Contacts of the strand formed by residues 87 - 98 (chain A) in PDB entry 3IT8


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 TYR 87 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  ALA*     3.1    19.5    +      -       +      +
     85A  VAL      3.3     0.8    -      -       -      -
     86A  SER*     1.3    81.2    -      -       -      +
     88A  GLN*     1.3    55.3    +      -       -      +
     89A  THR*     2.5    46.3    +      -       -      +
     91A  VAL*     4.3     4.7    -      -       +      -
     58F  HIS*     2.8    37.1    +      +       -      +
    153F  ALA      5.6     1.1    -      -       -      -
    157F  GLY*     3.7    24.9    -      -       -      +
    158F  PHE*     4.9     1.1    -      -       -      -
    160F  TYR*     4.3    14.1    -      -       +      -
    161F  MET*     4.1    19.3    -      -       +      -
    162F  GLY*     3.6    22.0    -      -       -      -
    165F  LEU*     4.1    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  ILE*     3.4    24.5    -      -       +      -
     84A  ALA      3.2     5.9    +      -       -      -
     85A  VAL*     3.0    32.5    +      -       -      +
     86A  SER      4.4     0.4    -      -       -      -
     87A  TYR*     1.3    64.9    -      -       -      +
     89A  THR*     1.3    65.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  ARG      3.1    13.0    -      -       -      +
     83A  ILE*     3.6     9.8    -      -       -      +
     84A  ALA      4.6     0.2    +      -       -      -
     87A  TYR*     2.5    38.5    +      -       -      +
     88A  GLN*     1.3    81.3    +      -       -      +
     90A  LYS*     1.3    78.3    +      -       -      +
     91A  VAL*     3.1     8.2    +      -       -      +
     58F  HIS*     4.6    15.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  GLN*     3.9    17.4    -      -       -      +
     81A  SER*     3.9    20.6    -      -       -      +
     82A  ARG      3.6     6.1    -      -       -      -
     83A  ILE*     4.2    13.3    -      -       +      +
     89A  THR*     1.3    83.0    -      -       +      +
     91A  VAL*     1.3    61.4    +      -       -      +
     92A  ASN*     5.2     2.4    -      -       -      +
    133A  SER*     4.1     9.0    -      -       -      -
    135A  GLU*     3.1    40.4    +      -       -      +
     58F  HIS*     5.2     2.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  SER*     4.3     0.7    -      -       -      -
     82A  ARG*     2.9    49.4    +      -       +      +
     84A  ALA*     5.8     1.1    -      -       +      +
     87A  TYR*     4.3     9.9    -      -       +      -
     89A  THR      3.6     8.5    -      -       -      +
     90A  LYS*     1.3    80.4    -      -       -      +
     92A  ASN*     1.3    64.1    +      -       -      +
     93A  LEU      3.5     0.2    +      -       -      -
     34C  ASN*     3.9    24.7    -      -       -      +
     58F  HIS*     4.6     5.6    -      -       +      +
    161F  MET*     4.2    12.8    -      -       -      -
    165F  LEU*     3.8    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  THR*     3.5    18.8    +      -       -      +
     80A  ILE      3.9     3.6    -      -       -      +
     81A  SER*     3.1    18.2    +      -       -      -
     90A  LYS*     5.2     2.1    -      -       -      +
     91A  VAL*     1.3    73.6    +      -       -      +
     93A  LEU*     1.3    64.5    +      -       -      +
     94A  LEU      4.8     2.5    -      -       -      +
     95A  SER*     4.7     6.1    +      -       -      -
     34C  ASN*     4.8     4.0    +      -       -      +
    146C  GLU*     2.6    39.0    +      -       -      +
    147C  SER*     4.1    14.6    +      -       -      -
    148C  GLY*     4.6     2.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  ILE*     3.9    27.6    -      -       +      -
     80A  ILE*     2.9    16.3    +      -       +      +
     81A  SER      4.7     1.1    -      -       -      -
     82A  ARG*     3.7    35.0    -      -       +      +
     91A  VAL      4.3     0.7    -      -       -      +
