Contacts of the strand formed by residues 54 - 67 (chain G) 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 G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52G  SER      3.5     0.2    +      -       -      -
     53G  GLU*     1.3    77.1    -      -       -      +
     55G  LEU*     1.3    60.9    +      -       -      -
     56G  TYR*     3.4    13.6    -      -       -      -
    124G  PHE      3.5     0.2    -      -       -      +
    125G  GLN*     3.5    16.7    +      -       -      +
    126G  LEU      2.8    37.5    +      -       -      -
      7H  THR      5.5     2.6    +      -       -      -
      8H  PRO      4.5     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 55 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54G  GLY*     1.3    72.7    -      -       -      -
     56G  TYR*     1.3    63.1    +      -       -      +
    123G  VAL*     4.1    17.0    -      -       +      -
    124G  PHE      3.4     0.9    -      -       -      +
    125G  GLN*     3.4    38.8    -      -       +      +
    156G  ALA*     3.7     2.4    -      -       -      +
    157G  LEU*     3.0    41.6    +      -       +      +
      8H  PRO*     3.6    14.9    +      -       +      +
      9H  SER*     3.3    27.5    -      -       -      +
     13H  VAL*     3.7    23.8    -      -       +      -
     36H  LEU*     3.9    16.8    -      -       +      -
    155H  ILE*     4.1    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 56 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12G  PRO*     3.7    17.9    -      -       +      +
     41G  VAL*     6.1     0.2    -      -       +      -
     50G  VAL*     3.0    34.7    -      -       +      +
     51G  PRO*     3.7     3.1    -      -       +      +
     52G  SER*     3.0    34.0    +      -       -      -
     53G  GLU      4.6     0.7    -      -       -      -
     54G  GLY*     3.4    25.1    -      -       -      -
     55G  LEU*     1.3    76.2    -      -       -      +
     57G  LEU*     1.3    60.9    +      -       -      +
     58G  ILE*     3.7     9.9    +      -       +      +
    122G  GLY      3.7     0.7    -      -       -      +
    123G  VAL*     3.2     7.9    -      -       -      +
    124G  PHE*     2.8    34.6    +      -       -      +
    126G  LEU*     3.8    26.5    -      -       +      -
    154G  ILE*     4.0    21.3    -      -       +      -
    155G  ILE      3.5     6.5    -      -       -      +
    156G  ALA*     3.7    31.0    -      -       +      -
    157G  LEU*     4.5     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 57 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56G  TYR*     1.3    72.3    -      -       -      +
     58G  ILE*     1.3    67.8    +      -       -      +
     59G  TYR*     4.4    14.2    -      -       +      -
    121G  GLY      5.0     1.6    -      -       -      -
    122G  GLY*     3.6    21.1    -      -       -      +
    123G  VAL*     4.3     9.4    -      -       +      +
    154G  ILE*     3.0     7.3    -      -       -      +
    155G  ILE*     2.9    51.3    +      -       +      +
    157G  LEU*     3.9    17.3    -      -       +      +
     57H  LEU*     4.0    15.5    -      -       +      -
     59H  TYR*     5.7     2.2    -      -       +      -
    119H  TYR*     5.8     1.8    -      -       -      +
     57I  LEU*     3.9    35.2    -      -       +      -
    123I  VAL*     5.1     0.4    -      -       +      -
    157I  LEU*     5.2     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 58 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56G  TYR*     4.2    12.3    -      -       +      +
     57G  LEU*     1.3    78.8    -      -       -      +
     59G  TYR*     1.3    66.4    +      -       -      +
     80G  ILE*     3.7    31.0    -      -       +      -
     93G  LEU*     4.0    17.3    -      -       +      -
     94G  LEU*     4.0     3.2    -      -       +      +
    121G  GLY*     3.1     3.3    -      -       -      -
    122G  GLY      2.9    35.0    +      -       -      +
    124G  PHE*     4.0    13.5    -      -       +      -
    126G  LEU*     4.0    10.1    -      -       +      -
    132G  LEU*     3.6    33.2    -      -       +      -
    152G  PHE*     4.2     4.9    -      -       +      -
    153G  GLY      3.6     3.6    -      -       -      +
    154G  ILE*     3.9    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 59 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14G  ALA      4.2     0.7    +      -       -      -
     15G  HIS*     2.7    36.8    +      -       -      +
     57G  LEU*     4.4    18.8    -      -       +      -
     58G  ILE*     1.3    79.1    -      -       -      +
     60G  SER*     1.3    66.5    +      -       -      +
     80G  ILE*     3.9     4.7    -      -       -      -
    119G  TYR*     3.5    15.9    -      -       +      +
    120G  LEU      3.1    14.8    -      -       -      +
    121G  GLY*     4.1     2.5    -      -       -      -
    151G  TYR*     3.7    14.6    -      +       -      -
    152G  PHE*     3.3     3.8    -      -       -      -
    153G  GLY*     2.9    57.4    +      -       -      +
    154G  ILE*     4.0     4.3    -      -       -      -
     57I  LEU*     5.7     1.6    -      -       +      -
    121I  GLY      3.6    13.9    -      -       -      -
    122I  GLY*     3.5    14.6    -      -       -      -
    123I  VAL*     2.9    39.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 60 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28G  TRP*     4.4     2.4    -      -       -      -
