Contacts of the strand formed by residues 113 - 126 (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 PRO 113 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  LYS*     4.6     5.4    -      -       -      -
     66A  GLY      3.2     8.1    -      -       -      +
     67A  GLN*     3.0    27.6    -      -       -      +
     68A  GLY      4.1     1.3    -      -       -      +
    112A  LYS*     1.3    94.0    -      -       +      +
    114A  TRP*     1.3    60.2    +      -       -      +
    115A  TYR*     4.4    20.7    -      -       +      +
     73B  HIS*     3.1    35.2    +      -       +      -
     75B  LEU*     5.7     1.1    -      -       +      -
     99B  SER*     4.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  PHE*     3.8    17.5    -      -       +      -
     65A  LYS*     3.1     9.8    -      -       -      +
     66A  GLY*     2.8    53.2    +      -       -      -
     68A  GLY      3.1    27.0    +      -       -      -
     69A  CYS*     4.5     2.2    -      -       -      -
     70A  PRO*     4.9     1.9    -      -       +      +
     74A  VAL*     5.9     0.2    -      -       +      -
     76A  LEU*     3.8    23.1    -      -       +      -
    100A  PRO*     3.7    38.6    -      -       +      -
    101A  CYS*     3.6    18.4    -      -       -      -
    112A  LYS      4.7     1.6    -      -       -      -
    113A  PRO*     1.3    75.6    -      -       -      +
    115A  TYR*     1.3    73.9    +      -       -      +
    116A  GLU*     4.1     6.7    -      -       +      +
    141A  TYR*     3.9    30.2    -      +       -      -
     73B  HIS*     6.1     0.4    -      -       +      -
     99B  SER*     3.5    11.0    -      -       -      +
    102B  GLN*     5.7     9.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  LEU*     4.3     4.9    -      -       +      -
     64A  PHE      3.3     4.3    -      -       -      +
     65A  LYS*     3.2    35.0    +      -       +      -
    113A  PRO*     4.4    16.7    -      -       +      +
    114A  TRP*     1.3    81.0    -      -       -      +
    116A  GLU*     1.3    76.1    +      -       -      +
    143A  LEU*     3.3    33.9    -      -       +      -
     75B  LEU*     3.9    37.1    -      -       +      +
     97B  ILE*     3.5    51.6    -      -       +      +
     98B  LYS*     4.0     5.8    -      -       -      +
     99B  SER*     3.2    20.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  LEU*     3.9     1.3    -      -       -      +
     64A  PHE*     2.9    41.8    +      -       +      +
     76A  LEU*     4.3    10.1    -      -       +      -
     98A  LYS*     3.1    53.9    +      -       +      -
     99A  SER      5.8     0.2    -      -       -      -
    100A  PRO*     4.4    17.1    -      -       +      +
    114A  TRP*     4.1    21.2    -      -       +      +
    115A  TYR*     1.3    83.7    +      -       -      +
    117A  PRO*     1.3    64.8    -      -       -      +
     98B  LYS*     3.7    14.0    -      -       -      +
     99B  SER*     4.9     4.0    +      -       -      +
    116B  GLU*     4.9     1.6    -      -       -      +
    116C  GLU*     4.9     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  GLN*     4.9     7.2    -      -       -      +
     62A  VAL      3.4    10.1    -      -       -      +
     63A  LEU*     4.3     7.9    -      -       +      -
     98A  LYS*     2.9    33.3    +      -       -      +
    116A  GLU*     1.3    82.6    -      -       -      +
    118A  ILE*     1.3    67.3    +      -       -      +
     96B  ALA*     4.1    24.2    -      -       +      -
     97B  ILE      3.5    21.5    -      -       -      +
     98B  LYS*     4.2    20.9    -      -       +      +
    117B  PRO      5.6     0.2    -      -       -      +
    118B  ILE*     5.1     7.9    -      -       +      -
    117C  PRO*     5.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  GLN*     3.3     8.7    -      -       -      +
     62A  VAL*     3.1    35.6    +      -       +      -
     64A  PHE*     4.0    26.7    -      -       +      -
     76A  LEU      4.3    10.5    -      -       -      +
     78A  HIS*     3.7    25.9    +      -       +      +
     96A  ALA*     3.8    31.6    -      -       +      +
     97A  ILE      4.7     1.3    -      -       -      -
     98A  LYS*     4.0    31.2    -      -       +      +
    117A  PRO*     1.3    81.5    -      -       -      +
    119A  TYR*     1.3    66.5    +      -       -      +
    120A  LEU*     4.2     1.1    -      -       +      -
    117C  PRO*     5.2     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  TYR*     3.5    17.8    -      +       +      +
     60A  SER      3.6    10.8    -      -       -      -
     61A  GLN*     4.0    10.1    -      -       +      +
    118A  ILE*     1.3    75.3    -      -       -      +
    120A  LEU*     1.3    96.4    +      -       -      +
    121A  GLY*     4.3     1.3    -      -       -      -
    151A  TYR*     3.6    21.1    -      +       -      -
     57B  LEU*     5.8     2.6    -      -       -      +
    119B  TYR*     3.5    31.1    -      +       +      +
    121B  GLY*     3.3    37.5    +      -       -      -
     61C  GLN*     3.3    11.8    +      -       -      -
