Contacts of the strand formed by residues 290 - 305 (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 LEU 290 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  HIS*     3.8    39.7    -      -       +      -
    166A  TRP      3.3    12.1    -      -       -      +
    167A  VAL*     4.0     5.8    -      -       +      -
    168A  MET*     3.7    11.7    -      -       -      +
    175A  PHE*     3.9    17.7    -      -       +      -
    286A  VAL*     3.3    20.4    -      -       +      +
    287A  LEU*     3.5    21.5    +      -       +      +
    288A  ALA      3.6     1.2    +      -       -      +
    289A  HIS*     1.3    77.1    -      -       -      +
    291A  ASP*     1.3    61.3    -      -       -      +
    292A  LYS      4.0     8.5    -      -       -      +
    293A  GLY      3.7    26.0    -      -       -      +
    294A  PRO*     3.8     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 291 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  TRP*     2.7    16.3    +      -       +      +
    168A  MET*     3.5    35.1    -      -       -      +
    169A  ASP      4.5     1.6    +      -       -      -
    250A  PRO*     3.4    31.0    -      -       +      +
    290A  LEU*     1.3    73.3    -      -       -      +
    292A  LYS*     1.3    58.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 292 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  ASP*     4.7     1.1    -      -       -      +
    165A  HIS*     3.6     3.6    -      -       -      -
    166A  TRP*     3.0    87.3    +      -       +      +
    290A  LEU*     3.5     6.5    -      -       -      +
    291A  ASP*     1.3    80.6    -      -       -      +
    293A  GLY*     1.3    67.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 293 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  TYR*     5.4     3.4    -      -       -      -
    164A  ASP      3.8     5.4    -      -       -      -
    287A  LEU*     4.9     0.9    -      -       -      +
    290A  LEU*     3.7    10.2    -      -       -      +
    292A  LYS*     1.3    84.1    -      -       -      +
    294A  PRO*     1.3    77.4    -      -       -      +
    295A  TYR*     3.9     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 294 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  MET*     3.6    33.0    -      -       +      +
     60A  TYR*     3.9     8.7    +      -       -      -
    164A  ASP      3.5     5.8    -      -       -      +
    165A  HIS*     3.3    28.7    -      -       +      +
    282A  HIS*     4.5     9.6    -      -       +      -
    287A  LEU*     3.5    30.3    -      -       +      -
    290A  LEU*     3.8     3.1    -      -       +      -
    293A  GLY*     1.3    84.6    -      -       -      +
    295A  TYR*     1.3    59.5    +      -       -      +
    296A  TYR*     3.7    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 295 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  GLN*     5.4     0.2    +      -       -      -
     53A  ILE*     3.3    31.6    -      -       +      +
     54A  HIS      5.4     0.4    -      -       -      -
     56A  MET*     5.1     0.4    -      -       -      -
     60A  TYR*     3.4    53.6    -      +       -      +
    162A  ILE      3.3     2.6    -      -       -      +
    163A  GLY*     3.2     0.5    -      -       -      -
    164A  ASP*     2.7    48.5    +      -       +      +
    293A  GLY*     5.0     3.1    -      -       -      -
    294A  PRO*     1.3    74.3    -      -       -      +
    296A  TYR*     1.3    63.4    +      -       -      +
    297A  MET*     3.7    30.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 296 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  ILE*     3.4     7.4    -      -       -      +
     54A  HIS*     3.0    44.2    +      +       +      +
     56A  MET*     4.6    14.3    -      -       +      -
     60A  TYR*     5.7     0.2    -      -       -      -
    161A  VAL*     3.2    26.7    -      -       +      -
    162A  ILE      3.3     0.7    -      -       -      -
    163A  GLY*     3.3    24.5    -      -       -      -
    165A  HIS*     3.8    15.3    +      +       -      -
    255A  VAL*     4.3    10.5    -      -       -      +
    257A  ILE*     4.1    10.5    -      -       +      +
    269A  LEU*     3.7    34.1    -      -       +      +
    282A  HIS*     5.0     8.9    +      +       -      -
    294A  PRO*     3.7    25.1    -      -       +      -
    295A  TYR*     1.3    80.4    -      -       -      +
    297A  MET*     1.3    60.8    +      -       -      +
    298A  PHE*     4.7     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 297 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  LYS*     4.2    16.6    -      -       -      +
     50A  GLN*     3.3    36.6    -      -       -      +
     52A  GLY      3.7     3.6    -      -       -      -
     53A  ILE*     4.3     0.9    -      -       +      +
     75A  GLY*     4.6     2.9    -      -       -      -
     77A  PHE*     4.4    17.9    -      -       +      -
    161A  VAL*     3.3     4.7    -      -       -      -
    162A  ILE*     3.0    36.1    +      -       +      +
    164A  ASP*     6.3     2.5    -      -       -      -
    295A  TYR*     3.7    30.5    -      -       +      -
    296A  TYR*     1.3    73.7    -      -       -      +
    298A  PHE*     1.3    63.3    +      -       -      +
    299A  PHE*     3.6    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 298 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  GLN*     3.3    11.8    -      -       -      +
