Contacts of the strand formed by residues 195 - 204 (chain C) in PDB entry 5TWV


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 ARG 195 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191C  PRO*     3.7     3.8    -      -       -      -
    192C  ARG      2.7    37.2    +      -       -      +
    193C  HIS*     4.7     5.8    -      -       -      +
    194C  GLY*     1.3    86.9    -      -       -      +
    196C  LEU*     1.3    61.4    +      -       -      +
    197C  CYS*     3.6     6.1    +      -       -      -
    260C  VAL*     4.3    29.7    -      -       +      +
    261C  ILE      6.1     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 196 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189C  ILE*     3.9    17.3    -      -       +      +
    190C  THR*     4.6     0.4    -      -       -      -
    191C  PRO*     3.7    31.0    -      -       +      +
    195C  ARG*     1.3    70.8    -      -       -      +
    197C  CYS*     1.3    63.1    +      -       -      +
    260C  VAL*     3.6     1.6    -      -       -      +
    261C  ILE*     3.0    44.6    +      -       +      +
    267C  LEU      5.3     3.4    -      -       -      +
    270C  LEU      5.8     0.7    -      -       -      +
    311C  TRP*     3.7    38.6    -      -       +      -
    342C  PRO*     6.3     0.9    -      -       +      -
    346C  ALA*     4.1    26.0    -      -       +      +
    349C  LEU*     4.5    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 197 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188C  VAL      4.0     0.2    -      -       -      +
    189C  ILE*     3.2     8.3    -      -       -      +
    190C  THR*     3.0    38.9    +      -       -      +
    192C  ARG*     4.5    17.7    -      -       +      +
    195C  ARG*     3.6    13.0    -      -       -      -
    196C  LEU*     1.3    82.6    -      -       -      +
    198C  PHE*     1.3    60.1    +      -       -      +
    199C  MET*     4.0     1.4    +      -       +      +
    258C  TYR*     4.3    17.9    -      -       +      -
    259C  HIS      3.2    12.3    -      -       -      +
    260C  VAL*     3.7    28.9    -      -       -      -
    261C  ILE*     5.3     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 198 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187C  ALA*     3.4    24.7    -      -       +      -
    188C  VAL      3.5     3.8    -      -       -      -
    189C  ILE*     3.5    29.6    -      -       +      -
    197C  CYS*     1.3    72.7    -      -       -      +
    199C  MET*     1.3    58.8    +      -       -      +
    200C  LEU*     3.4    44.4    -      -       +      -
    217C  MET*     4.9     8.5    -      -       -      -
    238C  ILE*     5.1     5.8    -      -       +      -
    257C  ILE*     3.1     7.6    -      -       +      +
    258C  TYR*     3.2     1.9    -      -       -      -
    259C  HIS*     2.8    52.4    +      -       +      +
    261C  ILE*     5.2     1.8    -      -       +      -
    267C  LEU*     5.2    11.7    -      -       +      -
    283C  ILE*     5.1    20.2    -      -       +      -
    304C  TYR*     5.6     3.8    -      -       +      -
    309C  ILE*     4.4    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 199 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187C  ALA*     3.8     1.2    -      -       -      +
    188C  VAL*     2.6    49.2    +      -       +      +
    190C  THR*     6.1     3.8    -      -       +      -
    197C  CYS*     4.0     2.0    +      -       +      +
    198C  PHE*     1.3    74.7    -      -       -      +
    200C  LEU*     1.3    66.6    +      -       -      +
    256C  ILE*     3.5    21.8    -      -       +      -
    257C  ILE      3.2     3.6    -      -       -      +
    258C  TYR*     5.3     2.9    -      -       +      -
    315C  PHE*     3.2    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 200 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184C  SER*     4.3     7.0    -      -       -      +
    187C  ALA*     3.5    28.9    -      -       +      -
    198C  PHE*     3.4    31.2    +      -       +      -
    199C  MET*     1.3    71.8    -      -       -      +
    201C  ARG*     1.3    60.8    +      -       -      +
    217C  MET*     4.0    25.6    -      -       +      -
    256C  ILE*     3.2     1.3    -      -       -      -
    257C  ILE*     2.6    44.2    +      -       +      +
    283C  ILE*     5.9     3.1    -      -       +      -
    285C  VAL*     4.0    27.4    -      -       +      -
    304C  TYR*     3.9    26.7    -      -       +      +
    315C  PHE*     3.9     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 201 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183C  PHE*     4.0     4.7    -      -       -      -
    184C  SER*     3.5    28.1    +      -       -      +
    200C  LEU*     1.3    77.4    -      -       -      +
    202C  VAL*     1.3    63.3    +      -       -      +
    254C  PRO*     4.2    15.5    -      -       +      -
    255C  LEU      3.4    13.0    -      -       -      +
    256C  ILE*     3.8    20.3    -      -       +      +
    315C  PHE*     3.2    49.4    +      -       +      +
    316C  VAL      2.9    32.5    +      -       -      +
    317C  PRO*     4.8     1.4    -      -       -      +
    318C  ILE*     3.5    16.3    -      -       -      +
    332C  LYS      3.5    12.1    +      -       -      -
    333C  PHE*     3.5    46.3    +      -       +      +
    335C  ASN      4.3     0.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 202 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181C  LEU*     5.3     2.2    -      -       +      -
    182C  ILE      3.5    14.1    -      -       -      +
    183C  PHE*     3.8    27.1    -      -       +      -
    201C  ARG*     1.3    75.5    -      -       -      +
    203C  GLY*     1.3    69.2    +      -       -      +
    215C  ILE*     6.2     3.1    -      -       +      -
    251C  LEU*     4.0    23.6    -      -       +      +
    254C  PRO*     3.1    20.3    -      -       -      +
    255C  LEU*     3.2    14.0    +      -       +      +
    257C  ILE*     4.2    14.1    -      -       +      -
    287C  LEU*     4.2    18.8    -      -       +      -
    333C  PHE*     4.0     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 203 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180C  THR      3.7     0.2    -      -       -      +
    181C  LEU*     3.7     6.1    -      -       -      +
    182C  ILE*     3.0    38.4    +      -       -      +
    202C  VAL*     1.3    78.8    -      -       -      +
    204C  ASP*     1.3    60.7    +      -       -      +
    251C  LEU*     4.2     7.2    -      -       -      -
    254C  PRO*     4.1    19.1    -      -       -      -
    330C  TYR*     4.7     5.4    -      -       -      -
    333C  PHE*     3.9     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 204 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  HIS*     3.7    11.8    +      -       -      -
    177C  ARG*     4.7     3.5    +      -       -      -
    180C  THR*     3.7    17.1    +      -       -      +
    181C  LEU*     3.8    18.1    -      -       +      +
    203C  GLY*     1.3    73.3    -      -       -      +
    205C  LEU*     1.3    65.6    +      -       -      +
    206C  ARG*     3.2    28.6    +      -       -      +
    208C  SER      3.3    16.2    -      -       -      +
    209C  MET*     5.1     2.9    -      -       -      +
    210C  ILE*     5.9     4.6    -      -       +      +
    251C  LEU*     3.9    25.6    -      -       +      +
    252C  VAL*     4.6     8.9    +      -       -      +
    254C  PRO*     5.2     0.4    -      -       -      +
    330C  TYR*     3.0    22.5    +      -       -      -
----------------------------------------------------------
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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