Contacts of the strand formed by residues 54 - 67 (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 GLY 54 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  SER      3.5     0.2    +      -       -      -
     53A  GLU*     1.3    77.3    -      -       -      +
     55A  LEU*     1.3    62.3    +      -       -      -
     56A  TYR*     3.3    13.7    -      -       -      -
    125A  GLN*     3.6    17.1    +      -       -      +
    126A  LEU      2.8    36.5    +      -       -      -
    156A  ALA*     6.4     0.2    -      -       -      -
      7C  THR      5.4     2.2    +      -       -      -
      8C  PRO      4.3     4.3    -      -       -      -
      9C  SER*     5.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  GLY*     1.3    71.8    -      -       -      -
     56A  TYR*     1.3    63.3    +      -       -      +
    123A  VAL*     4.1    15.7    -      -       +      -
    124A  PHE      3.4     1.3    -      -       -      +
    125A  GLN*     3.4    38.4    -      -       +      +
    156A  ALA*     3.7     2.3    -      -       -      +
    157A  LEU*     3.0    40.5    +      -       +      +
      8C  PRO*     3.6    14.4    +      -       +      +
      9C  SER*     3.2    26.6    -      -       -      +
     11C  LYS*     4.6     0.4    -      -       +      +
     13C  VAL*     3.7    24.5    -      -       +      -
     36C  LEU*     3.9    17.0    -      -       +      -
    155C  ILE*     4.0    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  PRO*     3.7    12.7    -      -       +      +
     50A  VAL*     3.0    33.7    -      -       +      +
     51A  PRO*     3.7     6.2    -      -       +      +
     52A  SER*     3.0    35.1    +      -       -      -
     53A  GLU      4.5     0.2    -      -       -      -
     54A  GLY*     3.3    24.7    -      -       -      -
     55A  LEU*     1.3    76.1    -      -       -      +
     57A  LEU*     1.3    61.9    +      -       -      +
     58A  ILE*     3.6     9.2    +      -       +      +
    122A  GLY      3.6     0.7    -      -       -      +
    123A  VAL*     3.2     8.1    -      -       -      +
    124A  PHE      2.8    37.6    +      -       -      +
    126A  LEU*     3.8    28.5    -      -       +      -
    154A  ILE*     4.0    20.6    -      -       +      -
    155A  ILE      3.5     6.1    -      -       -      -
    156A  ALA*     3.7    31.8    -      -       +      +
    157A  LEU*     4.9     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  TYR*     1.3    72.5    -      -       -      +
     58A  ILE*     1.3    69.1    +      -       -      +
     59A  TYR*     4.4    14.2    -      -       +      -
    121A  GLY*     5.0     1.8    -      -       -      -
    122A  GLY*     3.6    20.6    -      -       -      +
    123A  VAL*     4.3     9.2    -      -       +      +
    153A  GLY      4.0     0.2    -      -       -      +
    154A  ILE*     3.0    26.0    -      -       -      +
    155A  ILE*     2.9    32.5    +      -       +      +
    157A  LEU*     3.9    17.8    -      -       +      +
     57B  LEU*     3.9    24.2    -      -       +      -
    157B  LEU*     5.4     0.7    -      -       +      -
     57C  LEU*     3.9    26.2    -      -       +      -
     59C  TYR*     5.6     2.2    -      -       +      -
    119C  TYR*     5.7     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  TYR*     4.1    11.9    -      -       +      +
     57A  LEU*     1.3    78.1    -      -       -      +
     59A  TYR*     1.3    65.2    +      -       -      +
     80A  ILE*     3.7    31.0    -      -       +      -
     93A  LEU*     3.9    17.3    -      -       +      -
     94A  LEU*     4.0     4.1    -      -       +      +
    121A  GLY*     3.1     3.1    -      -       -      -
    122A  GLY      2.9    34.5    +      -       -      +
    124A  PHE*     4.0    13.2    -      -       +      -
    126A  LEU*     4.1    10.5    -      -       +      -
    132A  LEU*     3.6    32.8    -      -       +      -
    152A  PHE*     4.2     5.2    -      -       +      -
    153A  GLY      3.6     2.9    -      -       -      +
    154A  ILE*     3.9    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ALA      4.2     1.0    +      -       -      -
     15A  HIS*     2.7    35.6    +      -       -      +
     57A  LEU*     4.4    19.5    -      -       +      -
     58A  ILE*     1.3    81.1    -      -       -      +
     60A  SER*     1.3    65.9    +      -       -      +
     80A  ILE*     4.0     4.3    -      -       -      -
    119A  TYR*     3.5    15.7    -      -       -      +
    120A  LEU      3.1    14.1    -      -       -      +
    121A  GLY*     4.1     2.9    -      -       -      -
    151A  TYR*     3.7    14.8    -      +       -      -
    152A  PHE*     3.3     3.5    -      -       -      -
    153A  GLY*     2.9    57.0    +      -       -      +
    154A  ILE*     4.0     4.3    -      -       -      -
     57B  LEU*     5.7     1.8    -      -       +      -
    121B  GLY      3.7    12.8    -      -       -      -
    122B  GLY*     3.5    20.6    -      -       -      -
    123B  VAL*     2.9    34.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  TRP*     4.4     2.8    -      -       -      -
