Contacts of the strand formed by residues 191 - 201 (chain F) in PDB entry 3V56


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 191 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189F  GLU      3.6     1.8    +      -       -      -
    190F  THR*     1.3    77.9    -      -       -      +
    192F  TYR*     1.3    66.1    +      -       -      -
    193F  PHE*     3.5    10.4    -      -       -      -
    252F  LYS*     3.4     8.9    -      -       -      +
    253F  LEU      2.9    34.9    +      -       -      +
    283F  LYS*     4.4     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 192 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  HIS*     4.0    22.3    +      -       -      -
    220A  PHE*     4.6     0.2    -      +       -      -
    254A  GLU*     5.1     1.9    +      -       -      -
    172D  PHE*     3.4    46.1    -      +       +      -
    173D  LYS      4.6     2.1    +      -       -      -
    174D  ARG*     3.4    39.4    -      -       +      +
    191F  GLY*     1.3    75.9    -      -       -      -
    193F  PHE*     1.3    62.2    +      -       -      +
    250F  ILE*     4.3     5.4    -      -       +      -
    251F  ALA      3.6     2.5    -      -       -      -
    252F  LYS*     3.8    45.4    +      -       +      +
    283F  LYS*     3.7     2.6    -      -       -      +
    284F  LEU*     2.9    48.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 193 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177F  ALA*     4.3     4.5    -      -       +      -
    178F  LEU*     3.7    35.0    -      -       +      -
    187F  VAL*     4.0     8.1    -      -       +      -
    189F  GLU      3.4    25.8    -      -       -      -
    191F  GLY*     3.5    26.5    -      -       -      -
    192F  TYR*     1.3    77.1    -      -       -      +
    194F  PHE*     1.3    62.2    +      -       -      +
    195F  ILE*     3.5    18.7    +      -       +      +
    250F  ILE*     3.4     5.9    -      -       -      -
    251F  ALA      2.9    30.9    +      -       -      +
    253F  LEU*     3.7    29.2    -      -       +      -
    281F  ALA*     4.7     1.8    -      -       +      -
    282F  LEU      3.3     5.2    -      -       -      +
    283F  LYS*     3.5    44.6    -      -       +      -
    284F  LEU*     4.5     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 194 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194D  PHE*     3.9    32.3    -      +       -      -
    196D  TYR*     5.3     3.1    -      +       -      -
    246D  TYR*     4.5     3.1    -      -       -      -
    282D  LEU*     5.4     5.4    -      -       +      -
    194E  PHE*     3.8    26.5    -      +       -      -
    193F  PHE*     1.3    70.6    -      -       -      +
    195F  ILE*     1.4    56.2    +      -       -      +
    196F  TYR*     3.8    23.8    -      +       +      -
    246F  TYR*     4.0     5.8    -      -       -      -
    248F  ALA*     3.6    26.9    -      -       +      -
    249F  GLY*     3.4    20.0    -      -       -      -
    250F  ILE*     4.2    12.6    -      -       +      -
    281F  ALA*     3.3     2.3    -      -       -      -
    282F  LEU*     2.7    62.1    +      -       +      +
    284F  LEU*     4.3    16.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 195 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193F  PHE*     3.5    23.1    -      -       +      +
    194F  PHE*     1.4    75.4    -      -       -      +
    196F  TYR*     1.3    62.3    +      -       -      +
    212F  ILE*     3.5    30.1    -      -       +      -
    229F  LEU*     4.2     9.6    -      -       +      -
    230F  PHE*     4.3     8.9    -      -       +      -
    248F  ALA*     3.1     5.1    -      -       -      +
    249F  GLY      2.8    33.4    +      -       -      +
    251F  ALA*     3.8    23.6    -      -       +      +
    253F  LEU*     4.0    19.5    -      -       +      -
    259F  LEU*     3.8    23.6    -      -       +      -
    279F  PHE*     4.1     7.4    -      -       +      -
    280F  GLY      3.6    10.3    -      -       -      +
    281F  ALA*     4.2     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 196 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194E  PHE*     5.4     2.0    -      +       -      -
    248E  ALA      4.5     4.5    -      -       -      -
    249E  GLY*     4.4     7.4    -      -       -      -
    250E  ILE*     3.3    34.5    -      -       +      +
    147F  LEU      4.3     1.4    +      -       -      -
    148F  GLN*     2.7    41.9    +      -       -      +
    194F  PHE*     3.8    22.7    -      +       +      -