     59G  TYR*     1.3    82.0    -      -       -      +
     61G  GLN*     1.3    64.2    +      -       -      +
     78G  HIS*     2.8    31.1    +      -       -      -
     80G  ILE*     3.7    16.4    -      -       -      -
    119G  TYR*     3.5     5.1    -      -       -      -
    120G  LEU      2.9    31.8    +      -       -      +
    134G  ALA*     4.0     7.6    -      -       -      +
    151G  TYR*     3.0    16.9    +      -       -      -
    152G  PHE*     4.0     9.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 61 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60G  SER*     1.3    75.0    +      -       -      +
     62G  VAL*     1.3    74.7    +      -       -      +
     63G  LEU*     5.3     0.3    -      -       -      +
     78G  HIS*     3.9     0.2    -      -       -      -
    117G  PRO*     4.9     5.6    -      -       -      +
    118G  ILE      3.3    18.1    -      -       -      +
    119G  TYR*     4.0     8.0    -      -       +      +
    149G  GLN      3.1    17.8    -      -       -      +
    150G  VAL*     3.1     4.7    -      -       -      +
    151G  TYR*     2.8    64.4    +      -       +      +
     95I  SER      3.3    17.3    -      -       -      +
     96I  ALA*     4.0     9.9    -      -       -      +
    119I  TYR      3.3    11.9    +      -       -      -
    120I  LEU*     3.2    28.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26G  LEU*     4.6     7.4    -      -       +      -
     28G  TRP*     5.0     1.1    -      -       +      -
     60G  SER*     4.5     1.6    -      -       -      +
     61G  GLN*     1.3    81.8    -      -       -      +
     63G  LEU*     1.3    60.4    +      -       -      +
     64G  PHE*     3.4    33.2    -      -       +      -
     78G  HIS*     3.4    43.7    -      -       +      +
    116G  GLU      4.2     0.3    -      -       -      +
    117G  PRO*     3.4     2.3    -      -       -      +
    118G  ILE*     3.1    26.8    +      -       +      -
    136G  ILE*     3.7    14.4    -      -       +      -
    142G  LEU*     4.6     8.7    -      -       +      -
    149G  GLN      3.8     3.6    -      -       -      -
    150G  VAL*     4.2    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 63 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61G  GLN*     5.5     0.2    -      -       -      +
     62G  VAL*     1.3    76.3    -      -       -      +
     64G  PHE*     1.3    78.9    +      -       -      +
    115G  TYR*     4.3     6.3    -      -       +      -
    116G  GLU      3.8    17.9    -      -       -      +
    117G  PRO*     4.1     6.7    -      -       +      -
    142G  LEU*     3.8     4.7    -      -       -      +
    143G  LEU*     2.8    47.4    +      -       +      +
    149G  GLN*     3.5    53.3    +      -       +      +
    150G  VAL*     3.8     4.4    -      -       -      +
     96I  ALA*     4.6     3.6    -      -       -      -
     97I  ILE*     4.0    30.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 64 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62G  VAL*     3.4    21.8    -      -       +      -
     63G  LEU*     1.3    80.9    -      -       -      +
     65G  LYS*     1.3    61.1    +      -       -      +
     76G  LEU*     3.5    55.6    -      -       +      -
     77G  THR      4.0     9.6    -      -       -      -
    114G  TRP*     3.8     7.2    -      -       +      -
    115G  TYR*     3.3     2.1    -      -       -      -
    116G  GLU*     2.9    43.0    +      -       +      +
    118G  ILE*     3.9    15.9    -      -       +      -
    136G  ILE*     3.8    38.8    -      -       +      -
    137G  ASN*     4.7     0.4    -      -       -      -
    138G  ARG*     3.9    17.0    -      -       +      -
    141G  TYR*     3.2    21.5    -      -       +      +
    142G  LEU*     4.6     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 65 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64G  PHE*     1.3    77.4    -      -       -      +
     66G  GLY*     1.3    65.6    +      -       -      +
     67G  GLN*     4.0    22.2    -      -       -      +
    113G  PRO*     4.6     2.9    -      -       -      -
    114G  TRP*     3.1    15.9    -      -       -      +
    115G  TYR*     3.1    32.4    +      -       +      -
    141G  TYR*     2.7    32.2    +      -       -      +
    143G  LEU*     3.5    44.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 66 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65G  LYS*     1.3    76.8    -      -       -      +
     67G  GLN*     1.3    67.5    -      -       -      -
    113G  PRO*     3.2     2.4    -      -       -      +
    114G  TRP*     2.8    62.0    +      -       -      -
    141G  TYR*     4.0     9.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 67 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65G  LYS*     4.0    16.5    -      -       +      +
     66G  GLY*     1.3    69.9    -      -       -      +
     68G  GLY*     1.3    69.0    +      -       -      +
     69G  CYS*     4.6     1.2    -      -       -      -
     70G  PRO*     5.5     0.7    -      -       -      +
    111G  ALA      5.6     0.4    -      -       -      +
    112G  LYS      5.1     0.2    -      -       -      -
    113G  PRO*     3.0    34.6    -      -       -      +
    141G  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