Contacts of the strand formed by residues 54 - 67 (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 GLY 54 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52H  SER      3.6     0.4    +      -       -      -
     53H  GLU*     1.3    76.6    -      -       -      +
     55H  LEU*     1.3    60.7    +      -       -      -
     56H  TYR*     3.3    13.7    -      -       -      -
    125H  GLN*     3.5    17.5    +      -       -      +
    126H  LEU      2.8    37.2    +      -       -      -
    156H  ALA*     6.5     0.2    -      -       -      -
      7I  THR      5.3     2.6    +      -       -      -
      8I  PRO      4.2     4.3    -      -       -      -
      9I  SER*     5.8     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 55 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54H  GLY*     1.3    71.8    -      -       -      -
     56H  TYR*     1.3    64.1    +      -       -      +
    123H  VAL*     4.1    16.4    -      -       +      -
    124H  PHE      3.4     1.1    -      -       -      +
    125H  GLN*     3.3    38.4    -      -       +      +
    156H  ALA*     3.7     2.3    -      -       -      +
    157H  LEU*     3.0    41.7    +      -       +      +
      8I  PRO*     3.6    13.1    +      -       +      +
      9I  SER*     3.2    27.3    -      -       -      +
     13I  VAL*     3.6    29.4    -      -       +      -
     36I  LEU*     3.9    16.6    -      -       +      -
    155I  ILE*     4.0     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 56 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12H  PRO*     3.7    16.5    -      -       +      +
     50H  VAL*     3.0    25.8    -      -       +      +
     51H  PRO*     3.8     2.7    -      -       +      +
     52H  SER*     3.0    42.0    +      -       -      -
     53H  GLU      4.6     0.4    -      -       -      -
     54H  GLY*     3.3    25.6    -      -       -      -
     55H  LEU*     1.3    77.1    -      -       -      +
     57H  LEU*     1.3    63.0    +      -       -      +
     58H  ILE*     3.6     9.6    +      -       +      +
    122H  GLY      3.6     0.9    -      -       -      +
    123H  VAL*     3.2     7.1    -      -       -      +
    124H  PHE      2.8    38.1    +      -       -      +
    126H  LEU*     3.8    26.0    -      -       +      -
    154H  ILE*     4.0    21.1    -      -       +      -
    155H  ILE      3.5     7.2    -      -       -      -
    156H  ALA*     3.7    30.5    -      -       +      +
    157H  LEU*     4.5     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 57 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57G  LEU*     4.0    23.1    -      -       +      -
    157G  LEU*     5.3     0.7    -      -       +      -
     56H  TYR*     1.3    72.3    -      -       -      +
     58H  ILE*     1.3    67.6    +      -       -      +
     59H  TYR*     4.4    13.3    -      -       +      -
    121H  GLY*     4.9     1.6    -      -       -      -
    122H  GLY*     3.6    20.9    -      -       -      +
    123H  VAL*     4.3     9.2    -      -       +      +
    154H  ILE*     3.0    26.0    -      -       -      +
    155H  ILE*     2.9    34.2    +      -       +      +
    157H  LEU*     3.8    18.2    -      -       +      +
     57I  LEU*     3.8    27.6    -      -       +      -
     59I  TYR*     5.6     2.0    -      -       +      -
    119I  TYR*     5.7     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 58 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56H  TYR*     4.1    12.3    -      -       +      +
     57H  LEU*     1.3    77.9    -      -       -      +
     59H  TYR*     1.3    65.9    +      -       -      +
     80H  ILE*     3.7    30.7    -      -       +      -
     93H  LEU*     3.9    17.7    -      -       +      -
     94H  LEU*     4.0     3.6    -      -       +      +
    121H  GLY*     3.1     3.6    -      -       -      -
    122H  GLY      2.9    34.4    +      -       -      +
    124H  PHE*     4.0    12.8    -      -       +      -
    126H  LEU*     4.1     9.9    -      -       +      -
    132H  LEU*     3.6    32.1    -      -       +      -
    152H  PHE*     4.1     4.9    -      -       +      -
    153H  GLY      3.6     3.6    -      -       -      +
    154H  ILE*     3.9    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 59 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57G  LEU*     5.7     1.6    -      -       +      -
    121G  GLY      3.7    12.8    -      -       -      -
    122G  GLY*     3.5    14.1    -      -       -      -
    123G  VAL*     2.8    40.9    +      -       +      +
     14H  ALA      4.2     0.9    +      -       -      -
     15H  HIS*     2.6    36.3    +      -       -      +
     57H  LEU*     4.4    18.4    -      -       +      -
     58H  ILE*     1.3    80.5    -      -       -      +
     60H  SER*     1.3    66.8    +      -       -      +
     80H  ILE*     4.0     4.7    -      -       -      -
    119H  TYR*     3.5    15.9    -      -       -      +
    120H  LEU      3.0    13.7    -      -       -      +
    121H  GLY*     4.0     2.7    -      -       -      -
    151H  TYR*     3.7    15.0    -      +       -      -
    152H  PHE*     3.3     3.5    -      -       -      -
    153H  GLY*     2.9    58.5    +      -       -      +
    154H  ILE*     4.0     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 60 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28H  TRP*     4.4     2.8    -      -       -      -
     59H  TYR*     1.3    81.1    -      -       -      +
