Contacts of the strand formed by residues 193 - 204 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151B  LYS*     2.6    30.1    +      -       -      +
    183B  LEU*     4.5     5.2    -      -       +      +
    186B  MET*     3.3    49.8    -      -       +      +
    187B  LYS*     3.3    34.4    -      -       +      +
    190B  VAL      3.6    12.7    +      -       -      +
    191B  PRO      3.2     2.4    -      -       -      -
    192B  GLY*     1.3    74.5    -      -       -      +
    194B  VAL*     1.3    61.1    +      -       -      +
    195B  GLY      3.9    16.6    -      -       -      +
    196B  TRP*     4.6     4.0    -      -       -      -
    257B  ILE*     3.8    22.7    -      -       +      -
    258B  GLU      4.0     0.2    -      -       -      -
    259B  TRP*     3.5    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  PRO*     3.4    14.9    -      -       +      +
    151B  LYS*     3.4    15.0    -      -       +      +
    152B  VAL      3.8    16.8    -      -       -      +
    153B  ALA*     3.5    34.3    -      -       +      +
    158B  ARG*     4.6     4.0    -      -       +      -
    187B  LYS*     3.4    15.2    -      -       -      -
    192B  GLY      3.8    13.2    -      -       -      +
    193B  MET*     1.3    73.3    -      -       -      +
    195B  GLY*     1.3    60.4    +      -       -      +
    258B  GLU*     2.8    27.4    +      -       +      +
    259B  TRP      3.8    15.9    -      -       -      +
    260B  GLU*     3.8     7.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125B  ASP      3.1    14.6    -      -       -      -
    126B  LEU*     4.2     6.3    -      -       -      -
    127B  PRO*     4.1     6.5    -      -       -      -
    187B  LYS*     4.1     9.0    -      -       -      -
    193B  MET*     3.6     4.1    -      -       -      -
    194B  VAL*     1.3    81.9    -      -       -      +
    196B  TRP*     1.3    66.1    +      -       -      +
    257B  ILE*     3.4     6.6    -      -       -      +
    258B  GLU*     2.8    25.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  LYS*     3.4    45.5    -      -       +      -
    124B  SER*     3.4     4.9    -      -       -      -
    125B  ASP*     2.8    59.7    +      -       +      +
    126B  LEU*     3.7     8.5    -      -       -      +
    180B  THR*     4.3    12.1    -      -       +      -
    183B  LEU*     3.5    59.6    +      -       +      +
    184B  GLU*     3.9    26.8    -      -       +      +
    187B  LYS*     4.0    13.6    -      -       +      +
    193B  MET*     4.6     3.1    -      -       -      -
    195B  GLY*     1.3    78.9    -      -       -      +
    197B  MET*     1.3    72.0    +      -       -      +
    198B  ILE*     3.8    17.3    -      -       +      -
    256B  HIS      3.0    12.8    -      -       -      +
    257B  ILE*     4.5     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 197 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  ILE*     3.8    25.1    -      -       +      -
     79B  TYR*     3.9     4.7    -      -       +      -
    121B  VAL*     4.0    24.0    -      -       +      -
    123B  LYS      3.5     7.2    -      -       -      +
    124B  SER*     4.1     5.4    -      -       -      -
    126B  LEU*     3.8    19.7    -      -       +      -
    196B  TRP*     1.3    79.1    -      -       -      +
    198B  ILE*     1.3    65.6    +      -       -      +
    199B  MET*     3.7    32.1    -      -       +      +
    254B  LEU      3.8     0.5    -      -       -      +
    255B  VAL*     3.7     2.8    -      -       -      +
    256B  HIS*     2.8    58.1    +      -       +      +
    308B  TRP*     3.9    18.6    -      -       +      -
    312B  LEU*     5.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 198 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121B  VAL*     3.6     3.6    -      -       -      -
    122B  VAL*     2.8    51.4    +      -       +      -
    123B  LYS*     2.8    15.4    +      -       +      +
    175B  PHE*     4.6     9.2    -      -       +      -
    176B  GLU*     4.1     5.4    -      -       +      +
    179B  ALA*     3.6    13.0    -      -       +      -
    180B  THR*     3.4    40.8    -      -       -      +
    183B  LEU*     3.6    24.0    -      -       +      -
    196B  TRP*     3.8     9.4    -      -       +      -
    197B  MET*     1.3    71.8    -      -       -      +
    199B  MET*     1.3    58.0    +      -       -      +
    253B  TYR*     4.1    20.9    -      -       +      -
