Contacts of the strand formed by residues 101 - 111 (chain A) in PDB entry 1Q9S


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 ILE 101 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ARG*     3.8    32.1    -      -       +      -
     17A  GLY      3.5     3.6    -      -       -      +
     18A  GLN*     3.7    35.2    -      -       +      +
     19A  VAL*     4.9     0.2    -      -       -      -
     60A  VAL*     3.9     0.8    -      -       -      -
     61A  GLY*     2.9    33.5    +      -       -      +
     99A  GLY      4.4     2.7    -      -       -      +
    100A  GLU*     1.3    77.4    -      -       -      +
    102A  LEU*     1.3    62.3    +      -       -      +
    103A  ASN*     3.8    12.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ARG*     3.2     4.7    -      -       -      -
     17A  GLY      2.7    33.6    +      -       -      +
     19A  VAL*     3.7    12.6    -      -       +      -
     35A  ALA*     4.1    14.4    -      -       +      +
     37A  PHE*     3.6    25.6    -      -       +      -
     58A  ALA*     4.2     6.3    -      -       +      -
     59A  SER      3.4    21.5    -      -       -      +
     60A  VAL*     4.0    15.9    -      -       +      +
     87A  THR*     3.7    25.6    -      -       +      +
     89A  ILE*     4.1    13.7    -      -       +      -
     97A  PHE*     4.6     4.0    -      -       +      -
    100A  GLU      3.6     1.6    +      -       -      -
    101A  ILE*     1.3    71.9    -      -       -      +
    103A  ASN*     1.3    60.2    +      -       -      +
    104A  VAL*     3.7    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  CYS      4.0     3.4    -      -       -      -
     16A  ARG*     2.6    42.6    +      -       -      +
     58A  ALA*     3.1     7.8    -      -       -      +
     59A  SER*     2.8    54.6    +      -       -      +
     61A  GLY*     3.0    22.6    +      -       -      -
    101A  ILE*     3.8    14.3    +      -       -      +
    102A  LEU*     1.3    71.1    -      -       -      +
    104A  VAL*     1.3    62.6    +      -       -      +
    150A  PHE*     4.0     6.3    -      -       +      -
    151A  PHE*     3.6     4.8    -      -       +      -
    154A  SER*     3.4    12.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  PHE*     3.1     4.3    -      -       -      -
     15A  CYS*     2.8    44.2    +      -       -      +
     37A  PHE*     4.3     7.9    -      -       +      -
     57A  TRP      3.6     1.1    -      -       -      -
     58A  ALA*     3.7    18.6    -      -       +      -
     68A  MET*     3.7    21.1    -      -       +      -
     85A  MET*     4.2    14.6    -      -       +      -
     87A  THR*     4.2     6.1    -      -       -      +
    102A  LEU*     3.7    23.3    -      -       +      -
    103A  ASN*     1.3    80.3    -      -       -      +
    105A  ALA*     1.3    70.0    +      -       -      +
    106A  ILE*     4.0    13.9    -      -       +      -
    150A  PHE*     3.6     8.5    -      -       -      -
    151A  PHE*     4.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  PRO*     4.7     1.8    -      -       +      -
     13A  TYR      3.2     5.6    -      -       -      -
     14A  PHE*     3.6    30.3    -      -       +      -
     56A  GLY*     3.4     1.9    -      -       -      -
     57A  TRP*     3.1    31.3    +      -       +      +
     68A  MET*     3.7     1.0    -      -       -      +
    104A  VAL*     1.3    75.5    -      -       -      +
    106A  ILE*     1.3    64.4    +      -       -      +
    107A  VAL*     3.3     3.7    -      -       +      +
    145A  ILE*     4.2    12.3    -      -       +      -
    151A  PHE*     3.7    17.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  LEU*     3.5    10.2    -      -       +      +
     12A  PRO*     2.9     4.7    -      -       -      +
     13A  TYR*     2.8    60.7    +      -       +      +
