Contacts of the strand formed by residues 193 - 204 (chain A) in PDB entry 6QPA


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 MET 193 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  LYS*     2.8    31.4    +      -       -      +
    183A  LEU*     3.6    31.9    -      -       +      +
    186A  MET*     3.6    28.0    -      -       +      +
    187A  LYS*     3.7    19.8    -      -       -      +
    190A  VAL      3.5    15.6    +      -       -      +
    191A  PRO      3.3     2.2    +      -       -      -
    192A  GLY*     1.3    74.1    -      -       -      +
    194A  VAL*     1.3    65.4    +      -       -      +
    195A  GLY      3.9    14.8    -      -       -      +
    196A  TRP*     3.8    13.9    -      -       +      -
    257A  ILE*     3.8    19.5    -      -       +      -
    259A  TRP*     3.5    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  PRO*     3.4    17.7    -      -       +      +
    151A  LYS*     3.4    10.9    -      -       +      +
    152A  VAL      3.8    17.9    -      -       -      +
    153A  ALA*     3.5    35.4    -      -       +      +
    158A  ARG*     4.6     4.3    -      -       +      -
    187A  LYS*     3.3    15.7    -      -       -      -
    192A  GLY*     3.7    13.7    -      -       -      +
    193A  MET*     1.3    74.1    -      -       -      +
    195A  GLY*     1.3    59.8    +      -       -      +
    258A  GLU*     2.8    27.0    +      -       +      +
    259A  TRP      3.8     3.4    -      -       -      +
    260A  GLU*     3.8    19.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  ASP      3.2    13.2    -      -       -      -
    126A  LEU*     4.0     6.7    -      -       -      -
    127A  PRO*     4.0     7.0    -      -       -      -
    187A  LYS*     4.0     7.2    -      -       -      -
    193A  MET*     3.7     3.4    -      -       -      +
    194A  VAL*     1.3    82.0    -      -       -      +
    196A  TRP*     1.3    67.9    +      -       -      +
    257A  ILE*     3.5     6.8    -      -       -      +
    258A  GLU*     2.9    25.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  LYS*     3.4    46.4    -      -       +      -
    124A  SER*     3.4     5.9    -      -       -      -
    125A  ASP*     2.9    57.0    +      -       +      +
    126A  LEU*     3.6     9.9    -      -       -      +
    180A  THR*     4.5    12.6    -      -       +      -
    183A  LEU*     3.6    49.9    +      -       +      -
    184A  GLU*     3.9    25.3    -      -       +      +
    187A  LYS*     3.9    13.3    -      -       +      +
    193A  MET*     3.8    22.0    -      -       +      -
    195A  GLY*     1.3    76.8    -      -       -      +
    197A  MET*     1.3    70.7    +      -       -      +
    198A  ILE*     3.8    15.9    -      -       +      -
    256A  HIS      3.0    12.6    -      -       -      +
    257A  ILE*     4.5     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  ILE*     3.8    24.5    -      -       +      -
     79A  TYR*     4.0     6.1    -      -       +      -
    121A  VAL*     3.8    25.4    -      -       +      -
    123A  LYS      3.5     6.5    -      -       -      -
    124A  SER*     4.1     5.2    -      -       -      -
    126A  LEU*     3.9    24.5    -      -       +      -
    183A  LEU*     5.2     0.2    -      -       -      -
    196A  TRP*     1.3    79.1    -      -       -      +
    198A  ILE*     1.3    65.2    +      -       -      +
    199A  MET*     3.7    32.5    -      -       +      -
    254A  LEU      3.8     0.3    -      -       -      +
    255A  VAL*     3.7     3.6    -      -       -      +
    256A  HIS*     2.8    57.7    +      -       +      +
    308A  TRP*     4.0    11.2    -      -       +      -
    312A  LEU*     5.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  GLU      3.6     0.3    -      -       -      +
    121A  VAL*     3.6     4.2    -      -       -      -
    122A  VAL*     2.8    48.0    +      -       +      -
    123A  LYS*     2.9    17.0    +      -       +      +
    175A  PHE*     4.6     8.7    -      -       +      -
    176A  GLU*     4.1     6.3    -      -       +      +
    179A  ALA*     3.9    10.3    -      -       +      -
    180A  THR*     3.4    39.7    -      -       -      +
    183A  LEU*     3.7    20.6    -      -       +      -
    196A  TRP*     3.8    14.6    -      -       +      -
