Contacts of the strand formed by residues 174 - 186 (chain L) in PDB entry 4G7H


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 L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44L  LEU*     3.3    32.5    -      -       +      +
     45L  LEU*     4.1     7.3    -      -       +      +
     48L  ILE*     4.4     5.6    -      -       +      -
    172L  SER*     3.0    21.4    +      -       -      +
    173L  PRO*     1.3    78.9    -      -       +      +
    175L  ARG*     1.3    62.2    +      -       -      +
    176L  ARG      3.7    11.4    -      -       -      +
    177L  VAL*     3.6    27.8    -      -       +      -
    199L  ILE*     4.2     3.6    -      -       +      -
    200L  TRP      3.5     6.3    -      -       -      +
    201L  THR*     3.8     7.6    -      -       +      -
    210L  ALA*     3.8    29.2    -      -       +      -
    851N  LEU*     4.5     7.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 175 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45L  LEU*     5.0     3.9    -      -       -      +
     83L  LYS      5.0     4.8    +      -       -      -
     84L  GLU*     4.3    15.0    +      -       -      +
     86L  VAL*     3.9    15.4    -      -       -      +
    170L  VAL*     4.9    15.2    -      -       -      +
    172L  SER      5.3     4.1    +      -       -      +
    173L  PRO      3.4     1.5    +      -       -      +
    174L  VAL*     1.3    75.7    -      -       -      +
    176L  ARG*     1.3    60.5    +      -       -      +
    200L  TRP*     2.5    17.7    +      -       +      +
    201L  THR      3.9    18.2    -      -       -      -
    202L  ASP*     3.5    31.5    +      -       -      +
    845N  ASN*     4.7    19.8    +      -       -      +
    847N  ASP*     3.3    44.0    -      -       +      +
    848N  GLU*     6.3     0.4    -      -       -      +
    851N  LEU*     5.2     6.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 176 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45L  LEU*     4.6     3.6    -      -       -      -
    174L  VAL*     3.6     2.4    -      -       -      +
    175L  ARG*     1.3    81.7    -      -       -      +
    177L  VAL*     1.3    76.9    +      -       -      +
    178L  ALA*     4.6    10.3    -      -       -      +
    198L  ARG*     4.6     3.6    -      -       -      +
    199L  ILE*     3.6     0.2    -      -       -      -
    200L  TRP*     2.9    83.7    +      -       +      +
    847N  ASP*     4.4    10.2    +      -       -      +
    884N  ARG*     3.0    49.2    -      -       -      +
    888N  GLU*     2.5    41.7    +      -       -      -
    937N  TYR*     5.5     4.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 177 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41L  ARG*     3.4    50.2    +      -       +      -
     44L  LEU*     3.8    24.5    -      -       +      -
     45L  LEU*     4.1    14.4    -      -       +      +
    174L  VAL*     3.6    20.0    -      -       +      -
    176L  ARG*     1.3    86.2    -      -       -      +
    178L  ALA*     1.3    65.0    +      -       -      +
    179L  PHE      4.9     0.2    -      -       -      +
    197L  LEU*     3.7    27.8    -      -       +      -
    198L  ARG      3.4     4.9    -      -       -      +
    199L  ILE*     4.2     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 178 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41L  ARG*     5.3     0.4    -      -       -      +
    176L  ARG*     4.6    10.1    -      -       -      +
    177L  VAL*     1.3    76.8    -      -       -      +
    179L  PHE*     1.3    62.1    +      -       -      +
    197L  LEU*     3.7     0.7    -      -       -      +
    198L  ARG*     2.7    61.2    +      -       -      +
    200L  TRP*     4.0    18.1    -      -       +      -
    937N  TYR*     6.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 179 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34L  VAL*     4.0     8.1    -      -       +      -
     37L  GLY*     3.8    25.1    -      -       -      -
     38L  ASN*     3.2    42.2    -      -       -      -
     41L  ARG*     4.1    20.8    -      -       +      +
    178L  ALA*     1.3    75.8    -      -       -      +
    180L  GLN*     1.3    63.7    +      -       -      +