    119C  TYR*     3.4    56.8    +      +       +      +
----------------------------------------------------------
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Residues in contact with LEU 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  TYR*     3.1     5.5    -      -       -      +
     60A  SER      2.9    35.6    +      -       -      +
     78A  HIS*     3.5    43.1    -      -       +      +
     79A  THR*     3.8     3.6    -      -       -      -
     80A  ILE*     4.1    14.8    -      -       +      +
     94A  LEU*     3.7    33.9    -      -       +      +
     95A  SER      4.1     2.5    -      -       -      +
     96A  ALA*     3.7    22.0    -      -       +      +
    118A  ILE*     4.2     3.4    -      -       +      -
    119A  TYR*     1.3    93.0    -      -       -      +
    121A  GLY*     1.3    58.8    +      -       -      +
     61C  GLN*     3.3    19.1    -      -       -      +
    151C  TYR*     4.1     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  LEU*     5.0     1.3    -      -       -      -
     58A  ILE      3.1    11.9    -      -       -      -
     59A  TYR*     4.1     4.5    -      -       -      -
     94A  LEU*     3.6     9.8    -      -       -      +
    119A  TYR*     4.5     0.9    -      -       -      -
    120A  LEU*     1.3    75.2    -      -       -      +
    122A  GLY*     1.3    59.5    +      -       -      -
     59C  TYR*     3.6     1.4    -      -       -      -
    119C  TYR*     3.3    24.5    +      -       -      -
    151C  TYR*     3.0    30.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  LEU*     3.6     6.9    -      -       -      +
     58A  ILE      2.9    29.6    +      -       -      +
     94A  LEU*     3.7     5.6    -      -       -      +
    121A  GLY*     1.3    73.5    -      -       -      -
    123A  VAL*     1.3    64.1    +      -       -      -
    124A  PHE*     3.5    19.1    -      -       -      -
     15C  HIS*     4.3     0.9    -      -       -      -
     59C  TYR*     3.5    17.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  LEU*     4.1    18.8    -      -       +      -
     56A  TYR      3.2    11.0    -      -       -      +
     57A  LEU*     4.3     9.6    -      -       +      -
    122A  GLY*     1.3    74.5    -      -       -      +
    124A  PHE*     1.3    75.8    +      -       -      +
    157A  LEU*     4.3    11.4    -      -       +      -
     13C  VAL*     4.0    26.2    -      -       +      -
     14C  ALA      5.6     0.2    -      -       -      +
     15C  HIS*     3.7    20.3    +      -       +      +
     36C  LEU*     4.1     4.0    -      -       +      +
     57C  LEU*     5.3     0.4    -      -       +      -
     59C  TYR*     2.8    31.8    +      -       +      +
    154C  ILE      5.5     0.2    -      -       -      -
    155C  ILE*     3.9    26.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  GLY      3.5     0.5    -      -       -      +
     55A  LEU*     3.4     6.7    -      -       -      -
     56A  TYR*     2.8    40.4    +      -       -      +
     58A  ILE*     4.0    16.6    -      -       +      -
     93A  LEU*     3.6    46.9    -      -       +      -
     94A  LEU*     3.6    26.0    -      -       +      -
    122A  GLY      3.5    24.9    -      -       -      -
    123A  VAL*     1.3    78.2    -      -       -      +
    125A  GLN*     1.3    62.5    +      -       -      +
    126A  LEU*     3.6    19.1    +      -       +      +
     15C  HIS*     3.6    22.9    -      +       -      -
     34C  ASN*     3.5    31.2    -      -       +      -
     36C  LEU*     4.3     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  GLU*     5.5     2.3    -      -       -      +
     54A  GLY*     3.6    14.2    +      -       -      +
     55A  LEU*     3.4    15.8    -      -       +      +
     82A  ARG*     3.8    14.7    +      -       -      -
    124A  PHE*     1.3    70.7    -      -       -      +
    126A  LEU*     1.3    83.2    +      -       -      +
      6C  ARG*     5.0    16.1    -      -       -      +
      7C  THR      4.1     1.6    +      -       -      -
      8C  PRO*     2.9    48.5    +      -       +      +
     34C  ASN*     5.1     1.9    -      -       -      +
     36C  LEU*     4.0    23.9    -      -       +      +
    160F  TYR*     5.6     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  VAL*     3.6    30.1    -      -       +      -
     52A  SER      4.0     0.6    -      -       -      +
     53A  GLU*     3.3     5.7    -      -       -      +
     54A  GLY      2.8    33.1    +      -       -      -
     56A  TYR*     3.8    35.4    -      -       +      -
     58A  ILE*     4.1     8.1    -      -       +      -
     82A  ARG*     3.8    21.8    -      -       -      +
     93A  LEU*     5.0     0.9    -      -       +      -
    124A  PHE*     3.8    18.2    -      -       +      -
    125A  GLN*     1.3    93.0    +      -       -      +
    127A  GLU*     1.3    62.7    +      -       -      +
    130A  ASP*     3.5    13.2    -      -       +      +
    132A  LEU*     3.8    20.0    -      -       +      -
----------------------------------------------------------
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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