Contacts of the strand formed by residues 131 - 137 (chain B) in PDB entry 2I6A


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 ASN 131 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  PRO*     3.1    31.4    -      -       +      +
     36B  ASN*     2.8    21.9    +      -       -      +
    127B  ILE*     3.4     5.4    -      -       -      +
    128B  THR*     2.7    48.6    +      -       -      +
    129B  GLY*     4.8     0.5    -      -       -      -
    130B  ASP*     1.3    86.9    +      -       -      +
    132B  ARG*     1.3    65.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  SER*     5.0     3.8    -      -       -      -
     35B  PRO      3.1     3.1    +      -       -      -
     36B  ASN*     2.8    29.9    +      -       -      +
     37B  ASP      3.2     8.5    +      -       -      +
    125B  ALA*     3.8    21.9    -      -       +      +
    126B  CYS      3.9     3.6    -      -       -      -
    127B  ILE*     3.2    38.0    -      -       +      +
    130B  ASP      4.6     6.3    -      -       -      +
    131B  ASN*     1.3    80.4    -      -       -      +
    133B  SER*     1.3    60.3    +      -       -      +
    134B  LEU*     3.9    12.3    -      -       +      +
    292B  ILE*     5.6     7.5    -      -       -      +
    294B  ASP*     2.9    53.4    +      -       -      +
    295B  THR      5.0     1.6    -      -       -      +
    296B  ASN*     4.9    12.2    +      -       -      +
    332B  ARG*     5.1    11.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  LEU*     4.3     8.1    -      -       -      -
     33B  LEU*     3.6    20.4    -      -       -      +
     34B  LYS      2.9    25.4    +      -       -      -
     35B  PRO      3.4     5.4    +      -       -      -
     37B  ASP*     3.8     6.6    -      -       -      +
    124B  ALA      3.3     1.9    -      -       -      +
    126B  CYS*     2.8    51.6    +      -       -      +
    132B  ARG*     1.3    73.6    -      -       -      +
    134B  LEU*     1.3    58.6    +      -       -      +
    135B  ILE*     3.5    11.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  ASP*     6.0     1.8    -      -       -      +
     37B  ASP      3.0    14.7    +      -       -      +
     38B  GLN*     3.3    25.6    -      -       +      +
     39B  ILE*     2.8    33.8    +      -       -      +
    123B  CYS*     3.8    13.7    -      -       -      +
    124B  ALA      2.9     7.6    -      -       -      +
    125B  ALA*     3.2    37.9    -      -       +      -
    132B  ARG*     4.9    14.4    -      -       +      +
    133B  SER*     1.3    73.1    +      -       -      +
    135B  ILE*     1.3    59.6    +      -       -      +
    136B  ALA      4.2     0.2    -      -       -      -
    294B  ASP*     6.0     0.4    -      -       -      +
    296B  ASN*     4.1    15.5    -      -       +      +
    500B  5I5      4.0    35.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  LEU*     3.6    34.8    -      -       +      -
     39B  ILE*     3.4    17.3    -      -       +      -
     41B  ALA*     3.6    34.8    -      -       +      +
     45B  HIS*     4.3    10.3    -      -       +      -
     48B  LEU*     4.2     6.7    -      -       +      -
     49B  PHE*     3.5    16.6    -      -       +      -
    123B  CYS*     3.3     3.0    -      -       -      -
    124B  ALA*     2.8    36.1    +      -       +      +
    126B  CYS*     3.9    19.1    -      -       -      -
    133B  SER*     3.5    20.4    -      -       -      +
    134B  LEU*     1.3    80.3    -      -       -      +
    136B  ALA*     1.3    56.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  LEU*     4.2     4.5    -      -       +      -
     39B  ILE      2.9     9.9    +      -       -      -
     40B  LEU*     3.7    10.2    -      -       +      +
     41B  ALA*     2.8    26.7    +      -       -      +
    122B  THR      3.5     4.0    -      -       -      -
    123B  CYS*     3.9     6.7    -      -       -      -
    135B  ILE*     1.3    72.6    -      -       -      +
    137B  ASN*     1.3    59.3    +      -       -      +
    138B  LEU*     3.7    12.4    +      -       +      +
    500B  5I5      3.7    43.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  ALA*     4.1    10.2    -      -       +      +
     49B  PHE*     3.7    28.1    -      -       +      -
    119B  PRO*     5.6     2.4    -      -       -      +
    120B  THR      5.3     1.0    +      -       -      -
    121B  GLY*     3.3     1.2    -      -       -      -
    122B  THR*     2.5    51.2    +      -       -      +
    135B  ILE      4.0     1.2    +      -       -      -
    136B  ALA*     1.3    69.9    -      -       -      +
    138B  LEU*     1.3    63.4    +      -       -      +
    139B  ALA*     3.7    18.9    +      -       -      +
----------------------------------------------------------
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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