------------------------------------------------
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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