     45A  LEU*     5.2     0.9    -      -       +      -
     49A  ILE*     5.1     5.2    -      -       +      -
     54A  TYR*     3.3    44.6    -      -       +      -
     55A  TYR      4.2     2.9    -      -       -      -
     68A  MET*     4.7     1.8    -      -       -      -
     70A  VAL*     4.4    10.5    -      -       +      -
     72A  ILE*     4.0    18.8    -      -       +      -
     85A  MET*     3.8    23.1    -      -       +      -
    104A  VAL*     4.0    13.9    -      -       +      -
    105A  ALA*     1.3    72.3    -      -       -      +
    107A  VAL*     1.3    60.2    +      -       -      +
    108A  GLY      4.5     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  LEU*     3.5    20.5    -      -       -      +
     12A  PRO*     4.1     5.4    -      -       +      -
     55A  TYR*     3.2    29.5    +      -       +      -
     56A  GLY*     3.6    11.7    -      -       -      -
     57A  TRP*     3.8    20.6    -      -       +      -
    105A  ALA      3.3    17.9    -      -       -      +
    106A  ILE*     1.3    74.4    -      -       -      +
    108A  GLY*     1.3    61.5    +      -       -      +
    137A  LEU*     4.1     4.0    -      -       +      -
    142A  TYR*     3.8    33.6    +      -       +      -
    145A  ILE*     3.8    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  LEU*     3.7     7.2    -      -       -      +
     54A  TYR*     3.1    13.4    -      -       -      +
     55A  TYR*     3.0    50.6    +      -       -      -
    106A  ILE*     4.5     0.2    -      -       -      +
    107A  VAL*     1.3    83.2    -      -       -      +
    109A  TYR*     1.3    60.7    +      -       -      -
    142A  TYR*     5.3     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  ARG*     4.1    20.0    -      -       -      +
     11A  LEU*     4.4     4.1    -      -       +      +
     50A  SER*     5.1     3.4    -      -       -      -
     51A  THR      3.9     9.6    +      -       -      -
     52A  GLY*     3.9    14.8    -      -       -      -
     53A  ILE      3.7     9.0    -      -       -      -
     54A  TYR*     3.7    25.5    -      +       +      -
     55A  TYR*     3.9     0.4    -      -       -      -
    108A  GLY*     1.3    72.8    -      -       -      -
    110A  LEU*     1.3    64.1    +      -       -      +
    111A  ARG*     3.3    28.5    -      -       -      -
    112A  PRO*     3.1    32.9    -      -       +      +
    136A  ARG*     3.5    18.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  ILE*     2.9    19.1    +      -       +      +
     54A  TYR      4.4     7.2    -      -       -      +
     55A  TYR*     3.4    35.2    -      -       +      -
     69A  VAL*     4.3    11.4    -      -       +      -
    108A  GLY      3.9     0.2    +      -       -      -
    109A  TYR*     1.3    79.1    -      -       -      +
    111A  ARG*     1.3    67.7    +      -       +      +
    129A  ASP*     3.5    44.6    -      -       +      +
    132A  GLU*     3.7    28.9    -      -       +      -
    133A  ALA      4.6     1.6    -      -       -      +
    136A  ARG*     3.9    14.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  ILE*     2.7    37.9    +      -       +      +
    109A  TYR*     3.3    14.7    -      -       -      -
    110A  LEU*     1.3    82.9    -      -       -      +
    112A  PRO*     1.3    94.4    +      -       +      +
    114A  LYS*     3.8    31.1    -      -       -      +
    116A  PHE*     4.4     1.8    -      -       -      -
    125A  ALA*     4.0    23.9    -      -       -      +
    126A  ILE*     4.4     1.2    -      -       -      +
    129A  ASP*     2.9    41.3    +      -       -      +
    401A  FMN      3.0    41.2    +      -       -      -
----------------------------------------------------------
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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