Contacts of the strand formed by residues 177 - 183 (chain A) in PDB entry 3T2D


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 LYS 177 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  VAL      3.8     0.2    -      -       -      +
    171A  LEU*     3.7     3.0    -      -       -      +
    172A  ASP*     2.8    34.1    +      -       +      +
    175A  GLU*     2.7    44.2    +      -       +      +
    176A  HIS*     1.3    80.0    -      -       -      +
    178A  VAL*     1.3    63.8    +      -       -      +
    179A  TYR*     3.8    29.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  GLU*     3.7    29.6    -      -       +      -
    170A  VAL      3.3     6.1    -      -       -      +
    171A  LEU*     3.9    12.6    -      -       +      -
    176A  HIS      5.6     0.7    -      -       -      +
    177A  LYS*     1.3    78.2    -      -       -      +
    179A  TYR*     1.3    76.6    +      -       -      +
    180A  LEU*     5.0     6.3    -      -       +      -
    203A  ARG*     3.5    23.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 179 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168A  PHE      3.4     2.4    -      -       -      +
    169A  GLU*     3.5     2.8    -      -       -      -
    170A  VAL*     2.8    41.5    +      -       +      +
    172A  ASP*     4.1     5.6    +      -       +      -
    175A  GLU*     5.2     0.7    +      -       -      -
    177A  LYS*     3.8    42.8    +      -       +      +
    178A  VAL*     1.3    78.5    -      -       -      +
    180A  LEU*     1.3    63.1    +      -       -      +
    181A  LEU*     3.6    20.2    -      -       +      -
    193A  LEU*     4.2    18.6    -      -       +      -
    200A  TYR*     4.0    28.9    +      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 180 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  ILE*     4.1    20.0    -      -       +      -
    168A  PHE      3.4     2.7    -      -       -      +
    169A  GLU*     3.9    35.4    -      -       +      +
    178A  VAL*     5.0     5.2    -      -       +      -
    179A  TYR*     1.3    73.5    -      -       -      +
    181A  LEU*     1.3    64.0    +      -       -      +
    182A  LYS*     4.5     7.0    +      -       +      +
    186A  ASP*     4.5     3.1    -      -       -      +
    206A  PHE*     5.6     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  PHE      3.9     0.3    -      -       -      +
    167A  ILE*     3.5     2.9    -      -       -      +
    168A  PHE*     2.8    40.8    +      -       +      +
    170A  VAL*     4.0    20.4    -      -       +      -
    179A  TYR*     3.6    28.7    -      -       +      -
    180A  LEU*     1.3    76.6    -      -       -      +
    182A  LYS*     1.3    63.9    +      -       -      +
    186A  ASP*     3.6    15.3    -      -       +      +
    189A  SER*     4.0    15.9    -      -       -      +
    190A  LEU*     3.7    44.2    -      -       +      +
    193A  LEU*     4.1    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  PHE      3.4     4.7    -      -       -      +
    167A  ILE*     4.3    20.4    -      -       +      -
    180A  LEU*     4.8     6.7    -      -       +      +
    181A  LEU*     1.3    78.0    -      -       -      +
    183A  THR*     1.3    60.8    +      -       -      +
    185A  GLU*     3.5    20.1    +      -       -      +
    186A  ASP*     2.8    47.7    +      -       -      +
    208A  ARG*     3.7    29.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  PHE      4.1     2.4    +      -       -      -
    148A  ALA*     3.8    21.2    -      -       +      +
    165A  GLY*     3.4     3.7    -      -       -      -
    166A  PHE*     3.0    28.7    +      -       -      +
    168A  PHE*     3.4    32.2    -      -       +      -
    182A  LYS*     1.3    77.2    -      -       -      +
    184A  PRO*     1.3    66.9    -      -       -      +
    185A  GLU      3.6     0.9    -      -       -      -
    186A  ASP      4.7     0.2    -      -       -      -
    187A  ALA*     4.1    19.5    -      -       +      +
    190A  LEU*     3.7    18.6    -      -       +      -
    208A  ARG*     3.0    13.3    +      -       -      -
----------------------------------------------------------
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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