Contacts of the strand formed by residues 185 - 191 (chain A) in PDB entry 1POP


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 185 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  VAL*     4.1     9.5    -      -       -      +
    174A  LYS*     4.2     0.5    -      -       -      -
    175A  ASN*     3.0    36.1    +      -       -      +
    177A  TRP      6.2     0.2    -      -       -      -
    178A  GLY      3.5    17.5    -      -       -      -
    179A  THR      3.8     0.4    +      -       -      -
    181A  TRP*     2.9    24.2    +      -       -      -
    184A  ASN*     1.3    75.5    -      -       -      +
    186A  TYR*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  ARG*     3.5    50.2    -      -       -      +
     13A  VAL*     3.6    17.5    -      -       -      +
     14A  THR      4.4     2.3    +      -       -      -
     15A  PRO*     5.8     0.2    -      -       -      +
     16A  VAL*     3.6    25.9    -      -       +      +
    144A  TYR*     3.6     3.6    -      -       -      -
    164A  VAL*     4.1    13.5    -      -       +      -
    172A  LEU*     4.4    13.5    -      -       +      -
    173A  ILE      3.2    18.8    -      -       -      +
    174A  LYS*     3.7    24.7    -      -       +      +
    181A  TRP*     4.0     1.9    -      -       -      -
    182A  GLY*     3.7     1.9    -      -       -      -
    183A  GLU*     2.8    47.7    +      -       +      +
    184A  ASN*     3.8     9.2    -      -       +      -
    185A  GLY*     1.3    79.9    -      -       -      +
    187A  ILE*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  PHE*     3.9    23.6    -      -       +      -
    144A  TYR*     3.6    31.0    -      -       +      -
    149A  PHE*     3.7    27.6    -      -       +      -
    171A  ILE      3.7     0.2    -      -       -      +
    172A  LEU*     3.7     2.8    -      -       -      +
    173A  ILE*     2.9    59.6    +      -       +      +
    175A  ASN*     5.4     0.4    -      -       +      -
    181A  TRP*     3.7    21.1    -      -       +      -
    183A  GLU*     5.0     0.4    -      -       -      -
    186A  TYR*     1.3    75.5    -      -       -      +
    188A  ARG*     1.3    68.8    +      -       -      +
    189A  ILE*     3.8    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  TYR*     3.4     5.3    +      -       -      -
    147A  GLY*     3.8    14.1    +      -       -      +
    148A  ILE*     3.6    26.2    -      -       +      +
    149A  PHE*     2.8    27.5    +      -       -      +
    170A  TYR*     3.9    43.1    -      -       +      -
    171A  ILE      3.4     5.4    -      -       -      -
    172A  LEU*     3.9    21.3    -      -       +      -
    183A  GLU*     2.9    36.9    +      -       -      +
    187A  ILE*     1.3    74.5    -      -       -      +
    189A  ILE*     1.3    59.8    +      -       -      +
    426A  MOH      3.2    25.3    +      -       -      -
    427A  MOH      3.2     9.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 189 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  LEU*     3.5    32.1    -      -       +      -
    141A  PHE*     4.4     3.6    -      -       +      -
    148A  ILE*     4.6     0.2    -      -       -      -
    149A  PHE*     3.6    10.8    -      -       +      +
    170A  TYR*     3.2     3.1    -      -       -      -
    171A  ILE*     2.9    37.2    +      -       -      +
    173A  ILE*     4.5     7.6    -      -       +      -
    187A  ILE*     3.8    31.8    -      -       +      -
    188A  ARG*     1.3    75.0    -      -       -      +
    190A  LYS*     1.3    66.4    +      -       -      +
    199A  VAL*     3.7    40.6    -      -       +      +
    200A  CYS*     5.1     2.5    -      -       -      -
    202A  LEU*     4.5    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  ILE*     4.0    10.1    -      -       +      +
    149A  PHE      2.9    19.8    +      -       -      +
    150A  VAL*     4.1    16.4    -      -       +      -
    169A  ASN*     3.5    25.8    -      -       -      +
    171A  ILE*     5.7     0.7    -      -       -      +
    189A  ILE*     1.3    75.0    -      -       -      +
    191A  ARG*     1.3    75.3    +      -       -      +
    192A  GLY      4.8     3.8    +      -       -      -
    193A  THR*     3.8    23.5    -      -       +      +
    199A  VAL*     2.9    31.5    -      -       +      +
    202A  LEU*     5.9     1.0    -      -       -      +
    203A  TYR*     4.6     3.3    +      -       -      -
    416A  MOH      4.0    30.2    -      -       -      -
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Residues in contact with ARG 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  GLU      5.3     1.0    +      -       -      -
    118A  GLN*     2.9    32.5    +      -       -      +
    122A  LEU*     3.4    36.1    -      -       -      +
    166A  TYR*     4.8     7.7    -      -       -      -
    167A  GLY      2.9    25.3    +      -       -      -
    168A  PRO*     3.5    19.4    +      -       -      +
    169A  ASN*     3.1    14.0    +      -       -      +
    170A  TYR      3.6    25.3    +      -       -      +
    171A  ILE*     4.2     9.4    -      -       +      -
    189A  ILE      3.5     0.2    +      -       -      -
    190A  LYS*     1.3    94.6    +      -       -      +
    192A  GLY*     1.3    68.4    +      -       -      +
    193A  THR*     3.5     4.7    -      -       -      -
    203A  TYR*     3.8     8.5    -      -       -      +
----------------------------------------------------------
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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