Contacts of the strand formed by residues 174 - 184 (chain A) in PDB entry 4OIO


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 174 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  LEU*     3.3    31.6    -      -       +      +
     45A  LEU*     4.0    12.6    -      -       +      +
     48A  ILE*     4.4    10.8    -      -       +      -
    172A  SER*     3.2    15.2    +      -       -      +
    173A  PRO*     1.3    79.1    -      -       +      +
    175A  ARG*     1.3    65.8    +      -       -      +
    176A  ARG      3.9     4.9    -      -       -      +
    177A  VAL*     3.6    28.7    -      -       +      -
    199A  ILE*     4.9     2.7    -      -       +      -
    200A  TRP      3.7    12.6    -      -       -      +
    201A  THR*     4.4     4.5    -      -       +      +
    210A  ALA*     4.3    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 175 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  LEU*     4.9     3.4    -      -       -      +
     83A  LYS      5.5     4.2    +      -       -      -
     84A  GLU*     5.1    13.3    +      -       -      +
     85A  LEU      5.8     1.0    +      -       -      -
     86A  VAL*     5.1     3.8    -      -       -      +
    170A  VAL*     4.6    19.8    +      -       -      +
    172A  SER      4.5    12.9    +      -       -      -
    173A  PRO      3.4     0.8    +      -       -      -
    174A  VAL*     1.3    77.8    +      -       -      +
    176A  ARG*     1.3    62.7    +      -       +      +
    200A  TRP*     3.2    17.5    +      -       +      +
    201A  THR      4.3     1.6    -      -       -      -
    202A  ASP*     3.5    49.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 176 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  LEU*     4.6     3.8    -      -       -      -
    174A  VAL*     3.7     1.9    -      -       -      -
    175A  ARG*     1.3    82.5    -      -       +      +
    177A  VAL*     1.3    71.0    +      -       -      +
    200A  TRP*     2.8    80.7    +      -       +      +
    863C  ASP*     5.1     4.6    +      -       -      +
    864C  GLY*     3.5    39.2    -      -       -      +
    865C  THR*     3.2    27.1    -      -       -      +
    866C  PRO*     5.7     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  ARG*     2.8    53.5    +      -       +      -
     44A  LEU*     3.8    36.6    -      -       +      -
     45A  LEU*     4.2    10.5    -      -       +      +
    174A  VAL*     3.6    22.0    -      -       +      -
    176A  ARG*     1.3    83.2    -      -       -      +
    178A  ALA*     1.3    63.0    +      -       -      +
    197A  LEU*     4.0    10.1    -      -       +      -
    198A  ARG      3.5     9.0    -      -       -      +
    199A  ILE*     4.1    11.4    -      -       +      -
    200A  TRP*     4.5     0.2    -      -       -      -
    864C  GLY*     3.4    11.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  ARG*     4.7     3.1    -      -       -      +
    177A  VAL*     1.3    74.8    -      -       -      +
    179A  PHE*     1.3    60.8    +      -       -      +
    197A  LEU*     3.9     0.3    -      -       -      +
    198A  ARG*     2.7    47.6    +      -       +      +
    200A  TRP*     4.2    10.8    -      -       +      -
    860C  HIS*     6.0     2.0    -      -       +      +
    862C  PRO      3.8    10.3    -      -       -      +
    863C  ASP*     3.6    10.5    -      -       -      -
    864C  GLY*     3.3    28.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 179 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  GLY      4.0     0.2    -      -       -      -
     34A  VAL*     3.6    29.8    -      -       +      -
     37A  GLY*     3.7    12.8    -      -       -      -
     38A  ASN*     3.6    40.6    -      -       +      -
     41A  ARG*     4.1    18.6    -      -       +      -
    178A  ALA*     1.3    75.7    -      -       -      +
    180A  GLN*     1.3    64.5    +      -       -      +
    181A  VAL*     4.2     1.8    -      -       +      -
    195A  LEU*     3.6    20.6    -      -       +      -
    196A  THR      3.2     9.6    -      -       -      +
    197A  LEU*     3.6    20.0    -      -       +      -
    198A  ARG*     6.1     0.4    -      -       -      -
    860C  HIS*     5.1     6.7    -      +       -      -
    862C  PRO      4.6     7.3    -      -       -      +
    939C  ARG*     2.9    48.9    +      -       -      -
    975C  TYR*     4.8     2.6    -      -       -      -
    980C  GLY*     4.3     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 180 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  PHE*     1.3    79.1    -      -       -      +
    181A  VAL*     1.3    65.3    +      -       -      +
    182A  GLU*     4.0    17.0    +      -       +      -
    194A  LYS      3.3     3.6    -      -       -      +
    195A  LEU*     3.5     4.0    -      -       -      +
    196A  THR*     2.8    46.7    +      -       -      +
    198A  ARG*     5.0    11.4    +      -       -      -
    862C  PRO      4.7     8.0    -      -       -      +
    929C  ARG*     3.2    31.4    +      -       -      +
    934C  PHE*     3.8    25.9    -      -       +      +
    935C  GLY      2.9    28.7    +      -       -      -
    937C  ASP*     3.6    14.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  GLY*     3.7    30.3    -      -       -      +
     34A  VAL*     3.9    17.7    -      -       +      -
    179A  PHE*     4.2     3.1    -      -       +      -
    180A  GLN*     1.3    76.3    -      -       -      +
    182A  GLU*     1.3    63.1    +      -       -      +
    193A  ASP*     3.8    37.7    -      -       +      +
    194A  LYS      3.6     3.1    -      -       -      +
    195A  LEU*     4.5     1.1    -      -       +      -
    937C  ASP*     2.9    34.5    +      -       -      +
    938C  LYS*     3.1    27.0    +      -       +      +
    939C  ARG*     4.0     7.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  GLN*     4.0    16.7    -      -       +      +
    181A  VAL*     1.3    78.7    -      -       -      +
    183A  ASP*     1.3    64.2    +      -       -      +
    184A  THR      3.6     0.2    +      -       -      -
    192A  LEU      3.8     1.0    -      -       -      +
    193A  ASP*     3.7     2.1    -      -       -      -
    194A  LYS*     2.8    76.9    +      -       +      +
    196A  THR*     4.0     6.3    +      -       -      -
    933C  GLY      4.4     2.0    -      -       -      +
    934C  PHE*     3.5    18.3    -      -       -      +
    935C  GLY*     2.8    32.2    +      -       -      +
    936C  VAL      4.6    14.4    -      -       -      +
    938C  LYS*     4.5     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  GLU*     1.3    75.3    -      -       -      +
    184A  THR*     1.3    68.5    +      -       -      +
    190A  THR*     5.6     2.3    -      -       -      -
    191A  ASP*     3.6    17.9    +      -       -      -
    192A  LEU      3.4     5.7    -      -       -      +
    194A  LYS*     5.0     2.3    -      -       -      +
    936C  VAL      5.4     2.0    +      -       -      -
    938C  LYS*     3.3    31.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  GLU*     3.5    19.9    +      -       -      +
     27A  PRO*     4.1    16.7    -      -       +      +
    183A  ASP*     1.3    78.4    +      -       -      +
    185A  ARG*     1.3    73.7    +      -       -      +
    190A  THR*     4.7     0.2    -      -       -      -
    191A  ASP      4.3     3.1    +      -       -      -
    192A  LEU*     3.0    54.0    +      -       +      +
    193A  ASP      3.8    15.7    -      -       -      +
    194A  LYS*     4.1     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