Contacts of the strand formed by residues 42 - 53 (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 PHE 42 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  CSS      4.9     2.7    -      -       -      -
     36A  THR*     3.4    36.3    -      -       +      +
     37A  ALA*     3.5    31.9    -      -       +      -
     39A  HIS      3.0    16.5    +      -       -      +
     40A  PRO      4.4     3.1    -      -       -      +
     41A  GLY*     1.3    76.6    -      -       -      +
     43A  LEU*     1.3    65.0    +      -       -      +
     44A  GLY*     3.1    41.1    -      -       -      -
     45A  PHE*     3.7    19.5    -      +       +      -
     80A  THR*     4.1    11.4    -      -       +      -
     81A  VAL      3.8     5.6    -      -       -      -
     82A  TRP*     3.6    22.0    -      +       +      -
    305A  GLN*     4.6    11.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  GLU*     4.3     7.6    -      -       -      +
      6A  PRO*     3.7    20.6    -      -       +      -
     40A  PRO      5.1     0.9    -      -       -      +
     41A  GLY      3.6    12.8    -      -       -      +
     42A  PHE*     1.3    79.1    -      -       -      +
     44A  GLY*     1.3    55.9    +      -       -      +
     81A  VAL*     2.7    16.5    +      -       +      +
     82A  TRP      3.7    22.2    -      -       -      +
     83A  LYS*     3.7    27.1    -      -       +      +
    305A  GLN*     3.8    12.9    +      -       -      -
    307A  LEU*     4.1     3.1    -      -       -      +
    308A  TRP*     3.3    31.6    +      -       +      -
    311A  HIS*     3.9    28.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  PHE*     3.1    17.3    -      -       -      -
     43A  LEU*     1.3    80.8    -      -       -      +
     45A  PHE*     1.3    60.9    +      -       -      +
     81A  VAL*     2.8    27.2    +      -       -      +
    305A  GLN*     3.3    24.2    -      -       -      -
    308A  TRP*     3.8     9.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  CSS      3.8    45.8    -      -       +      -
     42A  PHE*     3.7    22.4    -      +       +      -
     44A  GLY*     1.3    74.4    -      -       -      +
     46A  GLU*     1.3    77.0    +      -       -      +
     47A  GLN*     4.1     9.6    -      -       +      -
     78A  GLN*     6.4     0.9    -      -       +      -
     79A  TYR      3.0    18.8    -      -       -      +
     80A  THR*     4.3     2.0    -      -       +      -
     81A  VAL*     4.7     2.0    -      -       -      -
    303A  MET*     3.9    36.3    -      -       +      -
    304A  GLU*     3.7     3.9    -      -       -      -
    305A  GLN*     3.1    56.8    +      -       +      +
    308A  TRP*     4.0     2.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  PHE*     1.3    81.2    -      -       -      +
     47A  GLN*     1.3    60.3    +      -       -      +
     48A  LEU*     3.8    13.7    -      -       +      +
     77A  PHE      3.5     1.9    -      -       -      +
     78A  GLN*     3.2     4.9    -      -       -      +
     79A  TYR*     2.7    66.2    +      -       +      +
    158A  ARG*     4.5     1.1    +      -       -      -
    160A  VAL*     5.9     0.7    -      -       -      +
    256A  HIS*     5.6     2.9    -      -       +      -
    258A  GLU*     5.4     0.4    -      -       -      -
    301A  PRO*     4.6     4.7    -      -       -      +
    303A  MET      3.9     2.5    -      -       -      -
    304A  GLU*     2.6    39.7    -      -       -      +
    306A  GLY*     4.8     1.7    -      -       -      -
    308A  TRP*     3.3    33.5    +      -       +      +
    309A  ARG*     3.6    15.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  MET*     4.3    26.6    +      -       -      +
     29A  GLY*     4.6     6.3    -      -       -      -
     45A  PHE*     4.1     7.5    -      -       +      -
     46A  GLU*     1.3    69.9    -      -       -      +
     48A  LEU*     1.3    59.4    +      -       -      +
     49A  LEU*     6.4     0.2    -      -       +      -
     76A  MET*     4.2    15.8    -      -       +      +
     77A  PHE      3.8     2.0    -      -       -      -
     78A  GLN*     3.4    35.3    -      -       +      +
    301A  PRO*     3.3     4.7    -      -       -      +
    302A  MET*     2.7    52.3    +      -       +      +
