Contacts of the strand formed by residues 109 - 115 (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 ASP 109 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  ASN*     3.0    28.6    +      -       -      +
     82D  LYS*     3.0    46.2    -      -       +      +
     84D  ALA      2.9    17.7    +      -       -      +
     85D  THR*     3.4    13.0    -      -       -      +
     86D  PHE      3.4     2.3    +      -       -      -
    107D  HIS      4.0     1.2    +      -       -      -
    108D  VAL*     1.3    71.6    -      -       -      +
    110D  ALA*     1.3    57.8    +      -       -      +
    111D  HIS*     2.9    42.0    +      -       -      -
    158D  LEU*     4.0     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 110 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86D  PHE*     3.4    18.2    -      -       +      +
    103D  ALA*     3.9    16.2    -      -       +      -
    108D  VAL*     3.0    11.0    +      -       +      +
    109D  ASP*     1.3    73.7    -      -       -      +
    111D  HIS*     1.3    67.9    +      -       -      +
    112D  TYR*     3.6    37.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 111 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85D  THR*     4.1     0.2    -      -       +      -
     86D  PHE      2.8     7.1    +      -       -      -
     87D  PHE*     3.0    48.3    -      +       +      -
     88D  GLY      3.5     0.3    +      -       -      -
    109D  ASP*     2.9    51.6    +      -       -      -
    110D  ALA*     1.3    76.2    +      -       -      +
    112D  TYR*     1.3    62.4    +      -       -      +
    149D  HIS*     3.7    11.7    +      -       +      +
    155D  ASN*     4.7    10.2    +      -       -      +
    158D  LEU*     3.3    27.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 112 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  ILE*     6.0     1.6    -      -       -      +
     15D  PRO*     3.9    16.2    -      -       +      -
     67D  GLN*     2.8    28.1    +      -       -      +
     86D  PHE*     3.8    19.0    -      +       -      -
     88D  GLY      3.1    19.5    -      -       -      +
     90D  ILE*     4.0    25.1    -      -       +      -
     99D  LEU*     3.7     8.1    +      -       +      -
    100D  LYS*     3.5    38.4    -      -       +      -
    103D  ALA*     3.3    19.1    -      -       -      +
    110D  ALA*     3.6    26.6    -      -       +      +
    111D  HIS*     1.3    77.2    -      -       -      +
    113D  TYR*     1.3    60.3    +      -       -      +
    114D  GLU*     3.8    12.0    +      -       +      +
    149D  HIS*     3.8     8.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 113 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116B  ASN*     3.7    27.0    +      -       +      +
    117B  GLU*     4.7     8.1    +      -       -      -
     88D  GLY      2.8    10.6    +      -       -      +
     89D  CYS*     3.3    22.1    -      -       +      -
     90D  ILE*     2.9    26.7    +      -       -      +
    112D  TYR*     1.3    73.6    -      -       -      +
    114D  GLU*     1.3    61.3    +      -       -      +
    115D  GLN*     3.6    28.5    -      -       +      +
    143D  CYS*     5.4     4.7    -      -       +      -
    144D  TYR*     4.8     4.9    -      +       +      -
    145D  LYS      6.3     0.9    -      -       -      -
    148D  LYS*     3.4    62.4    +      -       +      +
    149D  HIS*     3.6    23.9    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLU 114 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  ILE*     3.6    32.1    -      -       +      +
    116B  ASN*     2.8    32.4    +      -       -      +
     90D  ILE*     3.6    22.2    -      -       +      +
     91D  GLY      4.8     1.0    -      -       -      +
     92D  ILE*     3.6    27.4    -      -       +      +
    100D  LYS*     3.1    38.0    +      -       -      +
    112D  TYR*     3.8    11.6    +      -       +      +
    113D  TYR*     1.3    81.0    -      -       -      +
    115D  GLN*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 115 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116B  ASN*     5.0     0.9    -      -       -      +
     89D  CYS*     3.9    10.1    -      -       -      -
     90D  ILE      2.9    22.3    +      -       -      +
     91D  GLY*     3.4     1.0    -      -       -      -
     92D  ILE*     2.8    30.9    +      -       -      +
    113D  TYR*     3.6    27.1    -      -       +      +
    114D  GLU*     1.3    75.6    -      -       -      +
    116D  ASN*     1.3    60.6    +      -       -      +
    117D  GLU*     3.4    21.8    -      -       -      +
    118D  GLN*     2.6    57.5    -      -       -      +
    140D  ALA*     3.4     5.7    -      -       -      +
    143D  CYS*     4.0    12.6    -      -       +      -
----------------------------------------------------------
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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