Contacts of the strand formed by residues 260 - 266 (chain B) in PDB entry 2C10


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 260 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182B  MET*     3.5    12.3    -      -       -      +
    187B  GLU*     5.6     0.4    -      -       -      -
    249B  VAL*     3.6     5.0    -      -       -      +
    250B  ASN*     3.0    45.4    +      -       -      +
    258B  ARG      3.6    11.3    +      -       -      +
    259B  TRP*     1.3    81.7    -      -       -      +
    261B  ILE*     1.3    66.1    +      -       -      +
    262B  GLN*     4.5     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 261 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182B  MET*     3.7    15.9    -      -       +      -
    183B  ILE*     4.9     2.5    -      -       +      -
    187B  GLU*     3.3    40.3    +      -       +      +
    247B  LEU*     4.3    17.7    -      -       +      -
    248B  LEU      3.3     6.7    -      -       -      +
    249B  VAL*     3.8    24.0    -      -       +      -
    260B  THR*     1.3    78.0    -      -       -      +
    262B  GLN*     1.3    59.9    +      -       -      +
    263B  LYS      3.3    26.4    +      -       -      +
    264B  VAL*     3.9    16.6    -      -       +      -
    272B  ASP      4.5     8.1    -      -       -      +
    273B  SER*     6.0     2.2    -      -       -      -
    274B  LEU*     5.0     3.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 262 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224B  ALA*     3.7    14.9    -      -       -      +
    248B  LEU*     2.9    35.3    +      -       +      +
    250B  ASN*     3.2    43.7    -      -       +      +
    260B  THR*     3.9     5.1    -      -       -      +
    261B  ILE*     1.3    73.2    -      -       -      +
    263B  LYS*     1.3    70.4    +      -       -      +
    272B  ASP*     4.4     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 263 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    553A  TRP*     4.3    24.9    +      -       +      +
    226B  TRP*     3.8    23.3    -      -       +      -
    247B  LEU*     3.8     0.7    -      -       -      -
    248B  LEU*     3.0    36.6    +      -       +      -
    261B  ILE*     3.3    10.2    +      -       -      +
    262B  GLN*     1.3    85.8    -      -       -      +
    264B  VAL*     1.3    66.7    +      -       -      +
    270B  TYR*     4.2    30.2    -      -       +      +
    271B  TYR      3.8    13.9    -      -       -      +
    272B  ASP*     3.3    25.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 264 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226B  TRP*     4.6     2.9    -      -       -      -
    245B  LEU*     3.8    26.5    -      -       +      -
    246B  GLU      3.7     3.6    -      -       -      -
    247B  LEU*     3.9    17.7    -      -       +      -
    261B  ILE*     3.9    10.5    -      -       +      -
    263B  LYS*     1.3    80.9    -      -       -      +
    265B  PHE*     1.3    63.2    +      -       -      +
    270B  TYR*     3.4     8.1    -      -       -      +
    271B  TYR*     2.8    45.3    +      -       +      +
    273B  SER*     3.8    26.9    -      -       -      +
    274B  LEU*     4.0     6.7    -      -       +      +
    277B  LEU*     4.0    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 265 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226B  TRP*     4.3     4.7    -      -       +      -
    244B  GLY*     3.5     7.1    -      -       -      +
    245B  LEU*     3.4     5.7    -      -       -      +
    246B  GLU*     3.0    45.8    +      -       +      +
    264B  VAL*     1.3    76.1    -      -       -      +
    266B  TYR*     1.3    61.3    +      -       -      +
    267B  GLN*     4.7     1.6    -      -       -      -
    268B  GLY*     3.3    46.7    -      -       -      -
    269B  ARG      3.2    12.1    -      -       -      -
    270B  TYR*     3.9    24.9    -      +       +      -
    375B  ASN      4.1     4.7    -      -       -      -
    376B  SER*     3.3    22.0    -      -       -      -
    377B  PRO*     3.5    39.5    -      -       +      -
    499B  PHE*     6.4     0.4    -      +       -      -
    501B  PHE*     3.9    15.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with TYR 266 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194B  LEU*     3.9    27.2    -      -       +      +
    195B  LEU*     5.7     1.3    -      -       +      -
    198B  CYS*     3.2    32.2    -      -       -      +
    199B  CYS*     4.6     1.3    -      -       -      -
    243B  VAL      4.0    12.1    -      -       -      -
    244B  GLY      3.2    10.8    -      -       -      -
    245B  LEU*     3.7    22.2    -      -       +      -
    265B  PHE*     1.3    74.9    -      -       -      +
    267B  GLN*     1.3   107.2    +      -       +      +
    268B  GLY      3.2     1.8    -      -       -      -
    269B  ARG*     2.8    26.7    +      -       -      +
    271B  TYR*     4.0     9.1    +      +       +      -
    277B  LEU*     3.9    33.0    -      -       +      -
    286B  VAL*     4.2    17.7    -      -       +      -
    288B  VAL*     3.6     8.1    -      -       +      +
----------------------------------------------------------
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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