Contacts of the strand formed by residues 110 - 117 (chain A) in PDB entry 1Q21


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 PRO 110 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  GLU      3.4    20.6    -      -       -      +
     77A  GLY*     3.3     2.9    -      -       -      -
     78A  PHE*     2.9    27.2    +      -       -      -
    104A  LYS*     6.4     0.7    -      -       -      -
    109A  VAL*     1.3    85.3    -      -       +      +
    111A  MET*     1.4    60.9    +      -       -      +
    159A  LEU*     4.0     1.3    -      -       +      -
    162A  GLU*     3.9    19.1    -      -       +      +
    163A  ILE*     3.8    36.1    -      -       +      -
    166A  HIS*     3.8    33.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  PHE*     3.1    18.2    -      -       +      +
     80A  CYS*     3.9    24.0    -      -       -      -
     97A  ARG*     4.2    35.0    -      -       +      +
    100A  ILE*     3.5    36.1    -      -       +      -
    101A  LYS*     4.8     3.1    -      -       +      -
    109A  VAL*     3.3    22.7    +      -       +      +
    110A  PRO*     1.4    75.0    -      -       -      +
    112A  VAL*     1.3    71.4    +      -       -      +
    139A  ILE*     3.5    43.9    -      -       +      +
    140A  PRO*     3.5     5.4    -      -       -      +
    159A  LEU*     3.9     2.1    -      -       -      +
    162A  GLU*     4.5     4.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  PHE      3.0     5.5    +      -       -      -
     79A  LEU*     3.7    14.0    -      -       +      -
     80A  CYS*     2.9    27.2    +      -       -      +
    111A  MET*     1.3    80.4    -      -       -      +
    113A  LEU*     1.4    67.3    +      -       -      +
    114A  VAL*     4.3     8.0    -      -       +      +
    139A  ILE*     4.2     3.4    -      -       -      -
    140A  PRO*     3.8    14.8    -      -       +      +
    142A  ILE*     3.7    29.8    -      -       +      -
    155A  ALA      4.5     6.1    -      -       -      +
    158A  THR*     3.9    13.5    -      -       +      -
    159A  LEU*     3.7    33.9    -      -       +      +
    162A  GLU*     4.2     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  CYS*     3.5    19.7    -      -       +      +
     82A  PHE*     3.9    23.6    -      -       +      -
     90A  PHE*     4.9     0.9    -      -       +      -
     93A  ILE*     3.9    26.7    -      -       +      -
    112A  VAL*     1.4    71.3    -      -       -      +
    114A  VAL*     1.3    62.7    +      -       -      +
    130A  ALA*     3.9    23.6    -      -       +      +
    133A  LEU*     4.4    18.6    -      -       +      -
    134A  ALA*     4.3     9.0    -      -       +      +
    137A  TYR*     5.1     1.1    -      -       +      -
    139A  ILE*     3.8    16.2    -      -       +      +
    140A  PRO      2.8    15.5    +      -       -      +
    141A  TYR*     3.4    18.3    -      -       +      -
    142A  ILE      2.9    25.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  LEU*     4.1    15.7    -      -       +      -
     79A  LEU*     3.6    37.9    -      -       +      -
     80A  CYS      2.7    12.3    +      -       -      +
     81A  VAL*     3.3    11.2    -      -       +      -
     82A  PHE*     2.9    34.6    +      -       -      +
    112A  VAL*     4.3     6.1    -      -       +      +
    113A  LEU*     1.3    79.5    -      -       -      +
    115A  GLY*     1.4    60.4    +      -       -      +
    116A  ASN      4.3     0.7    -      -       -      +
    142A  ILE*     3.3     2.9    -      -       +      +
    144A  THR*     3.2    38.8    -      -       +      +
    155A  ALA*     4.2    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  PHE*     3.6    15.7    -      -       -      -
     84A  ILE*     3.5    24.7    -      -       -      +
    114A  VAL*     1.4    69.1    -      -       -      +
    116A  ASN*     1.3    61.3    +      -       -      -
    118A  CYS*     4.5     0.7    -      -       -      +
    141A  TYR*     3.6     8.6    -      -       -      -
    142A  ILE      3.0    12.1    +      -       -      -
    143A  GLU*     3.3     8.3    -      -       -      +
    144A  THR*     3.0    24.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  VAL      3.2    16.4    +      -       -      +
     15A  GLY*     4.0     4.4    -      -       -      -
     19A  LEU*     3.5    11.5    -      -       +      +
     81A  VAL*     4.0    17.0    -      -       +      -
     82A  PHE      2.8    15.8    +      -       -      +
     83A  ALA*     3.4     2.6    -      -       -      -
     84A  ILE*     2.8    27.0    +      -       -      +
    114A  VAL*     3.6     0.8    +      -       +      -
    115A  GLY*     1.3    74.8    -      -       -      +
    117A  LYS*     1.4    78.6    +      -       -      +
    118A  CYS      3.4     1.1    -      -       -      -
    144A  THR*     2.8    25.4    +      -       -      +
    146A  ALA*     3.1    23.3    +      -       -      +
    180A  GDP      3.0    31.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  GLY      2.6    22.4    +      -       -      -
     14A  VAL      3.2    21.3    -      -       -      +
     83A  ALA*     4.2     6.6    -      -       +      +
     84A  ILE*     3.9     6.9    -      -       +      +
     85A  ASN*     4.2    15.5    +      -       -      +
    116A  ASN*     1.4    89.6    +      -       -      +
    118A  CYS*     1.3    50.5    +      -       -      +
    119A  ASP*     2.6    30.2    +      -       -      -
    120A  LEU*     2.7    43.4    +      -       +      +
    144A  THR      3.2     0.4    +      -       -      -
    180A  GDP      2.7    56.7    +      -       +      +
----------------------------------------------------------
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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