    303A  MET*     3.0    48.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  GLU*     4.4    16.4    -      -       +      +
     47A  GLN*     1.3    75.4    -      -       -      +
     49A  LEU*     1.3    59.0    +      -       -      +
     76A  MET*     3.4     8.9    -      -       -      +
     77A  PHE*     2.8    45.8    +      -       +      +
     79A  TYR*     3.5    39.9    -      -       +      +
    160A  VAL*     4.1    27.6    -      -       +      -
    162A  ILE*     4.0    14.8    -      -       +      -
    256A  HIS*     5.6     1.1    -      -       +      -
    299A  PHE*     3.6    16.3    -      -       +      -
    300A  SER      3.5     1.6    -      -       -      -
    301A  PRO*     3.8    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ILE*     4.3     7.2    -      -       +      -
     22A  TYR*     3.6    31.2    -      -       +      +
     25A  MET*     4.3    11.2    -      -       +      -
     47A  GLN*     4.1     0.8    +      -       +      -
     48A  LEU*     1.3    73.1    -      -       -      +
     50A  GLN*     1.3    71.2    +      -       -      +
     51A  THR*     3.4     4.8    +      -       +      +
     74A  MET*     4.0    26.5    -      -       +      -
     75A  GLY      3.6    15.0    -      -       -      +
     76A  MET*     3.8    17.5    -      -       +      -
    299A  PHE*     3.2     2.0    -      -       -      -
    300A  SER*     2.8    33.7    +      -       -      +
    302A  MET*     4.0    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  LYS*     4.3     4.7    +      -       -      -
     49A  LEU*     1.3    74.4    -      -       -      +
     51A  THR*     1.3    63.0    +      -       -      +
     52A  GLY      3.1    18.6    +      -       -      +
     53A  ILE*     3.7    17.0    -      -       -      +
     68A  ARG*     5.0     0.3    -      -       -      +
     71A  LEU*     3.4    28.4    -      -       +      +
     73A  PRO      5.0     0.2    -      -       -      +
     74A  MET*     3.4    26.9    -      -       -      +
     75A  GLY*     2.8    43.1    +      -       -      +
    297A  MET*     3.3    28.8    -      -       +      +
    298A  PHE      3.3    14.8    -      -       -      +
    299A  PHE*     3.4    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  LEU*     3.9    11.4    -      -       +      +
     50A  GLN*     1.3    76.4    -      -       -      +
     52A  GLY*     1.3    53.2    +      -       -      +
     65A  VAL      3.4     5.9    +      -       -      +
     66A  ASP*     3.6     2.2    -      -       -      -
     67A  MET*     2.6    31.5    +      -       -      -
     68A  ARG*     3.4    37.6    +      -       +      +
     71A  LEU*     4.4     4.0    -      -       -      -
    159A  THR*     5.7     0.9    -      -       -      +
    262A  PRO*     5.6     6.1    -      -       -      +
    298A  PHE*     2.8    26.9    +      -       -      +
    299A  PHE*     3.8     3.0    +      -       -      -
    300A  SER*     4.0    20.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  GLN*     3.1    19.3    +      -       -      +
     51A  THR*     1.3    81.7    +      -       -      +
     53A  ILE*     1.3    61.5    +      -       -      +
     64A  ALA      3.5     6.3    -      -       -      -
     65A  VAL      3.2    10.5    -      -       -      -
     67A  MET*     4.0    12.6    -      -       -      -
     71A  LEU*     4.5     0.9    -      -       -      -
    298A  PHE*     2.8    27.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  GLN*     3.7    15.5    -      -       -      +
     52A  GLY*     1.3    79.3    -      -       -      +
     54A  HIS*     1.3    66.8    +      -       -      +
     55A  PRO*     3.5     1.6    -      -       -      +
     60A  TYR*     3.6    33.2    -      -       +      +
     63A  GLY*     3.8    17.9    -      -       -      +
     64A  ALA      2.9    32.6    +      -       -      +
     65A  VAL*     3.2    16.9    +      -       -      +
     67A  MET*     4.2     7.2    -      -       -      -
     71A  LEU*     6.0     0.7    -      -       +      -
    295A  TYR*     3.3    33.7    -      -       +      +
    296A  TYR      3.4    12.6    -      -       -      +
    297A  MET*     4.5     1.1    -      -       -      -
    298A  PHE*     3.8     8.2    -      -       -      -
----------------------------------------------------------
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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