    181L  VAL*     3.9    20.6    -      -       +      -
    195L  LEU*     3.8    17.0    -      -       +      -
    196L  THR      3.2    11.2    -      -       -      +
    197L  LEU*     3.8    19.3    -      -       +      -
    936N  TYR*     4.5     7.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 180 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179L  PHE*     1.3    77.1    -      -       -      +
    181L  VAL*     1.3    74.2    +      -       -      +
    182L  GLU*     4.2    19.2    +      -       -      +
    194L  LYS      3.6     1.9    -      -       -      +
    195L  LEU*     3.9     0.2    -      -       -      -
    196L  THR*     2.9    46.6    +      -       +      +
    638N  LYS*     5.3     9.7    -      -       -      +
    936N  TYR*     4.0    35.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 181 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33L  GLY*     3.4    33.0    -      -       -      +
     34L  VAL*     3.6    17.9    -      -       +      +
    179L  PHE*     3.9    14.3    -      -       +      -
    180L  GLN*     1.3    83.3    +      -       -      +
    182L  GLU*     1.3    66.8    +      -       -      +
    193L  ASP*     3.3    36.3    -      -       +      +
    194L  LYS      3.3     8.5    -      -       -      +
    195L  LEU*     4.2     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 182 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180L  GLN*     4.2    24.5    +      -       +      +
    181L  VAL*     1.3    79.9    -      -       -      +
    183L  ASP*     1.3    69.8    +      -       -      +
    193L  ASP*     3.8     1.3    -      -       -      -
    194L  LYS*     2.9    72.1    +      -       +      +
    196L  THR*     5.4     4.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 183 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182L  GLU*     1.3    82.5    -      -       -      +
    184L  THR*     1.3    60.9    +      -       -      +
    190L  THR*     4.3    12.8    -      -       +      +
    191L  ASP*     3.9    18.0    -      -       -      +
    192L  LEU      3.4    10.8    -      -       -      +
    193L  ASP*     4.1     6.6    -      -       -      +
    194L  LYS*     5.7     0.2    -      -       -      +
    851M  LYS*     4.3    16.5    +      -       -      -
    636N  GLN*     6.0     2.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 184 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26L  GLU*     3.4    18.9    +      -       -      +
     27L  PRO*     4.4     9.9    -      -       +      -
    183L  ASP*     1.3    77.2    -      -       -      +
    185L  ARG*     1.3    70.6    +      -       -      +
    190L  THR*     3.0     7.6    -      -       -      +
    192L  LEU*     2.9    55.7    +      -       +      +
    193L  ASP      3.7    14.4    -      -       -      +
    194L  LYS*     4.1    15.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 185 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27L  PRO*     6.2     0.7    -      -       -      -
    184L  THR*     1.3    83.1    +      -       -      +
    186L  LEU*     1.3    57.5    +      -       -      +
    187L  GLY      3.2    30.4    +      -       -      +
    189L  ARG      3.1    14.6    -      -       -      +
    190L  THR*     3.6    27.1    -      -       +      +
    192L  LEU*     4.6     1.8    -      -       -      -
    688N  TRP*     6.2     1.4    -      -       -      +
    689N  ASP*     3.5    22.4    +      -       -      +
    692N  GLU*     3.4    44.9    +      -       -      +
     51O  LEU*     5.3     8.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 186 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6L  LEU*     3.8    26.2    -      -       +      -
      7L  LYS*     4.6    20.2    -      -       +      -
     27L  PRO*     4.6    13.2    -      -       +      -
    185L  ARG*     1.3    71.8    -      -       -      +
    187L  GLY*     1.3    71.3    +      -       -      +
    188L  GLN*     3.2     5.4    +      -       -      -
    189L  ARG*     3.0    27.3    +      -       -      +
    192L  LEU*     3.5    17.8    -      -       +      +
----------------------------------------------------------
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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