Contacts of the strand formed by residues 115 - 121 (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 GLY 115 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111J  GLU*     4.2     2.2    -      -       -      -
    112J  THR*     2.8    33.0    +      -       -      +
    113J  ALA      3.3     1.2    -      -       -      -
    114J  ASN*     1.3    80.2    -      -       -      +
    116J  PRO*     1.3    79.3    -      -       -      +
    117J  LEU*     4.2     1.0    -      -       -      +
    243J  TYR*     4.9     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 116 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111J  GLU*     3.9     9.0    -      -       +      -
    115J  GLY*     1.3    84.2    -      -       -      +
    117J  LEU*     1.3    62.8    +      -       -      +
    130J  MET*     3.6    27.4    -      -       +      -
    131J  THR*     3.7    20.4    +      -       -      +
    242J  ASN*     4.0    27.6    -      -       +      +
    243J  TYR*     3.1    38.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 117 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80J  ILE*     4.1    21.1    -      -       +      -
     86J  THR*     5.8     5.2    -      -       +      -
     91J  LEU*     4.5     0.2    -      -       +      -
    110J  VAL*     2.9    29.0    +      -       +      +
    111J  GLU*     4.4     3.8    -      -       -      -
    112J  THR*     4.1    16.6    -      -       -      +
    115J  GLY      3.4     3.1    +      -       -      +
    116J  PRO*     1.3    75.3    -      -       -      +
    118J  ALA*     1.3    60.4    +      -       -      +
    129J  LYS*     3.9     3.3    -      -       -      -
    130J  MET*     3.1    24.9    +      -       -      +
    131J  THR*     4.4     1.7    +      -       -      -
    134J  GLY      4.2     9.0    -      -       -      +
    135J  PHE*     3.7    29.7    -      -       +      +
    136J  PRO*     4.2    12.3    -      -       +      -
    141J  LEU*     4.0    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 118 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109J  TYR*     3.2     1.7    -      -       -      -
    110J  VAL*     2.7    34.7    +      -       +      +
    117J  LEU*     1.3    81.6    -      -       +      +
    119J  ARG*     1.3    58.3    +      -       -      +
    127J  PHE*     3.7    24.6    -      -       +      -
    128J  THR      3.5     6.1    -      -       -      +
    130J  MET*     3.3     6.3    -      -       -      +
    135J  PHE*     3.7    28.3    -      -       +      -
    141J  LEU*     4.2    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 119 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108J  GLY      4.4     4.5    -      -       -      +
    109J  TYR*     3.8     6.5    -      -       +      -
    118J  ALA*     1.3    73.6    -      -       -      +
    120J  TYR*     1.3    67.3    +      -       -      +
    121J  HIS*     3.5    33.1    +      -       +      +
    127J  PHE*     3.3     2.8    -      -       -      -
    128J  THR*     2.7    39.5    +      -       -      +
    129J  LYS      4.4     3.8    +      -       -      -
    130J  MET*     3.4    38.4    -      -       +      +
    242J  ASN      2.9    25.5    +      -       -      -
    243J  TYR*     3.7     0.2    -      -       -      +
    244J  GLU*     3.3    28.3    +      -       -      +
    247J  GLU*     2.8    41.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 120 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108J  GLY      2.8    21.3    +      -       -      +
    119J  ARG*     1.3    76.6    -      -       -      +
    121J  HIS*     1.3    73.2    +      -       -      +
    122J  THR*     4.2     8.3    -      -       -      -
    125J  LYS*     3.6    25.3    -      -       -      +
    126J  ARG*     3.7    28.9    -      -       -      -
    127J  PHE*     3.7    28.8    -      +       +      -
    148J  TRP*     4.1    12.3    -      +       -      -
    151J  VAL*     5.2     1.3    -      -       +      -
    152J  LYS*     3.8    22.2    +      -       +      +
    155J  LEU*     3.9    12.6    -      -       +      -
    156J  GLY*     3.4    33.6    -      -       -      -
    159J  GLU*     3.1    36.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 121 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119J  ARG*     3.5    33.3    +      -       -      -
    120J  TYR*     1.3    76.2    +      -       -      +
    122J  THR*     1.3    61.0    +      -       -      +
    123J  GLY      3.2     1.8    -      -       -      +
    124J  ASP*     3.6    25.1    -      -       -      +
    125J  LYS*     2.9    31.0    +      -       -      -
    126J  ARG      3.0    14.1    +      -       -      +
    128J  THR*     3.0    38.2    +      -       +      +
    159J  GLU*     5.0     0.2    -      -       -      -
    244J  GLU*     4.8     8.7    -      -       -      -
----------------------------------------------------------
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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