     92A  ASN*     1.3    77.1    -      -       -      +
     94A  LEU*     1.3    73.6    +      -       +      +
    124A  PHE*     3.6    33.0    -      -       +      -
    126A  LEU*     5.0     0.4    -      -       +      -
    132A  LEU*     4.1     7.2    -      -       +      -
     15C  HIS*     4.8     2.9    +      -       -      -
     34C  ASN*     3.5    44.4    -      -       +      +
    148C  GLY*     3.4    15.6    -      -       -      -
    151C  TYR*     5.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  ILE*     4.0     6.5    -      -       +      +
     79A  THR*     3.2     1.2    +      -       -      -
     80A  ILE*     2.8    54.6    +      -       +      +
     92A  ASN*     4.9     0.6    -      -       -      +
     93A  LEU*     1.3    90.6    +      -       +      +
     95A  SER*     1.3    65.0    -      -       -      +
    120A  LEU*     3.7    15.7    -      -       +      -
    121A  GLY*     3.6    28.9    -      -       -      +
    122A  GLY*     3.7     5.2    -      -       -      +
    124A  PHE*     3.6    25.6    -      -       +      -
    148C  GLY*     3.4     5.2    -      -       -      +
    151C  TYR*     3.4    37.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  THR*     5.5     1.4    -      -       -      -
     78A  HIS      3.3    11.8    +      -       -      -
     79A  THR*     3.7    16.2    -      -       -      +
     92A  ASN*     4.7     3.7    +      -       -      -
     94A  LEU*     1.3    77.5    -      -       -      +
     96A  ALA*     1.3    65.8    +      -       -      +
     97A  ILE*     5.1     2.1    -      -       -      +
    120A  LEU*     4.0     6.0    -      -       -      +
     61C  GLN*     3.4     6.2    -      -       -      +
    146C  GLU*     3.8    30.5    +      -       -      +
    148C  GLY*     2.8    19.2    +      -       -      +
    149C  GLN*     3.3    22.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  THR*     3.4     5.0    -      -       -      -
     78A  HIS      3.0    30.3    +      -       -      +
     95A  SER*     1.3    77.6    +      -       -      +
     97A  ILE*     1.3    68.3    +      -       -      +
    118A  ILE*     3.8    20.0    -      -       +      +
    120A  LEU*     3.7    19.2    -      -       +      +
     61C  GLN*     4.1     5.6    -      -       -      +
     63C  LEU*     4.7     7.0    -      -       +      -
    117C  PRO*     4.1    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  LEU*     4.4    17.7    -      -       +      -
     76A  LEU      3.2    11.7    -      -       -      +
     77A  THR*     4.2    17.5    -      -       +      -
     95A  SER*     5.1     2.7    -      -       -      +
     96A  ALA*     1.3    81.3    -      -       -      +
     98A  LYS*     1.3    66.5    +      -       -      +
    118A  ILE*     4.7     1.8    -      -       -      -
     63C  LEU*     4.2     8.2    -      -       +      +
    115C  TYR*     3.5    54.8    -      -       +      +
    117C  PRO*     3.5    19.9    -      -       -      +
    143C  LEU*     4.6     1.3    -      -       +      -
    149C  GLN*     3.5    26.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  LEU*     3.9     0.9    -      -       -      -
     76A  LEU*     2.8    39.5    +      -       +      +
     97A  ILE*     1.3    79.6    -      -       -      +
     99A  SER*     1.3    62.2    +      -       -      +
    100A  PRO*     3.3     5.9    -      -       -      +
    116A  GLU*     3.1    47.0    +      -       +      +
    117A  PRO*     2.9    28.8    +      -       -      +
    118A  ILE*     4.0    19.1    -      -       +      -
     98B  LYS*     3.5    24.0    -      -       -      +
     98C  LYS*     3.5    20.2    -      -       -      +
    115C  TYR*     4.0     7.9    -      -       -      +
    116C  GLU*     3.7     8.1    -      -       -      +
    117C  PRO*     4.2    13.0    -      -       +      +
----------------------------------------------------------
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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