Contacts of the strand formed by residues 179 - 185 (chain B) in PDB entry 6CU0


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 LEU 179 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143B  VAL*     3.8    28.3    -      -       +      +
    144B  PHE*     4.1     3.1    -      -       -      -
    145B  PHE*     3.7    45.1    -      -       +      +
    164B  ALA*     3.6     0.9    -      -       -      -
    165B  LEU*     2.8    44.5    +      -       +      +
    177B  ALA*     3.8     3.3    -      -       -      +
    178B  ALA*     1.3    76.5    -      -       -      +
    180B  ALA*     1.3    63.5    +      -       -      +
    200B  GLN*     3.7    21.8    -      -       +      +
    202B  ARG*     3.4    43.7    -      -       +      +
    204B  LEU*     5.2     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 180 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  GLU*     5.8     1.6    -      -       -      +
    197A  PHE*     3.3    18.3    -      -       +      -
    145B  PHE*     3.9     2.9    -      -       -      -
    163B  LEU      3.6    10.5    -      -       -      +
    164B  ALA*     4.6     2.7    -      -       +      -
    177B  ALA*     4.3    15.9    -      -       +      +
    179B  LEU*     1.3    76.5    -      -       -      +
    181B  LEU*     1.3    61.8    +      -       -      +
    200B  GLN*     2.9    29.7    +      -       -      +
    202B  ARG*     5.7     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 181 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  PHE*     4.0    15.2    -      -       +      -
    145B  PHE*     3.8    31.9    -      -       +      +
    147B  LEU*     4.4    15.3    -      -       +      -
    162B  SER*     3.2     2.6    -      -       -      -
    163B  LEU*     3.1    34.7    +      -       +      +
    180B  ALA*     1.3    73.5    -      -       -      +
    182B  THR*     1.3    89.3    +      -       -      +
    183B  VAL*     4.2     2.2    -      -       +      -
    198B  GLY*     3.3    44.0    -      -       -      +
    199B  PHE*     3.8     7.0    -      -       -      +
    200B  GLN*     4.0    15.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 182 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  SER*     5.0     5.6    +      -       -      +
    197A  PHE*     3.8    35.3    -      -       -      +
    160B  SER*     3.3    27.1    -      -       -      +
    161B  VAL      3.4     8.1    -      -       -      +
    162B  SER*     3.6    12.8    +      -       -      +
    181B  LEU*     1.3    90.2    +      -       -      +
    183B  VAL*     1.3    69.3    +      -       -      +
    184B  ASP*     4.3     8.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  LEU*     3.9    20.6    -      -       +      +
    149B  LEU*     3.6    18.4    -      -       +      -
    160B  SER*     3.5     2.8    -      -       -      -
    161B  VAL*     2.9    33.0    +      -       -      +
    181B  LEU*     4.2     3.4    -      -       +      -
    182B  THR*     1.3    79.4    -      -       -      +
    184B  ASP*     1.3    65.2    +      -       -      +
    185B  LEU*     3.7     1.0    +      -       -      +
    196B  ALA*     3.4    34.3    -      -       +      +
    197B  PHE      3.6    23.8    -      -       -      +
    198B  GLY*     3.8    16.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  PRO*     5.5     2.9    -      -       -      +
    193A  ARG*     3.5    27.5    -      -       -      +
    195A  SER      5.4     2.3    -      -       -      +
    159B  GLY      3.7     8.1    -      -       -      +
    160B  SER*     4.6     4.6    -      -       -      +
    182B  THR*     4.6    10.6    -      -       -      +
    183B  VAL*     1.3    76.8    -      -       -      +
    185B  LEU*     1.3    63.2    +      -       -      +
    186B  PRO*     3.6     6.7    -      -       +      +
    196B  ALA*     3.6    19.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  LEU*     4.6     3.1    -      -       +      -
    149B  LEU*     3.6    31.6    -      -       +      -
    158B  SER*     3.7     9.3    -      -       -      +
    159B  GLY      2.8    35.8    +      -       -      +
    160B  SER*     4.3     9.2    -      -       -      +
    161B  VAL*     3.8    22.4    -      -       +      -
    183B  VAL      4.5     0.7    -      -       -      +
    184B  ASP*     1.3    76.0    -      -       -      +
    186B  PRO*     1.3    70.9    -      -       -      +
    187B  PRO*     3.7     1.7    -      -       -      +
    196B  ALA*     4.3     1.8    -      -       +      -
    218B  THR*     5.8     1.1    -      -       -      +
    219B  GLU      5.7     0.9    -      -       -      +
    223B  ARG*     6.4     1.8    -      -       -      -
    226B  TRP*     3.7    57.7    -      -       +      +
----------------------------------------------------------
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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