    195F  ILE*     1.3    73.0    -      -       -      +
    197F  GLY*     1.3    58.5    +      -       -      +
    212F  ILE*     3.8     6.1    -      -       -      -
    246F  TYR*     3.4    24.5    -      -       +      +
    247F  SER      3.6     6.5    -      -       -      -
    248F  ALA*     3.6     6.1    -      -       +      -
    278F  PHE*     4.2    25.1    -      +       -      -
    279F  PHE*     3.3     8.1    -      -       -      -
    280F  GLY*     2.9    60.2    +      -       -      +
    281F  ALA*     3.8     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 197 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196F  TYR*     1.3    79.0    -      -       -      +
    198F  GLN*     1.3    60.3    +      -       -      -
    210F  HIS*     3.5    11.9    +      -       -      -
    212F  ILE*     3.7     9.3    -      -       -      +
    246F  TYR*     3.5     6.4    -      -       -      -
    247F  SER      3.1    32.8    +      -       -      +
    261F  LEU*     4.3     6.7    -      -       -      -
    278F  PHE      3.4    11.9    -      -       -      -
    279F  PHE*     4.2     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 198 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231E  ARG      2.8    27.9    +      -       -      -
    246E  TYR      4.0     1.7    -      -       -      +
    247E  SER*     2.7    29.6    +      -       -      -
    197F  GLY*     1.3    74.1    -      -       -      +
    199F  VAL*     1.4    75.5    +      -       -      +
    210F  HIS*     4.2     0.4    -      -       -      -
    244F  SER*     4.0    14.7    +      -       -      -
    245F  CYS      3.2    17.5    -      -       -      +
    246F  TYR*     3.7    16.6    +      -       +      +
    261F  LEU*     4.6     0.6    -      -       -      +
    276F  VAL*     3.0    18.8    +      -       -      +
    277F  THR*     3.2     2.1    -      -       -      +
    278F  PHE*     2.9    58.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 199 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166F  VAL*     4.8     0.4    -      -       +      -
    198F  GLN*     1.4    80.9    -      -       -      +
    200F  LEU*     1.3    63.2    +      -       -      +
    201F  TYR*     3.5    38.1    -      -       +      +
    210F  HIS*     3.5    18.4    -      -       +      +
    244F  SER*     3.3     1.8    -      -       -      -
    245F  CYS      2.9    28.8    +      -       -      -
    261F  LEU*     3.6    26.9    -      -       +      -
    263F  ILE*     4.2     6.7    -      -       +      -
    270F  ILE*     3.8    21.3    -      -       +      -
    276F  VAL      3.9     3.6    -      -       -      -
    277F  THR*     3.7    19.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 200 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231E  ARG*     4.3     4.9    -      -       -      +
    233E  ILE*     3.6    32.1    -      -       +      -
    199F  VAL*     1.3    71.2    -      -       -      +
    201F  TYR*     1.3    66.2    +      -       -      +
    202F  THR*     4.3     9.9    -      -       +      -
    242F  ASN*     3.9    10.5    -      -       +      +
    243F  ASN      3.6    29.8    -      -       -      +
    244F  SER*     3.7     6.5    -      -       -      +
    270F  ILE*     3.2     7.3    -      -       -      +
    271F  SER*     2.9    47.8    +      -       -      +
    276F  VAL*     3.6    32.7    +      -       +      +
    277F  THR*     3.3     7.5    +      -       -      -
     29K  VAL      5.5     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 201 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199F  VAL*     3.5    34.4    -      -       +      +
    200F  LEU*     1.3    73.1    -      -       -      +
    202F  THR*     1.3    61.2    +      -       -      +
    203F  ASP      3.5     0.7    -      -       -      -
    208F  MET*     3.6    37.5    -      -       +      -
    209F  GLY*     3.0    35.6    -      -       -      -
    210F  HIS*     2.6    34.1    +      -       -      +
    234F  GLN*     5.2     2.7    -      -       +      -
    236F  MET*     3.4    21.5    -      -       +      +
    242F  ASN*     3.4     5.2    -      -       -      -
    243F  ASN      2.8    43.8    +      -       -      +
    245F  CYS*     4.2    12.3    -      -       +      -
    263F  ILE*     3.9     6.4    -      -       +      +
    269F  GLN      3.8     1.8    -      -       -      +
    270F  ILE*     3.6    18.8    -      -       +      -
----------------------------------------------------------
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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