     59A  TYR*     1.3    81.6    -      -       -      +
     61A  GLN*     1.3    64.2    +      -       -      +
     78A  HIS*     2.8    32.3    +      -       -      -
     80A  ILE*     3.7    16.4    -      -       -      -
    119A  TYR*     3.6     4.6    -      -       -      -
    120A  LEU*     2.9    32.1    +      -       -      +
    134A  ALA*     4.0     6.8    -      -       -      +
    151A  TYR*     3.0    16.2    +      -       -      -
    152A  PHE*     4.0     9.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  SER*     1.3    75.5    +      -       -      +
     62A  VAL*     1.3    75.4    +      -       -      +
     63A  LEU*     5.3     0.5    -      -       -      +
     78A  HIS*     3.9     0.4    -      -       -      -
    117A  PRO*     4.9     6.0    -      -       -      +
    118A  ILE      3.3    16.4    -      -       -      +
    119A  TYR*     4.0     8.0    -      -       +      +
    149A  GLN      3.1    18.1    -      -       -      +
    150A  VAL*     3.1     5.2    -      -       -      +
    151A  TYR*     2.8    68.5    +      -       +      +
     95B  SER      3.4    16.3    -      -       -      +
     96B  ALA*     4.2     9.4    -      -       -      +
    119B  TYR      3.3    24.9    +      -       -      -
    120B  LEU*     3.3    15.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  LEU*     4.6     8.1    -      -       +      -
     28A  TRP*     5.0     1.1    -      -       +      -
     60A  SER*     4.5     1.6    -      -       -      +
     61A  GLN*     1.3    81.2    -      -       -      +
     63A  LEU*     1.3    59.8    +      -       -      +
     64A  PHE*     3.4    33.7    -      -       +      -
     78A  HIS*     3.4    43.1    -      -       +      +
    116A  GLU      4.2     0.2    -      -       -      +
    117A  PRO*     3.4     2.3    -      -       -      +
    118A  ILE*     3.1    27.4    +      -       +      -
    136A  ILE*     3.7    14.1    -      -       +      -
    142A  LEU*     4.6     8.1    -      -       +      -
    149A  GLN      3.8     4.0    -      -       -      -
    150A  VAL*     4.2    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  GLN*     5.3     0.4    -      -       -      +
     62A  VAL*     1.3    74.1    -      -       -      +
     64A  PHE*     1.3    78.7    +      -       -      +
    115A  TYR*     4.3     6.5    -      -       +      -
    116A  GLU      3.8    17.5    -      -       -      +
    117A  PRO*     4.1     8.5    -      -       +      -
    142A  LEU*     3.8     4.6    -      -       -      +
    143A  LEU*     2.8    47.2    +      -       +      +
    149A  GLN*     3.5    53.1    +      -       +      +
    150A  VAL*     3.8     4.6    -      -       -      +
     96B  ALA*     4.6     4.0    -      -       +      -
     97B  ILE*     4.2    28.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  VAL*     3.4    22.9    -      -       +      -
     63A  LEU*     1.3    81.5    -      -       -      +
     65A  LYS*     1.3    61.2    +      -       -      +
     76A  LEU*     3.5    54.3    -      -       +      -
     77A  THR      4.1     9.9    -      -       -      -
    114A  TRP*     3.8     7.0    -      -       +      -
    115A  TYR*     3.3     2.3    -      -       -      -
    116A  GLU      2.9    43.6    +      -       -      +
    118A  ILE*     4.0    15.7    -      -       +      -
    136A  ILE*     3.8    39.3    -      -       +      -
    137A  ASN*     4.7     0.2    -      -       -      -
    138A  ARG*     3.9    17.0    -      -       +      -
    141A  TYR*     3.3    17.9    -      -       +      +
    142A  LEU*     4.5     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  PHE*     1.3    75.8    -      -       -      +
     66A  GLY*     1.3    66.5    +      -       -      +
     67A  GLN*     4.0    22.4    -      -       +      +
    113A  PRO*     4.6     3.4    -      -       -      -
    114A  TRP*     3.1    17.0    -      -       -      +
    115A  TYR*     3.2    33.0    +      -       +      -
    140A  ASP      5.0     0.2    -      -       -      +
    141A  TYR*     2.8    32.8    +      -       -      +
    143A  LEU*     3.5    44.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  LYS*     1.3    77.5    -      -       -      +
     67A  GLN*     1.3    66.2    +      -       -      +
     68A  GLY      4.8     0.2    -      -       -      -
    113A  PRO*     3.2     1.9    -      -       -      +
    114A  TRP*     2.8    61.1    +      -       -      -
    141A  TYR*     4.0     9.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  LYS*     4.0    16.4    -      -       -      +
     66A  GLY*     1.3    70.1    -      -       -      +
     68A  GLY*     1.3    69.2    +      -       -      +
     69A  CYS*     4.6     1.0    -      -       -      -
     70A  PRO*     5.5     0.5    -      -       -      +
    111A  ALA      5.6     0.7    -      -       -      +
    113A  PRO*     3.0    27.3    -      -       -      +
    141A  TYR*     5.3     1.2    -      -       -      -
----------------------------------------------------------
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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