Contacts of the strand formed by residues 103 - 112 (chain J) 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 LEU 103 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98J  TYR*     4.0    11.4    -      -       +      +
     99J  GLU*     3.5     2.6    -      -       -      +
    100J  THR*     3.0    31.4    +      -       -      +
    101J  GLY      3.7     1.2    -      -       -      +
    102J  LEU*     1.3    79.9    -      -       +      +
    104J  PHE*     1.3    65.9    +      -       -      +
    213J  ILE*     3.5    39.7    -      -       +      -
    215J  LYS*     4.2    21.8    -      -       -      +
    228J  TYR*     5.0     3.4    -      -       +      +
    284J  PHE*     3.5    44.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 104 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30G  ASN*     3.8    23.1    -      -       -      -
     31G  ARG*     3.2    49.4    -      -       +      +
     32G  ARG      4.8     4.5    -      -       -      -
     98J  TYR*     3.2    24.6    +      -       -      +
     99J  GLU*     4.1     8.5    -      -       +      -
    102J  LEU      3.4    11.7    -      -       -      -
    103J  LEU*     1.3    77.2    -      -       -      +
    105J  GLY*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 105 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97J  CYS*     3.2     4.9    -      -       -      +
     98J  TYR*     3.0    50.0    +      -       -      +
    104J  PHE*     1.3    79.3    -      -       -      +
    106J  SER*     1.3    60.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 106 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96J  GLY      3.3    13.2    -      -       -      -
     97J  CYS*     3.9     9.4    -      -       -      +
     98J  TYR*     4.1     1.5    -      -       -      -
    105J  GLY*     1.3    75.4    -      -       -      -
    107J  TYR*     1.3    67.6    +      -       -      +
    159J  GLU*     2.6    44.2    +      -       -      +
    163J  CYS*     5.2     2.7    -      -       -      -
    164J  SER*     5.9     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 107 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2J  THR*     5.5     1.9    -      -       -      +
      3J  LEU      3.5    16.5    +      -       -      -
      4J  LYS*     3.6    18.5    -      -       -      +
     94J  ILE*     3.8    11.7    -      -       +      -
     95J  THR*     2.8    29.6    +      -       -      -
     96J  GLY*     2.8    46.2    +      -       -      +
     97J  CYS*     3.8    10.5    +      -       -      -
     98J  TYR*     4.5     4.9    -      +       +      -
    106J  SER*     1.3    80.4    -      -       -      +
    108J  GLY*     1.3    59.0    +      -       -      +
    109J  TYR*     4.0     6.3    -      +       +      -
    159J  GLU*     3.5    14.7    -      -       -      +
    246J  GLY      3.5    26.5    -      -       -      -
    247J  GLU*     4.0    28.7    -      -       +      +
    248J  PRO*     3.3    23.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 108 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94J  ILE      3.2     8.3    -      -       -      -
     95J  THR*     3.8     8.7    -      -       -      -
    107J  TYR*     1.3    78.7    -      -       -      +
    109J  TYR*     1.3    61.7    +      -       -      +
    119J  ARG*     3.9     3.4    -      -       -      +
    120J  TYR*     2.8    34.5    +      -       -      +
    155J  LEU*     4.1    10.1    -      -       -      -
    159J  GLU*     3.4    14.7    +      -       -      +
    247J  GLU*     5.4     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 109 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92J  SER      3.9     0.2    -      -       -      +
     93J  LEU*     3.7     5.2    -      -       -      +
     94J  ILE*     2.8    61.7    +      -       +      +
    107J  TYR*     4.0     9.2    -      +       -      -
    108J  GLY*     1.3    77.0    -      -       -      +
    110J  VAL*     1.3    69.0    +      -       -      +
    111J  GLU*     3.3    25.2    +      -       +      -
    118J  ALA      3.2    14.4    -      -       -      +
    119J  ARG*     3.8     9.0    -      -       +      -
    120J  TYR      4.5     0.2    -      -       -      +
    127J  PHE*     4.9     2.0    -      -       -      -
    130J  MET*     3.6    23.6    -      -       +      -
    243J  TYR*     3.7    11.8    -      +       -      -
    247J  GLU*     3.7    35.7    -      -       +      -
    248J  PRO*     3.4    10.1    -      -       +      +
    249J  GLY*     3.2    26.9    +      -       -      -
    325J  NAG      4.6     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 110 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91J  LEU*     3.5    33.4    -      -       +      -
     92J  SER      3.3     8.3    -      -       -      +
     93J  LEU*     3.9    19.7    -      -       +      -
    109J  TYR*     1.3    75.3    -      -       -      +
    111J  GLU*     1.3    61.5    +      -       -      +
    117J  LEU*     2.9    36.9    +      -       +      +
    118J  ALA      2.7    16.4    +      -       -      +
    127J  PHE*     4.0    17.5    -      -       +      -
    130J  MET*     3.2     3.4    -      -       -      +
    140J  MET*     4.0    19.7    -      -       +      -
    141J  LEU*     4.3    13.5    -      -       +      -
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Residues in contact with GLU 111 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91J  LEU*     3.4     7.5    -      -       -      +
     92J  SER*     2.9    46.8    +      -       -      -
     94J  ILE*     4.0    16.3    -      -       +      +
    109J  TYR*     3.3    18.9    +      -       +      -
    110J  VAL*     1.3    75.5    -      -       -      +
    112J  THR*     1.3    64.4    +      -       -      +
    115J  GLY*     3.9     5.8    -      -       -      +
    116J  PRO*     3.9    16.6    -      -       +      -
    117J  LEU*     3.9     2.0    -      -       -      +
    243J  TYR*     3.1    19.9    +      -       -      -
    249J  GLY*     5.4     1.0    -      -       -      -
    325J  NAG      3.9    24.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 112 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77J  LEU*     6.1     0.2    -      -       -      +
     80J  ILE*     4.7     5.2    -      -       -      +
     86J  THR*     5.9     1.6    -      -       +      +
     88J  THR*     3.3    14.3    +      -       +      +
     90J  SER*     3.8     8.4    +      -       -      -
     91J  LEU*     3.7    17.5    -      -       -      +
    111J  GLU*     1.3    78.3    -      -       -      +
    113J  ALA*     1.3    59.8    +      -       -      +
    114J  ASN*     2.8    45.3    -      -       +      +
    115J  GLY*     2.8    28.6    +      -       -      +
    117J  LEU*     4.1    16.7    -      -       +      +
----------------------------------------------------------
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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