Contacts of the strand formed by residues 131 - 137 (chain D) 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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35D  PRO*     2.9    30.7    -      -       -      +
     36D  ASN*     3.0    22.3    +      -       -      +
    127D  ILE*     3.3     7.6    -      -       -      +
    128D  THR*     2.7    52.7    +      -       -      +
    130D  ASP*     1.3    78.8    +      -       -      +
    132D  ARG*     1.3    66.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 132 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20D  SER*     4.9     3.8    +      -       -      -
     35D  PRO      3.0     4.5    +      -       -      -
     36D  ASN*     2.9    17.3    +      -       -      +
     37D  ASP      3.2    22.0    +      -       -      +
    125D  ALA*     4.2    16.9    -      -       +      +
    126D  CYS      3.7     3.8    -      -       -      -
    127D  ILE*     3.3    34.9    -      -       +      +
    130D  ASP      5.1     4.9    -      -       -      +
    131D  ASN*     1.3    79.0    -      -       -      +
    133D  SER*     1.3    60.0    +      -       -      +
    134D  LEU*     4.0    15.4    -      -       +      +
    292D  ILE*     6.1     3.0    -      -       -      +
    293D  ILE      5.1     2.0    -      -       -      -
    294D  ASP*     2.9    56.5    +      -       -      +
    295D  THR      5.1     1.3    -      -       -      +
    296D  ASN*     4.8     9.8    -      -       -      +
    332D  ARG*     4.6    17.0    +      -       -      +
    334D  THR*     5.0     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 133 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28D  LEU*     4.0     9.9    -      -       -      -
     33D  LEU*     3.8    15.1    -      -       -      +
     34D  LYS      2.4    29.5    +      -       -      -
     35D  PRO      3.7     2.2    +      -       -      -
     37D  ASP*     3.9    10.6    -      -       -      +
    124D  ALA      3.1     2.9    -      -       -      +
    125D  ALA*     3.5     0.3    -      -       -      -
    126D  CYS*     2.7    55.9    +      -       -      +
    132D  ARG*     1.3    70.7    -      -       -      +
    134D  LEU*     1.3    61.3    +      -       -      +
    135D  ILE*     3.6     6.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 134 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18D  ASP*     6.5     0.9    -      -       -      -
     37D  ASP*     3.1    17.4    +      -       -      +
     38D  GLN*     3.3    28.7    -      -       +      +
     39D  ILE*     2.8    34.8    +      -       -      +
    123D  CYS*     4.0    12.8    -      -       -      -
    124D  ALA      3.1     6.7    -      -       -      +
    125D  ALA*     3.6    32.8    -      -       +      +
    132D  ARG*     4.7    16.8    -      -       +      +
    133D  SER*     1.3    73.9    +      -       -      +
    135D  ILE*     1.3    56.9    +      -       -      +
    136D  ALA      4.1     0.7    -      -       -      -
    294D  ASP*     5.9     0.7    -      -       -      +
    296D  ASN*     4.4    11.2    -      -       +      +
    500D  5I5      3.9    40.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 135 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33D  LEU*     3.7    25.4    -      -       +      -
     39D  ILE*     3.3    17.0    -      -       +      -
     41D  ALA*     3.8    31.2    -      -       +      +
     45D  HIS*     4.5     9.4    -      -       +      -
     48D  LEU*     3.9    13.9    -      -       +      -
     49D  PHE*     3.5    17.5    -      -       +      -
    123D  CYS*     3.4     1.9    -      -       -      -
    124D  ALA*     2.8    33.9    +      -       +      +
    126D  CYS*     3.6    24.2    -      -       +      -
    133D  SER*     3.6    20.6    -      -       -      +
    134D  LEU*     1.3    75.7    -      -       -      +
    136D  ALA*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 136 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16D  LEU*     4.1     2.7    -      -       +      -
     39D  ILE      2.9    10.7    +      -       -      -
     40D  LEU*     3.7     7.3    -      -       +      +
     41D  ALA*     2.8    28.7    +      -       -      +
    122D  THR      3.6     5.8    -      -       -      +
    123D  CYS*     4.0     6.7    -      -       -      +
    135D  ILE*     1.3    74.3    -      -       -      +
    137D  ASN*     1.3    59.0    +      -       -      +
    138D  LEU*     3.5    15.8    +      -       +      +
    500D  5I5      3.6    44.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 137 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  ALA*     4.2    11.7    -      -       -      +
     46D  LYS*     5.4     7.4    -      -       -      +
     49D  PHE*     3.8    26.3    -      -       +      -
    119D  PRO*     5.9     0.8    -      -       -      +
    121D  GLY*     3.2     2.1    -      -       -      -
    122D  THR*     2.6    50.6    +      -       -      +
    135D  ILE      3.9     1.4    +      -       -      -
    136D  ALA*     1.3    68.8    -      -       -      +
    138D  LEU*     1.3    66.1    +      -       -      +
    139D  ALA*     3.2    20.5    +      -       -      +
----------------------------------------------------------
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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