Contacts of the strand formed by residues 113 - 126 (chain H) 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 H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73G  HIS*     3.0    35.2    +      -       +      -
     75G  LEU*     5.7     1.6    -      -       +      -
     99G  SER*     4.4     0.3    -      -       -      -
     65H  LYS*     4.6     5.6    -      -       -      -
     66H  GLY      3.2     7.4    -      -       -      +
     67H  GLN*     3.0    27.6    -      -       -      +
     68H  GLY      4.1     0.7    -      -       -      +
    111H  ALA      4.7     0.4    -      -       -      +
    112H  LYS*     1.3    94.9    -      -       +      +
    114H  TRP*     1.3    60.6    +      -       -      +
    115H  TYR*     4.4    20.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 114 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73G  HIS*     5.9     0.4    -      -       +      -
     99G  SER*     3.5    12.1    -      -       -      +
    102G  GLN*     5.8     8.3    -      -       +      +
     64H  PHE*     3.8    18.4    -      -       +      -
     65H  LYS*     3.2    10.1    -      -       -      +
     66H  GLY*     2.8    53.1    +      -       -      -
     68H  GLY      3.0    27.7    +      -       -      -
     69H  CYS*     4.5     2.2    -      -       -      -
     70H  PRO*     4.8     1.7    -      -       +      +
     74H  VAL*     5.9     0.4    -      -       +      -
     76H  LEU*     3.8    22.9    -      -       +      -
    100H  PRO*     3.7    37.9    -      -       +      -
    101H  CYS*     3.6    17.7    -      -       -      -
    112H  LYS      4.8     1.6    -      -       -      -
    113H  PRO*     1.3    76.5    -      -       -      +
    115H  TYR*     1.3    74.1    +      -       -      +
    116H  GLU*     4.1     6.7    -      -       +      +
    141H  TYR*     3.9    28.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with TYR 115 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75G  LEU*     3.8    40.6    -      -       +      +
     97G  ILE*     3.5    50.6    -      -       +      +
     98G  LYS*     3.9     4.8    -      -       -      +
     99G  SER*     3.2    20.1    +      -       -      +
     63H  LEU*     4.3     4.9    -      -       +      -
     64H  PHE      3.4     4.0    -      -       -      +
     65H  LYS*     3.1    37.1    +      -       +      -
    113H  PRO*     4.4    15.3    -      -       +      +
    114H  TRP*     1.3    81.5    -      -       -      +
    116H  GLU*     1.3    74.2    +      -       -      +
    143H  LEU*     3.3    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 116 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98G  LYS*     3.7    15.1    -      -       -      +
     99G  SER*     4.8     5.4    +      -       -      +
    116G  GLU*     5.0     1.4    -      -       -      +
     63H  LEU*     3.9     1.5    -      -       -      +
     64H  PHE*     2.9    41.3    +      -       +      +
     76H  LEU*     4.3     8.7    -      -       +      -
     98H  LYS*     3.1    53.3    +      -       +      -
     99H  SER      5.9     0.2    -      -       -      -
    100H  PRO*     4.4    16.7    -      -       +      +
    114H  TRP*     4.1    21.4    -      -       +      +
    115H  TYR*     1.3    83.3    -      -       -      +
    117H  PRO*     1.3    64.7    -      -       -      +
    116I  GLU*     5.0     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 117 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96G  ALA*     4.0    25.4    -      -       +      -
     97G  ILE      3.2    22.7    -      -       -      +
     98G  LYS*     4.2    20.9    -      -       +      +
    118G  ILE*     5.1     7.6    -      -       +      -
     61H  GLN*     4.9     7.2    -      -       -      +
     62H  VAL      3.4    10.5    -      -       -      +
     63H  LEU*     4.3     7.2    -      -       +      -
     98H  LYS*     2.9    33.1    +      -       -      +
    116H  GLU*     1.3    82.2    -      -       -      +
    118H  ILE*     1.3    67.5    +      -       -      +
    117I  PRO*     5.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 118 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61H  GLN*     3.3     8.8    -      -       -      +
     62H  VAL*     3.0    35.9    +      -       +      -
     64H  PHE*     3.9    27.1    -      -       +      -
     76H  LEU      4.3    10.1    -      -       -      +
     78H  HIS*     3.7    24.9    +      -       +      +
     96H  ALA*     3.8    31.0    -      -       +      +
     97H  ILE      4.7     1.3    -      -       -      -
     98H  LYS*     4.0    31.4    -      -       +      +
    116H  GLU      4.7     0.2    -      -       -      +
    117H  PRO*     1.3    81.4    -      -       -      +
    119H  TYR*     1.3    67.1    +      -       -      +
    120H  LEU*     4.2     1.3    -      -       +      -
    117I  PRO*     5.3     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 119 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57G  LEU*     5.8     2.3    -      -       -      +
    119G  TYR*     3.5    32.6    -      +       +      +
    121G  GLY*     3.2    37.7    +      -       -      -
     59H  TYR*     3.5    17.6    -      +       +      +
     60H  SER      3.6     9.4    -      -       -      -
     61H  GLN*     4.0     9.4    -      -       +      +
    118H  ILE*     1.3    76.7    -      -       -      +
    120H  LEU*     1.3    95.9    +      -       -      +
    121H  GLY*     4.5     0.9    -      -       -      -
    151H  TYR*     3.6    22.0    -      +       -      -
     61I  GLN*     3.3    12.0    +      -       -      -