    197A  MET*     1.3    71.4    -      -       -      +
    199A  MET*     1.3    62.9    +      -       -      +
    253A  TYR*     3.9    22.9    -      -       +      -
    254A  LEU      4.0     3.4    -      -       -      +
    255A  VAL*     4.9     6.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  ILE*     4.0    13.7    -      -       -      -
     10A  ILE*     3.8    22.0    -      -       +      -
     79A  TYR*     3.5    24.5    -      -       -      +
    119A  PHE*     3.8    20.6    -      -       +      -
    120A  GLU      3.2     6.3    -      -       -      +
    121A  VAL*     4.8     4.3    -      -       +      -
    162A  ILE*     5.2     1.3    -      -       +      -
    197A  MET*     3.7    32.5    -      -       +      +
    198A  ILE*     1.3    78.2    -      -       -      +
    200A  LYS*     1.3    60.1    +      -       -      +
    253A  TYR*     3.2     7.8    -      -       -      +
    254A  LEU*     2.7    60.6    +      -       +      +
    256A  HIS*     3.9    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  PHE*     3.3     3.7    -      -       -      -
    120A  GLU*     2.9    47.5    +      -       +      +
    122A  VAL*     3.7    11.9    -      -       +      +
    172A  GLU*     4.5     9.3    -      -       -      +
    176A  GLU*     3.8     8.7    +      -       -      +
    199A  MET*     1.3    72.7    -      -       -      +
    201A  GLN*     1.3    70.2    +      -       -      +
    202A  PHE*     3.4     8.4    +      -       +      -
    251A  THR*     3.9    21.1    -      -       +      -
    252A  GLN      3.7     3.4    -      -       -      -
    253A  TYR*     3.5    41.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  TRP*     5.2     3.8    +      -       -      +
    117A  PRO*     3.8    20.9    -      -       +      +
    118A  TYR      3.4    12.6    -      -       -      +
    119A  PHE*     3.5    15.3    -      -       +      -
    200A  LYS*     1.3    79.8    -      -       -      +
    202A  PHE*     1.3    62.2    +      -       -      +
    203A  GLY      3.9     9.2    -      -       -      +
    204A  VAL*     3.8    13.3    -      -       -      +
    247A  GLY*     3.6     8.6    -      -       -      -
    248A  GLN*     3.0    41.9    +      -       -      +
    251A  THR*     4.3     9.5    -      -       -      +
    252A  GLN*     2.7    55.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 202 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ILE*     3.9    18.6    -      -       +      -
     85A  VAL*     3.8    21.5    -      -       +      -
    118A  TYR*     3.1    16.0    +      -       +      -
    119A  PHE      3.5    28.3    -      -       -      -
    120A  GLU*     3.6    26.5    -      -       +      +
    200A  LYS*     3.8     7.2    -      -       +      +
    201A  GLN*     1.3    74.0    -      -       -      +
    203A  GLY*     1.3    57.9    +      -       -      +
    243A  PRO*     3.7    29.7    -      -       +      +
    246A  PRO*     5.0     0.9    -      -       -      +
    247A  GLY*     3.6    14.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  PRO*     3.3     6.1    -      -       -      +
    118A  TYR*     2.6    32.8    +      -       -      +
    201A  GLN*     3.8     1.4    -      -       -      +
    202A  PHE*     1.3    79.7    -      -       -      +
    204A  VAL*     1.3    62.1    +      -       -      +
    243A  PRO*     3.6    15.0    -      -       -      +
    245A  ILE      3.4    12.3    -      -       -      -
    247A  GLY*     3.5    10.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  TRP*     3.7    40.4    -      -       +      -
    116A  GLU      3.5    10.8    -      -       -      +
    117A  PRO*     3.9     7.2    -      -       +      -
    118A  TYR*     3.9     4.5    -      -       -      -
    201A  GLN*     3.8    16.8    -      -       -      +
    203A  GLY*     1.3    78.3    -      -       -      +
    205A  SER*     1.3    67.2    +      -       -      +
    209A  SER*     3.4    22.4    -      -       -      +
    243A  PRO*     3.6     1.4    -      -       -      +
    244A  PRO*     3.2    20.8    -      -       -      +
    245A  ILE*     2.9    35.7    +      -       +      +
    246A  PRO      4.2     4.5    -      -       -      +
----------------------------------------------------------
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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