Contacts of the strand formed by residues 159 - 167 (chain D) 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 THR 159 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51D  THR*     5.7     1.1    -      -       -      +
    158D  ARG*     1.3    78.2    +      -       -      +
    160D  VAL*     1.3    73.2    +      -       -      +
    161D  VAL*     4.2     1.3    -      -       +      -
    257D  ILE      3.9     0.2    -      -       -      +
    258D  GLU*     3.3     4.7    -      -       -      +
    259D  TRP*     2.8    33.6    +      -       -      +
    260D  GLU      4.4     0.2    +      -       -      -
    261D  SER*     3.4    12.5    -      -       -      -
    262D  PRO*     3.2    31.5    -      -       +      +
    265D  ALA*     4.1    22.4    -      -       +      -
    298D  PHE*     4.2    18.4    -      -       +      -
    299D  PHE      3.7    10.3    +      -       -      +
    300D  SER*     5.4     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 160 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46D  GLU*     6.1     0.7    -      -       -      +
     48D  LEU*     4.1    34.8    -      -       +      -
    158D  ARG*     4.8     5.6    -      -       -      +
    159D  THR*     1.3    78.3    -      -       -      +
    161D  VAL*     1.3    68.5    +      -       -      +
    162D  ILE*     4.4     3.4    -      -       +      -
    256D  HIS*     3.4    32.3    -      -       +      +
    257D  ILE      3.6     2.9    -      -       -      +
    258D  GLU*     4.1    21.8    -      -       +      +
    298D  PHE*     3.7     0.9    -      -       -      -
    299D  PHE*     2.7    45.4    +      -       +      +
    301D  PRO*     4.4    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 161 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159D  THR*     4.2     1.8    -      -       +      -
    160D  VAL*     1.3    78.0    -      -       -      +
    162D  ILE*     1.3    62.2    +      -       -      +
    255D  VAL      3.5     0.3    -      -       -      +
    256D  HIS*     3.5     3.6    -      -       -      -
    257D  ILE*     2.7    44.0    +      -       +      +
    259D  TRP*     4.1     6.1    -      -       +      +
    265D  ALA*     3.8    22.0    -      -       +      -
    269D  LEU*     3.8    12.6    -      -       +      -
    296D  TYR*     3.2    36.3    -      -       +      -
    297D  MET      3.4     4.7    -      -       -      +
    298D  PHE*     3.7    33.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 162 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48D  LEU*     4.0     8.1    -      -       +      -
     77D  PHE*     3.7    24.9    -      -       +      -
     79D  TYR*     3.5    25.4    -      -       +      +
    160D  VAL*     4.4     5.8    -      -       +      -
    161D  VAL*     1.3    78.2    -      -       -      +
    163D  GLY*     1.3    61.1    -      -       -      +
    164D  ASP*     3.8     1.1    +      -       +      +
    199D  MET*     5.2     0.9    -      -       +      -
    254D  LEU*     3.9    39.9    -      -       +      -
    255D  VAL      3.3     5.6    -      -       -      +
    256D  HIS*     4.8     2.2    -      -       -      +
    295D  TYR      3.3     3.6    -      -       -      +
    296D  TYR*     3.4     2.9    -      -       -      -
    297D  MET*     3.0    34.0    +      -       +      +
    299D  PHE*     3.4    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 163 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162D  ILE*     1.3    71.2    -      -       -      +
    164D  ASP*     1.3    60.8    +      -       -      -
    165D  HIS*     3.0    13.7    +      -       -      -
    254D  LEU*     3.3     7.2    -      -       -      -
    255D  VAL      2.7    38.2    +      -       -      -
    295D  TYR      3.4     2.5    -      -       -      -
    296D  TYR*     3.3    31.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 164 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162D  ILE*     3.8     1.7    +      -       +      +
    163D  GLY*     1.3    71.5    -      -       -      -
    165D  HIS*     1.3    61.9    +      -       -      +
    166D  TRP*     3.6    18.8    +      -       -      -
    252D  GLN*     3.0    33.8    +      -       -      +
    253D  TYR      3.9     1.8    -      -       -      -
    254D  LEU*     3.9     8.2    -      -       +      +
    292D  LYS*     4.2     0.6    -      -       -      +
    293D  GLY*     3.7     5.5    -      -       -      -
    294D  PRO*     3.4     8.3    -      -       -      +
    295D  TYR*     2.8    45.1    +      -       +      +
    297D  MET*     6.3     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 165 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163D  GLY*     3.0    32.4    +      -       -      -
    164D  ASP*     1.3    72.7    +      -       -      +
    166D  TRP*     1.3    64.3    +      -       -      +
    167D  VAL*     4.1     1.5    +      -       +      -
    175D  PHE*     3.8    28.5    -      +       +      -
    251D  THR      3.8     0.2    -      -       -      +
    252D  GLN*     3.4     3.6    -      -       -      -
    253D  TYR*     2.8    44.0    +      -       +      +
    255D  VAL*     3.4    27.6    -      -       +      +
    282D  HIS*     5.2     1.4    +      -       -      -
    286D  VAL*     3.9    11.4    -      -       +      +
    290D  LEU*     3.9    26.0    -      -       +      -
    292D  LYS      3.6     4.9    -      -       -      -
    294D  PRO*     3.5    26.7    -      -       +      +
    296D  TYR*     3.8    16.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 166 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164D  ASP*     3.6    20.9    +      -       -      -
    165D  HIS*     1.3    80.5    -      -       -      +
    167D  VAL*     1.3    56.7    +      -       -      +
    248D  GLN*     3.5    33.5    +      -       -      +
    249D  THR      5.6     0.2    -      -       -      -
    250D  PRO*     4.1    29.6    -      -       +      -
    251D  THR      3.5     4.0    -      -       -      +
    252D  GLN*     4.2    12.7    -      -       +      +
    290D  LEU*     3.3     6.3    -      -       -      +
    291D  ASP*     2.7    31.7    +      -       +      -
    292D  LYS*     3.0    64.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 167 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165D  HIS*     4.7     2.7    -      -       +      -
    166D  TRP*     1.3    75.7    -      -       -      +
    168D  MET*     1.3    76.8    +      -       -      +
    169D  ASP*     3.4     1.0    +      -       -      -
    171D  HIS      3.7    25.1    -      -       -      +
    172D  GLU*     3.8    14.7    -      -       +      +
    175D  PHE*     3.6    29.4    -      -       +      -
    250D  PRO*     3.3    18.0    -      -       -      +
    251D  THR*     2.9    18.8    +      -       -      +
    253D  TYR*     3.4    30.3    -      -       +      -
    289D  HIS      3.5     8.7    -      -       -      +
    290D  LEU*     4.1     5.6    -      -       +      -
    291D  ASP*     4.2     1.6    -      -       -      -
----------------------------------------------------------
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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