Contacts of the strand formed by residues 173 - 182 (chain A) in PDB entry 2IL1


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 VAL 173 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  THR*     3.0    35.9    +      -       -      +
    171A  VAL      4.0     6.1    -      -       -      +
    172A  GLY*     1.3    85.8    -      -       -      +
    174A  ASP*     1.3    71.9    +      -       -      +
    192A  TRP*     4.1    11.7    -      -       +      -
    193A  ASP      3.3     7.0    -      -       -      +
    194A  THR*     4.0    19.5    -      -       +      -
    203A  ILE*     5.2     0.2    -      -       +      -
    204A  THR*     4.4     4.9    -      -       +      -
    207A  TYR*     3.5    58.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 174 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  MET*     5.0     5.2    -      -       +      -
    170A  THR*     5.2     1.3    -      -       -      -
    173A  VAL*     1.3    81.0    +      -       -      +
    175A  PHE*     1.3    63.7    +      -       -      +
    192A  TRP*     3.5     7.8    -      -       -      -
    193A  ASP*     2.8    52.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 175 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  MET*     4.6     3.1    -      -       -      -
    170A  THR*     5.8     3.1    -      -       -      -
    174A  ASP*     1.3    78.7    -      -       -      +
    176A  LYS*     1.3    72.4    +      -       -      +
    177A  ILE*     3.5    29.8    -      -       +      -
    190A  GLN*     3.6    21.8    -      -       +      +
    191A  ILE      3.1    14.8    -      -       -      +
    192A  TRP*     3.6    34.3    -      +       +      -
    193A  ASP      4.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 176 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  MET*     3.7    30.2    -      -       +      -
    156A  GLU*     4.6     9.6    +      -       -      -
    159A  THR*     3.5    33.7    -      -       +      +
    160A  ASP*     3.3    42.6    +      -       -      +
    175A  PHE*     1.3    79.0    +      -       -      +
    177A  ILE*     1.3    63.9    +      -       -      +
    178A  LYS      4.2     0.2    -      -       -      -
    189A  LEU      3.7     1.0    -      -       -      +
    190A  GLN*     3.7     2.3    -      -       -      -
    191A  ILE*     2.9    33.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  THR*     5.1     2.3    -      -       -      +
    160A  ASP*     5.6     1.6    -      -       -      +
    175A  PHE*     3.5    24.2    -      -       +      -
    176A  LYS*     1.3    73.9    -      -       -      +
    178A  LYS*     1.3    66.2    +      -       -      +
    179A  THR*     5.1     1.8    -      -       -      +
    188A  ARG*     3.7    56.5    -      -       +      +
    189A  LEU      3.3     6.5    -      -       -      +
    190A  GLN*     3.7    35.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158A  PHE*     3.0    55.5    +      -       +      +
    159A  THR*     4.0    23.6    -      -       +      +
    176A  LYS      4.2     0.2    -      -       -      -
    177A  ILE*     1.3    77.4    -      -       -      +
    179A  THR*     1.3    67.7    +      -       -      +
    180A  VAL*     3.7    17.0    +      -       +      +
    187A  ILE      3.5     0.3    -      -       -      +
    189A  LEU*     2.7    49.1    +      -       +      +
    191A  ILE*     4.8     2.5    -      -       +      -
    290A  ASP*     5.7     0.4    +      -       -      -
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Residues in contact with THR 179 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  ALA*     5.7     0.7    -      -       +      -
    177A  ILE*     5.1     2.5    -      -       -      +
    178A  LYS*     1.3    82.0    -      -       -      +
    180A  VAL*     1.3    65.8    +      -       -      +
    181A  GLU*     4.3     2.0    +      -       +      -
    186A  LYS*     3.7    34.3    -      -       +      -
    187A  ILE      3.4     7.4    -      -       -      +
    188A  ARG*     4.3    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 180 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158A  PHE*     3.9    21.1    -      -       +      -
    178A  LYS*     3.7    28.0    -      -       +      +
    179A  THR*     1.3    78.8    -      -       -      +
    181A  GLU*     1.3    61.5    +      -       -      +
    182A  LEU*     4.8     6.1    -      -       +      -
    185A  LYS      3.4     1.9    -      -       -      +
    186A  LYS*     3.5     2.6    -      -       -      -
    187A  ILE*     2.8    64.3    +      -       +      +
    189A  LEU*     4.7    10.5    -      -       +      -
    294A  LEU*     4.2    22.0    -      -       +      -
    297A  VAL*     4.8     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  THR*     4.3     2.6    +      -       +      -
    180A  VAL*     1.3    77.8    -      -       -      +
    182A  LEU*     1.3    61.1    +      -       -      +
    184A  GLY*     5.3     4.9    -      -       -      +
    185A  LYS      3.3     8.3    -      -       -      +
    186A  LYS*     4.7    14.4    -      -       +      -
    294A  LEU*     5.1     3.8    -      -       -      +
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Residues in contact with LEU 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  VAL*     4.8     6.3    -      -       +      -
    181A  GLU*     1.3    74.1    -      -       -      +
    183A  ARG*     1.3    78.2    +      -       +      +
    184A  GLY      3.2     0.6    -      -       -      +
    185A  LYS*     2.8    32.1    +      -       -      +
    187A  ILE*     4.7     8.3    -      -       +      -
    294A  LEU*     3.9    41.5    -      -       +      +
    297A  VAL*     3.8    15.0    -      -       +      -
    298A  ASP*     4.1    23.6    -      -       +      +
    301A  LEU*     3.8    28.3    -      -       +      +
----------------------------------------------------------
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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