     61H  GLN*     1.3    65.6    +      -       -      +
     78H  HIS*     2.9    30.7    +      -       -      -
     80H  ILE*     3.8    16.6    -      -       -      -
    119H  TYR*     3.6     4.2    -      -       -      -
    120H  LEU*     2.9    33.1    +      -       -      +
    134H  ALA*     4.0     7.3    -      -       -      +
    151H  TYR*     2.9    16.6    +      -       -      -
    152H  PHE*     3.9     9.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 61 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95G  SER      3.3    16.9    -      -       -      +
     96G  ALA*     4.1     9.1    -      -       -      +
    119G  TYR      3.3    11.1    +      -       -      -
    120G  LEU*     3.2    28.7    -      -       -      +
     60H  SER*     1.3    76.5    +      -       -      +
     62H  VAL*     1.3    75.2    +      -       -      +
     63H  LEU*     5.3     0.3    -      -       -      +
     78H  HIS*     3.9     0.4    -      -       -      -
    117H  PRO*     4.9     5.2    -      -       -      +
    118H  ILE      3.3    17.7    -      -       -      +
    119H  TYR*     4.0     7.3    -      -       +      +
    149H  GLN      3.1    18.4    -      -       -      +
    150H  VAL*     3.1     4.9    -      -       -      +
    151H  TYR*     2.8    65.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26H  LEU*     4.6     7.9    -      -       +      -
     28H  TRP*     5.0     1.6    -      -       +      -
     60H  SER*     4.5     1.3    -      -       -      +
     61H  GLN*     1.3    81.6    -      -       -      +
     63H  LEU*     1.3    60.3    +      -       -      +
     64H  PHE*     3.4    33.4    -      -       +      -
     78H  HIS*     3.4    40.2    -      -       +      +
    116H  GLU      4.2     0.2    -      -       -      +
    117H  PRO*     3.4     2.1    -      -       -      +
    118H  ILE*     3.0    31.9    +      -       +      -
    136H  ILE*     3.7    17.0    -      -       +      -
    142H  LEU*     4.6     8.7    -      -       +      -
    149H  GLN      3.8     4.7    -      -       -      -
    150H  VAL*     4.2    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 63 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96G  ALA*     4.6     3.8    -      -       -      -
     97G  ILE*     4.2    30.3    -      -       +      +
     61H  GLN*     5.3     0.9    -      -       -      +
     62H  VAL*     1.3    75.2    -      -       -      +
     64H  PHE*     1.3    78.7    +      -       -      +
    115H  TYR*     4.3     7.2    -      -       +      -
    116H  GLU      3.8    17.5    -      -       -      +
    117H  PRO*     4.2     8.1    -      -       +      -
    142H  LEU*     3.8     5.0    -      -       -      +
    143H  LEU*     2.8    46.8    +      -       +      +
    149H  GLN*     3.5    53.3    +      -       +      +
    150H  VAL*     3.8     4.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 64 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62H  VAL*     3.4    22.2    -      -       +      -
     63H  LEU*     1.3    81.0    -      -       -      +
     65H  LYS*     1.3    59.8    +      -       -      +
     76H  LEU*     3.5    56.1    -      -       +      -
     77H  THR      4.1     8.7    -      -       -      -
    114H  TRP*     3.8     7.0    -      -       +      -
    115H  TYR*     3.4     1.9    -      -       -      -
    116H  GLU      2.9    43.3    +      -       -      +
    118H  ILE*     3.9    15.7    -      -       +      -
    136H  ILE*     3.8    38.4    -      -       +      -
    137H  ASN*     4.7     0.4    -      -       -      -
    138H  ARG*     3.9    17.3    -      -       +      -
    141H  TYR*     3.3    18.8    -      -       +      +
    142H  LEU*     4.5     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 65 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64H  PHE*     1.3    76.6    -      -       -      +
     66H  GLY*     1.3    65.8    +      -       -      +
     67H  GLN*     4.0    23.1    -      -       +      +
    113H  PRO*     4.6     3.4    -      -       -      -
    114H  TRP*     3.2    16.6    -      -       -      +
    115H  TYR*     3.1    32.0    +      -       +      -
    140H  ASP      5.0     0.2    -      -       -      +
    141H  TYR*     2.7    31.9    +      -       -      +
    143H  LEU*     3.5    43.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 66 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65H  LYS*     1.3    77.2    -      -       -      +
     67H  GLN*     1.3    67.2    +      -       -      -
    113H  PRO*     3.2     2.3    -      -       -      +
    114H  TRP*     2.8    61.7    +      -       -      -
    141H  TYR*     4.0     9.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 67 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65H  LYS*     4.0    15.7    -      -       -      +
     66H  GLY*     1.3    70.8    -      -       -      +
     68H  GLY*     1.3    69.0    +      -       -      +
     69H  CYS      5.0     1.2    -      -       -      -
     70H  PRO*     5.5     0.7    -      -       -      +
    111H  ALA      5.3     0.7    -      -       -      +
    112H  LYS      5.1     0.2    -      -       -      -
    113H  PRO*     3.0    28.0    -      -       -      +
    141H  TYR*     5.4     1.0    -      -       -      -
----------------------------------------------------------
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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