Contacts of the strand formed by residues 141 - 147 (chain B) in PDB entry 6CIM


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 SER 141 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76B  ALA*     4.2     2.0    -      -       -      +
     77B  THR      5.9     0.4    -      -       -      +
    140B  HIS*     1.3    74.5    -      -       -      +
    142B  ILE*     1.3    61.6    +      -       -      +
    143B  ASP*     4.2     1.1    -      -       -      -
    154B  VAL      4.3     0.4    -      -       -      -
    155B  LEU*     3.1     7.5    -      -       -      +
    156B  PHE*     2.9    39.4    +      -       -      +
    207B  HIS*     2.5    34.2    +      -       -      -
    209B  SER*     3.5    27.8    -      -       -      -
    218B  ILE*     4.0     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 142 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76B  ALA*     4.0    20.5    -      -       +      +
     77B  THR*     3.3    19.8    +      -       -      +
     78B  CYS*     2.9    35.5    -      -       +      +
     92B  ILE*     4.0    22.9    -      -       +      +
     94B  HIS*     4.5     8.1    -      -       +      -
    107B  ILE*     5.1     1.1    -      -       +      -
    141B  SER*     1.3    75.0    -      -       -      +
    143B  ASP*     1.3    75.8    +      -       -      +
    153B  GLY*     5.1     0.9    -      -       -      -
    154B  VAL      3.1    15.3    -      -       -      +
    155B  LEU*     3.9    23.3    -      -       +      -
    185B  ILE*     4.4     9.6    -      -       +      -
    187B  PHE*     4.4    15.7    -      -       +      -
    209B  SER*     4.6     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78B  CYS*     3.8    11.8    -      -       -      +
    141B  SER*     4.2     1.0    -      -       -      -
    142B  ILE*     1.3    84.5    +      -       -      +
    144B  VAL*     1.3    64.7    +      -       -      +
    153B  GLY*     3.4     4.5    -      -       -      -
    154B  VAL*     2.9    33.2    +      -       -      +
    187B  PHE*     5.7     0.2    -      -       -      -
    209B  SER*     2.6    45.3    +      -       -      +
    211B  ALA*     3.6    26.0    +      -       +      +
    216B  VAL*     3.8    14.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78B  CYS*     4.1    18.5    -      -       -      +
     79B  SER      4.1    15.4    +      -       -      +
     80B  TYR*     4.2    16.2    -      -       +      -
     92B  ILE*     4.3     1.3    -      -       +      -
    143B  ASP*     1.3    78.4    -      -       -      +
    145B  VAL*     1.3    69.6    +      -       -      +
    146B  TYR*     3.7    40.4    -      -       +      +
    151B  SER*     4.4     9.4    -      -       -      -
    152B  MET      3.5     8.5    -      -       -      +
    187B  PHE*     4.2    19.1    -      -       +      -
    211B  ALA*     3.7    18.4    -      -       -      +
    213B  ASN      4.6     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 145 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  VAL*     1.3    78.8    -      -       -      +
    146B  TYR*     1.3    64.4    +      -       -      +
    147B  SER*     5.7     0.2    -      -       -      -
    150B  LYS      3.7     0.5    -      -       -      +
    151B  SER*     3.4     4.5    -      -       -      -
    152B  MET*     2.9    53.7    +      -       +      +
    154B  VAL*     4.0    19.5    -      -       +      -
    213B  ASN      3.3    12.6    -      -       -      +
    214B  ASP*     4.0    20.6    -      -       -      +
    215B  THR      4.0     4.0    -      -       -      +
    216B  VAL*     3.7    27.8    -      -       +      +
    236B  ILE      5.6     0.4    -      -       -      +
    238B  VAL*     4.1    19.3    -      -       +      -
    240B  LEU*     5.2     1.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 146 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  SER      5.4     0.3    +      -       -      -
     80B  TYR*     3.8     5.6    -      +       -      -
     81B  LYS*     3.6    36.0    +      -       +      +
    144B  VAL*     3.7    30.1    -      -       +      +
    145B  VAL*     1.3    74.3    -      -       -      +
    147B  SER*     1.3    59.3    +      -       -      +
    149B  GLY*     5.5     2.2    -      -       -      +
    150B  LYS      3.1    10.1    -      -       -      +
    151B  SER*     3.8    25.6    -      -       -      -
    213B  ASN*     2.8    23.5    +      -       -      +
    214B  ASP*     3.3    21.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 147 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145B  VAL*     4.2     1.3    +      -       -      -
    146B  TYR*     1.3    75.8    -      -       -      +
    148B  ARG*     1.3    72.1    +      -       -      +
    149B  GLY      3.3     1.1    -      -       -      -
    150B  LYS*     2.9    26.3    +      -       -      +
    214B  ASP*     3.9     7.3    +      -       -      +
    238B  VAL*     3.4    20.7    +      -       -      -
    239B  ASP*     3.0    28.8    +      -       -      -
    240B  LEU*     3.0    22.1    +      -       -      +
----------------------------------------------------------
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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