    254B  LEU      3.9     3.8    -      -       -      +
    255B  VAL*     4.7     6.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 199 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  ILE*     4.1    14.4    -      -       +      -
     10B  ILE*     3.8    20.6    -      -       +      -
     79B  TYR*     3.5    23.8    -      -       -      +
    119B  PHE*     3.7    22.4    -      -       +      -
    120B  GLU      3.2     6.5    -      -       -      +
    121B  VAL*     5.0     2.0    -      -       +      -
    162B  ILE*     5.2     1.6    -      -       +      -
    197B  MET*     3.7    33.4    -      -       +      -
    198B  ILE*     1.3    78.1    -      -       -      +
    200B  LYS*     1.3    60.6    +      -       -      +
    253B  TYR*     3.1     9.8    -      -       -      +
    254B  LEU*     2.9    59.8    +      -       +      +
    256B  HIS*     3.8    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  PHE*     3.2     3.7    -      -       -      -
    120B  GLU*     2.8    54.5    +      -       +      +
    122B  VAL*     3.7    11.4    -      -       +      -
    172B  GLU*     4.5    10.7    -      -       -      +
    176B  GLU*     3.8     9.6    +      -       -      +
    199B  MET*     1.3    72.6    -      -       -      +
    201B  GLN*     1.3    70.8    +      -       -      +
    202B  PHE*     3.4     7.4    +      -       +      -
    251B  THR*     4.0    19.5    -      -       +      -
    252B  GLN      3.8     2.9    -      -       -      -
    253B  TYR*     3.3    41.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 201 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115B  TRP*     5.3     2.5    +      -       -      +
    117B  PRO*     3.9    21.9    -      -       +      +
    118B  TYR      3.3    12.3    -      -       -      +
    119B  PHE*     3.4    17.1    -      -       +      -
    200B  LYS*     1.3    80.0    -      -       -      +
    202B  PHE*     1.3    61.2    +      -       -      +
    203B  GLY      3.9    10.3    -      -       -      +
    204B  VAL*     3.8    11.8    -      -       -      +
    247B  GLY*     3.6     7.9    -      -       -      -
    248B  GLN*     3.0    48.5    +      -       -      +
    251B  THR*     4.2    10.4    -      -       -      +
    252B  GLN*     2.7    52.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 202 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  ILE*     4.1    15.5    -      -       +      -
     85B  VAL*     3.7    22.2    -      -       +      -
    118B  TYR*     3.0    21.3    +      -       +      -
    119B  PHE      3.6    22.0    -      -       -      -
    120B  GLU*     3.5    30.5    -      -       +      +
    200B  LYS*     3.8     7.2    -      -       +      +
    201B  GLN*     1.3    73.7    -      -       -      +
    203B  GLY*     1.3    57.3    +      -       -      +
    243B  PRO*     3.6    30.0    -      -       +      +
    246B  PRO*     4.9     1.0    -      -       -      +
    247B  GLY*     3.6    13.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 203 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117B  PRO*     3.2     7.1    -      -       -      +
    118B  TYR*     2.7    32.5    +      -       -      +
    201B  GLN*     3.7     1.6    -      -       -      +
    202B  PHE*     1.3    80.4    -      -       -      +
    204B  VAL*     1.3    62.0    +      -       -      +
    243B  PRO*     3.5    12.6    -      -       -      -
    245B  ILE      3.3    14.1    -      -       -      -
    247B  GLY*     3.5    11.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 204 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115B  TRP*     3.6    37.9    -      -       +      +
    116B  GLU      3.4    13.7    -      -       -      +
    117B  PRO*     3.9     6.5    -      -       +      -
    118B  TYR*     3.9     5.2    -      -       -      -
    201B  GLN*     3.8    17.0    -      -       -      +
    203B  GLY*     1.3    80.2    -      -       -      +
    205B  SER*     1.3    67.6    +      -       -      +
    209B  SER*     3.3    22.9    -      -       -      +
    243B  PRO*     3.6     1.2    -      -       -      +
    244B  PRO*     3.2    20.6    -      -       -      +
    245B  ILE*     2.9    36.1    +      -       +      +
    246B  PRO      4.3     2.7    -      -       -      +
----------------------------------------------------------
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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