Contacts of the strand formed by residues 215 - 219 (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 THR 215 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145B  VAL*     4.0     2.9    -      -       -      +
    210B  ILE      4.5     0.2    -      -       -      -
    211B  ALA*     3.3     3.5    -      -       -      +
    212B  ARG*     2.9    35.3    +      -       -      -
    213B  ASN      3.3     1.0    +      -       -      -
    214B  ASP*     1.3    92.7    +      -       -      +
    216B  VAL*     1.3    68.3    +      -       -      +
    217B  TYR*     3.9    20.2    -      -       +      +
    235B  ARG*     3.3    36.8    -      -       +      -
    236B  ILE      3.3     9.2    -      -       -      +
    237B  ARG*     3.7    18.2    +      -       -      +
    294B  ASP      5.7     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 216 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143B  ASP*     3.8    20.4    -      -       +      +
    145B  VAL*     3.7    17.5    -      -       +      -
    154B  VAL*     3.8    28.0    -      -       +      -
    210B  ILE      3.3     6.7    -      -       -      +
    211B  ALA*     3.8    17.9    -      -       +      -
    215B  THR*     1.3    79.2    -      -       -      +
    217B  TYR*     1.3    63.7    +      -       -      +
    218B  ILE*     4.1     9.4    +      -       +      +
    234B  TYR      3.9     0.9    -      -       -      +
    235B  ARG      3.8     0.2    -      -       -      -
    236B  ILE*     2.9    56.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 217 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208B  VAL      3.6     1.0    -      -       -      +
    209B  SER*     3.2     7.4    -      -       -      -
    210B  ILE*     2.8    56.4    +      -       +      +
    212B  ARG*     5.4     6.5    -      -       +      -
    215B  THR*     3.9    15.4    -      -       +      +
    216B  VAL*     1.3    74.5    -      -       -      +
    218B  ILE*     1.3    61.0    +      -       -      +
    219B  LEU*     5.2     1.3    -      -       +      -
    233B  LEU*     4.0    20.2    -      -       +      -
    234B  TYR      3.2     5.8    -      -       -      +
    235B  ARG*     3.6    49.6    +      -       +      -
    237B  ARG*     5.2     1.2    +      -       -      -
    252B  LEU*     4.7     8.5    -      -       +      -
    292B  LEU*     4.4    25.1    -      -       +      -
    293B  GLY      4.6     3.9    +      -       -      -
    294B  ASP      5.4     0.9    +      -       -      -
    295B  ASN*     4.5     3.1    -      -       -      -
    296B  THR      4.2    14.0    +      -       -      -
    297B  ILE*     4.0    25.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 218 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141B  SER*     4.0     6.3    -      -       -      +
    156B  PHE*     4.2    20.9    -      -       +      -
    200B  LEU*     6.2     0.9    -      -       +      -
    204B  LEU*     3.7    29.4    -      -       +      -
    207B  HIS*     3.9    18.8    -      -       +      +
    208B  VAL      3.5     0.2    -      -       -      -
    209B  SER*     3.6    28.7    -      -       -      -
    216B  VAL*     4.9    11.0    -      -       +      +
    217B  TYR*     1.3    75.6    -      -       -      +
    219B  LEU*     1.3    63.1    +      -       -      +
    232B  ASN      4.0     0.2    -      -       -      +
    233B  LEU*     3.3     7.6    -      -       -      +
    234B  TYR*     2.8    52.6    +      -       +      +
    236B  ILE*     4.9    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 219 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207B  HIS*     3.2     2.5    -      -       -      +
    208B  VAL*     2.9    44.6    +      -       +      +
    210B  ILE*     3.5    29.4    -      -       +      -
    217B  TYR*     5.2     2.2    -      -       +      -
    218B  ILE*     1.3    73.1    -      -       -      +
    220B  GLY*     1.3    68.3    +      -       -      +
    221B  GLY      3.4     0.2    +      -       -      -
    232B  ASN      4.2     0.4    -      -       -      -
    233B  LEU*     3.5    34.8    -      -       +      -
    255B  GLY*     4.5     0.2    -      -       -      -
    256B  ILE*     3.8    25.8    -      -       +      +
    258B  VAL*     5.4     0.2    -      -       -      -
    273B  ILE*     3.9    17.5    -      -       +      -
    290B  VAL*     4.7     6.1    -      -       +      -
    299B  ILE*     3.8    26.2    -      -       +      -
----------------------------------------------------------
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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