Contacts of the strand formed by residues 110 - 119 (chain A) in PDB entry 1A9R


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 THR 110 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  GLN*     3.2    16.9    +      -       -      -
     27A  VAL*     3.4     5.2    -      -       +      -
     28A  ALA      2.9    25.8    +      -       -      -
    108A  VAL*     3.3     7.8    -      -       -      +
    109A  GLU*     1.3    77.4    -      -       -      +
    111A  LEU*     1.3    70.1    +      -       -      +
    112A  VAL*     4.3     6.1    -      -       +      -
    170A  MET*     5.6     4.3    -      -       +      -
    233A  LEU*     4.7     0.9    -      -       -      -
    234A  ARG*     2.8    46.7    +      -       +      +
    236A  PHE*     5.6     2.7    -      -       +      -
    282A  ILE*     3.9    31.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  ALA*     3.4    26.7    -      -       +      +
     30A  ILE*     4.1    27.6    -      -       +      -
    100A  VAL*     4.5     7.6    -      -       +      -
    103A  PHE*     4.4     8.1    -      -       +      -
    110A  THR*     1.3    75.9    -      -       -      +
    112A  VAL*     1.3    63.6    +      -       -      +
    113A  VAL*     3.8    22.9    -      -       +      -
    224A  GLU      4.4     7.6    -      -       -      +
    228A  ALA*     3.6    26.5    -      -       +      -
    233A  LEU*     4.2    15.5    -      -       +      +
    234A  ARG      2.8    14.6    +      -       -      +
    235A  VAL*     3.4    11.9    -      -       +      +
    236A  PHE      3.0    25.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  VAL*     4.2    19.7    -      -       +      -
     28A  ALA      2.9    10.1    +      -       -      +
     29A  VAL*     3.3    21.7    -      -       +      +
     30A  ILE*     2.9    27.2    +      -       -      +
    110A  THR*     4.5     4.3    -      -       +      -
    111A  LEU*     1.3    77.4    -      -       -      +
    113A  VAL*     1.3    64.4    +      -       -      +
    114A  THR*     4.4    13.2    -      -       +      -
    236A  PHE*     3.1    34.3    -      -       +      +
    238A  PHE*     4.6     4.0    -      -       +      -
    275A  VAL*     5.1     8.7    -      -       +      -
    279A  MET*     4.6     4.3    -      -       +      -
    282A  ILE*     4.4    14.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  ILE*     4.0    20.4    -      -       +      -
     84A  ARG*     4.5     5.4    -      -       -      +
    111A  LEU*     3.8    26.5    -      -       +      -
    112A  VAL*     1.3    76.9    -      -       -      +
    114A  THR*     1.3    66.5    +      -       -      +
    132A  ILE*     5.1     2.5    -      -       +      -
    166A  TYR*     5.1     1.3    -      -       +      -
    221A  THR*     3.8    29.4    -      -       +      -
    224A  GLU*     4.7     7.2    -      -       +      -
    225A  VAL*     4.3     6.1    -      -       +      -
    235A  VAL*     4.2    12.1    -      -       +      -
    236A  PHE      2.9    11.2    +      -       -      +
    237A  GLY*     2.9    39.6    -      -       -      -
    238A  PHE      3.1     3.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  VAL*     5.1     0.4    -      -       +      -
     30A  ILE      3.2    10.2    +      -       -      +
     31A  CYS      3.6     0.2    -      -       -      -
     32A  GLY*     2.8    29.2    +      -       -      -
     33A  SER*     4.9     3.6    -      -       -      -
     35A  LEU*     3.5    27.6    -      -       +      +
     84A  ARG*     2.9    25.2    +      -       -      -
    112A  VAL*     4.4     8.5    -      -       +      -
    113A  VAL*     1.3    80.8    -      -       -      +
    115A  ASN*     1.3    64.6    +      -       -      +
    221A  THR*     4.7     0.2    -      -       -      -
    238A  PHE*     3.3    40.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  GLY*     4.5     2.5    -      -       -      -
     33A  SER*     3.9     7.3    +      -       -      -
    114A  THR*     1.3    78.9    -      -       -      +
    116A  ALA*     1.3    69.6    +      -       -      +
    132A  ILE*     4.0     6.1    -      -       -      +
    192A  TYR*     3.6    20.4    -      -       -      -
    220A  SER*     4.1     0.2    -      -       -      +
    221A  THR*     2.9    31.7    +      -       -      +
    238A  PHE*     3.2     4.6    +      -       -      +
    239A  SER*     2.7    33.2    +      -       -      -
    240A  LEU*     2.9    27.7    +      -       -      +
    291A  SO4      3.1    27.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  SER*     4.3    12.1    -      -       -      -
    115A  ASN*     1.3    80.9    +      -       -      +
    117A  ALA*     1.3    62.7    +      -       -      +
    218A  GLY*     4.5     5.9    -      -       -      -
    219A  MET      5.5     0.3    +      -       -      -
    240A  LEU      3.4     6.3    -      -       -      -
    242A  THR*     3.7    23.6    -      -       +      +
    260A  VAL*     5.4     4.7    -      -       +      -
    290A  HPA      3.6    17.2    +      -       +      +
    291A  SO4      3.0    21.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  ASN*     3.9     4.5    -      -       -      +
    116A  ALA*     1.3    75.4    -      -       -      +
    118A  GLY*     1.3    61.3    +      -       -      +
    192A  TYR*     4.1     4.7    -      -       +      -
    216A  ALA*     3.8    24.2    -      -       +      -
    217A  VAL      3.3    13.2    -      -       -      +
    239A  SER*     3.8    18.4    -      -       -      +
    240A  LEU      2.9     7.6    +      -       -      +
    241A  ILE*     3.4     8.3    -      -       +      -
    242A  THR*     3.0    25.1    +      -       -      -
    290A  HPA      3.6     7.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  ALA*     1.3    73.9    -      -       -      +
    119A  GLY*     1.3    63.2    +      -       -      -
    216A  ALA*     3.3     6.0    -      -       -      -
    217A  VAL*     2.9    34.6    +      -       -      +
    241A  ILE*     4.6     0.2    -      -       -      -
    243A  ASN*     3.5     9.2    -      -       -      -
    245A  VAL*     4.0     6.5    -      -       -      -
    290A  HPA      3.4    29.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  GLY*     1.3    71.0    -      -       -      -
    120A  LEU*     1.3    61.6    +      -       -      -
    121A  ASN      3.6     1.1    -      -       -      -
    124A  PHE*     4.7     3.6    -      -       -      -
    215A  ASP      3.9     4.0    -      -       -      -
    241A  ILE*     3.8    21.7    -      -       -      +
    243A  ASN      2.8    17.8    +      -       -      -
    244A  LYS*     3.9    15.4    +      -       -      -
    245A  VAL*     3.2    28.3    +      -       -      +
----------------------------------------------------------
 Back to top of page


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