     51A  THR*     2.8    39.6    +      -       -      +
     52A  GLY*     2.8    21.2    +      -       -      +
     53A  ILE      3.8    11.7    -      -       -      -
     54A  HIS*     3.6    36.6    -      +       +      -
     65A  VAL*     3.6    26.9    -      -       +      +
    159A  THR*     4.3    11.0    -      -       +      -
    160A  VAL      3.8     3.4    -      -       -      -
    161A  VAL*     3.5    19.3    -      -       +      -
    262A  PRO*     3.6    26.2    -      -       +      -
    265A  ALA*     3.7    17.0    -      -       +      -
    266A  HIS*     4.0    11.2    -      -       +      -
    269A  LEU*     4.2     5.4    -      -       +      -
    296A  TYR      4.3     1.3    -      -       -      -
    297A  MET*     1.3    76.6    -      -       -      +
    299A  PHE*     1.3    56.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 299 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  LEU*     3.6    27.8    -      -       +      -
     49A  LEU      3.2     9.0    -      -       -      +
     50A  GLN*     3.4    32.5    -      -       +      -
     51A  THR*     4.1     5.8    -      -       -      -
     75A  GLY      4.3     3.8    -      -       -      -
     77A  PHE*     3.8    35.9    -      +       -      -
    159A  THR*     3.7     8.5    +      -       -      +
    160A  VAL*     2.7    45.8    +      -       +      +
    162A  ILE*     3.6    26.5    -      -       +      -
    297A  MET*     3.6    47.1    -      -       +      -
    298A  PHE*     1.3    75.6    -      -       -      +
    300A  SER*     1.3    59.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 300 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  LEU*     3.5     0.2    -      -       -      -
     49A  LEU*     2.8    31.4    +      -       -      -
     51A  THR*     4.0    18.3    -      -       -      +
    156A  SER      5.4     2.6    +      -       -      -
    158A  ARG      4.3     4.5    +      -       -      -
    159A  THR*     5.3     0.2    -      -       -      +
    299A  PHE*     1.3    76.0    -      -       -      +
    301A  PRO*     1.3    73.1    +      -       -      +
    302A  MET*     3.2    21.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 301 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  GLU*     4.6     0.7    -      -       -      +
     47A  GLN      3.3     7.9    -      -       -      +
     48A  LEU*     3.8    16.4    -      -       +      -
    156A  SER*     3.5    22.6    -      -       -      +
    158A  ARG*     3.0    45.3    -      -       +      +
    160A  VAL*     4.3    14.8    -      -       +      -
    299A  PHE      4.0     3.8    -      -       -      +
    300A  SER*     1.3    86.8    +      -       -      +
    302A  MET*     1.3    63.8    +      -       -      +
    303A  MET      3.6     0.4    -      -       -      -
    304A  GLU*     3.8    25.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 302 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  TYR*     6.1     3.6    -      -       +      -
     25A  MET*     5.8     5.4    -      -       +      -
     47A  GLN*     2.7    35.5    +      -       +      +
     49A  LEU*     4.0    34.1    -      -       +      -
    156A  SER*     3.2    15.2    +      -       -      -
    300A  SER*     3.2    24.4    +      -       -      +
    301A  PRO*     1.3    72.7    -      -       -      +
    303A  MET*     1.3    64.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 303 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  MET*     3.9    20.6    -      -       +      +
     26A  MET*     4.5     9.2    -      -       +      -
     29A  GLY      5.2     0.9    -      -       -      -
     30A  PRO*     4.0    28.3    -      -       +      -
     33A  CSS      6.2     1.3    -      -       -      -
     45A  PHE*     3.9    21.9    -      -       +      -
     47A  GLN*     3.0    53.9    +      -       +      +
    156A  SER*     4.0     2.2    -      -       -      -
    302A  MET*     1.3    83.6    -      -       +      +
    304A  GLU*     1.3    68.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 304 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  PHE*     3.7    12.1    -      -       -      +
     46A  GLU*     2.6    32.0    -      -       -      +
    129A  ILE*     3.9    22.0    -      -       +      +
    155A  SER*     3.6     7.8    +      -       -      +
    156A  SER*     2.8    35.6    +      -       -      +
    158A  ARG*     2.8    35.5    +      -       -      -
    301A  PRO*     3.8    15.6    -      -       +      +
    303A  MET*     1.3    81.5    -      -       -      +
    305A  GLN*     1.3    60.8    +      -       -      +
    306A  GLY      3.8     1.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 305 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  PHE*     4.6    10.4    +      -       +      -
     43A  LEU      3.8    13.4    +      -       -      -
     44A  GLY*     3.5    18.4    -      -       -      -
     45A  PHE*     3.1    49.8    +      -       +      +
    304A  GLU*     1.3    72.3    -      -       -      +
    306A  GLY*     1.3    58.3    +      -       -      +
    307A  LEU*     3.0    34.2    +      -       -      +
    308A  TRP*     3.3     8.7    -      -       -      -
----------------------------------------------------------
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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