    119I  TYR*     3.5    55.1    -      +       +      +
----------------------------------------------------------
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Residues in contact with LEU 120 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59H  TYR*     3.0     6.1    -      -       -      +
     60H  SER      2.9    35.6    +      -       -      +
     78H  HIS*     3.5    43.3    -      -       +      +
     79H  THR*     3.8     3.4    -      -       -      -
     80H  ILE*     4.1    13.5    -      -       +      +
     94H  LEU*     3.7    34.5    -      -       +      +
     95H  SER      4.1     5.2    -      -       -      +
     96H  ALA*     3.7    20.0    -      -       +      -
    118H  ILE*     4.2     2.9    -      -       +      -
    119H  TYR*     1.3    93.8    -      -       -      +
    121H  GLY*     1.3    57.0    +      -       -      +
     61I  GLN*     3.4    17.9    -      -       -      +
    151I  TYR*     4.1     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 121 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57H  LEU*     4.9     2.0    -      -       -      -
     58H  ILE      3.1    12.3    -      -       -      -
     59H  TYR*     4.0     4.5    -      -       -      -
     94H  LEU*     3.6     8.5    -      -       -      +
    119H  TYR*     4.5     0.9    -      -       -      -
    120H  LEU*     1.3    75.4    -      -       -      +
    122H  GLY*     1.3    58.2    +      -       -      -
     59I  TYR*     3.6     1.4    -      -       -      -
    119I  TYR*     3.2    26.6    +      -       -      -
    151I  TYR*     3.0    30.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 122 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57H  LEU*     3.6     7.1    -      -       -      +
     58H  ILE      2.9    30.7    +      -       -      +
     94H  LEU*     3.7     5.2    -      -       -      +
    121H  GLY*     1.3    74.8    -      -       -      -
    123H  VAL*     1.3    62.8    +      -       -      -
    124H  PHE*     3.5    19.0    -      -       -      -
     15I  HIS*     4.3     0.9    -      -       -      -
     59I  TYR*     3.5    17.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 123 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55H  LEU*     4.1    17.9    -      -       +      -
     56H  TYR      3.2    11.4    -      -       -      +
     57H  LEU*     4.3     9.2    -      -       +      -
    122H  GLY*     1.3    72.8    -      -       -      +
    124H  PHE*     1.3    76.3    +      -       -      +
    157H  LEU*     4.3    11.4    -      -       +      -
     13I  VAL*     4.0    26.9    -      -       +      -
     14I  ALA      5.6     0.4    -      -       -      +
     15I  HIS*     3.7    19.9    -      -       +      +
     36I  LEU*     4.1     3.4    -      -       +      +
     57I  LEU*     5.2     0.4    -      -       +      -
     59I  TYR*     2.8    29.9    +      -       +      +
    154I  ILE      5.5     0.2    -      -       -      -
    155I  ILE*     3.9    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 124 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54H  GLY      3.5     0.9    -      -       -      +
     55H  LEU*     3.4     6.6    -      -       -      -
     56H  TYR*     2.8    39.5    +      -       -      +
     58H  ILE*     4.0    16.8    -      -       +      -
     93H  LEU*     3.6    46.9    -      -       +      -
     94H  LEU*     3.7    28.0    -      -       +      -
    122H  GLY*     3.5    29.4    -      -       -      -
    123H  VAL*     1.3    88.6    -      -       -      +
    125H  GLN*     1.3    63.2    +      -       -      +
    126H  LEU*     3.6    17.4    +      -       +      +
     15I  HIS*     3.7    17.5    -      +       -      -
     34I  ASN*     3.6    30.7    -      -       +      -
     36I  LEU*     4.3     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 125 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53H  GLU*     5.5     2.1    -      -       -      +
     54H  GLY*     3.5    14.2    +      -       -      +
     55H  LEU*     3.3    15.8    -      -       +      +
     82H  ARG*     3.8    14.4    +      -       -      -
    124H  PHE*     1.3    71.7    -      -       -      +
    126H  LEU*     1.3    82.4    +      -       -      +
      6I  ARG*     5.0    16.7    -      -       -      +
      7I  THR      4.0     2.0    +      -       -      -
      8I  PRO*     2.9    50.7    +      -       +      +
     34I  ASN*     5.2     1.7    -      -       -      +
     36I  LEU*     4.0    25.0    -      -       +      +
    160L  TYR*     5.6     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 126 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50H  VAL*     3.6    29.4    -      -       +      -
     52H  SER      3.9     0.4    -      -       -      +
     53H  GLU*     3.3     5.0    -      -       -      +
     54H  GLY      2.8    32.2    +      -       -      -
     56H  TYR*     3.8    35.9    -      -       +      -
     58H  ILE*     4.1     7.9    -      -       +      -
     82H  ARG*     3.8    20.9    -      -       -      +
     93H  LEU*     5.1     0.9    -      -       +      -
    124H  PHE*     3.8    18.2    -      -       +      -
    125H  GLN*     1.3    93.9    +      -       -      +
    127H  GLU*     1.3    61.4    +      -       -      +
    130H  ASP*     3.5    13.0    -      -       +      +
    132H  LEU*     3.8    19.3    -      -       +      -
----------------------------------------------------------
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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