Contacts of the strand formed by residues 74 - 82 (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 MET 74 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14D  LYS*     3.4     3.8    -      -       -      -
     15D  ILE*     3.0    48.4    +      -       +      +
     16D  ALA      4.7     2.0    -      -       -      +
     17D  ASN*     3.6    29.6    -      -       +      +
     22D  TYR*     3.6    28.9    -      -       -      +
     25D  MET*     6.1     0.2    -      -       -      -
     49D  LEU*     3.9    25.4    -      -       +      -
     50D  GLN      3.2    24.0    -      -       -      +
     68D  ARG*     5.0     9.0    -      -       +      +
     71D  LEU*     4.0    23.1    -      -       +      +
     72D  ASN*     4.1     0.6    -      -       -      +
     73D  PRO*     1.3    75.2    -      -       -      +
     75D  GLY*     1.3    63.7    +      -       -      +
     76D  MET      3.6     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 75 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13D  ALA      3.5     7.4    -      -       -      -
     14D  LYS*     4.4    12.6    -      -       -      +
     49D  LEU*     3.7     4.3    -      -       -      +
     50D  GLN*     2.8    56.2    +      -       -      +
     74D  MET*     1.3    75.2    -      -       -      +
     76D  MET*     1.3    58.1    +      -       -      +
     77D  PHE*     4.9     2.9    -      -       -      -
    297D  MET*     4.6     6.1    -      -       -      -
    299D  PHE*     4.4     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 76 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11D  ASN*     3.5     3.3    -      -       -      +
     13D  ALA*     2.7    43.5    +      -       +      +
     15D  ILE*     4.0    24.5    -      -       +      -
     25D  MET*     4.1    21.5    -      -       +      +
     47D  GLN*     4.4    12.3    -      -       +      +
     48D  LEU      3.4     6.5    -      -       -      +
     49D  LEU*     3.7    23.3    -      -       +      -
     75D  GLY*     1.3    71.9    -      -       -      +
     77D  PHE*     1.3    63.1    +      -       -      +
     78D  GLN*     3.5    38.5    -      -       -      +
    109D  MET*     4.3    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 77 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10D  ILE*     3.8    22.9    -      -       +      -
     11D  ASN      3.2     3.1    -      -       -      -
     12D  MET*     3.7    42.2    -      -       +      -
     13D  ALA      4.6     4.0    -      -       -      -
     14D  LYS*     5.8     3.6    -      -       +      -
     46D  GLU      3.5     1.7    -      -       -      +
     47D  GLN*     3.8     0.9    -      -       -      -
     48D  LEU*     2.8    52.2    +      -       +      +
     75D  GLY*     4.2     1.5    -      -       -      -
     76D  MET*     1.3    86.7    -      -       -      +
     78D  GLN*     1.3    62.3    +      -       -      +
     79D  TYR*     4.0     1.6    -      +       +      -
    162D  ILE*     3.7    30.3    -      -       +      -
    254D  LEU*     5.0     2.7    -      -       +      -
    297D  MET*     4.3    19.3    -      -       +      -
    299D  PHE*     3.8    24.2    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLN 78 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9D  ALA      3.3     2.4    -      -       -      +
     10D  ILE*     3.4     0.2    -      -       -      -
     11D  ASN*     2.8    56.1    +      -       +      +
     29D  GLY*     6.0     3.0    -      -       -      -
     32D  VAL*     4.8    14.8    -      -       -      +
     33D  CSS      4.8    12.4    -      -       -      -
     46D  GLU      3.4     4.3    -      -       -      +
     47D  GLN*     4.3    22.3    -      -       +      +
     76D  MET*     3.5    35.3    -      -       -      +
     77D  PHE*     1.3    76.4    -      -       -      +
     79D  TYR*     1.3    65.7    +      -       -      +
     80D  THR*     3.6     7.9    +      -       +      +
    103D  CSS      5.7     6.9    -      -       -      -
    106D  CYS*     6.3     0.4    -      -       -      -
    116D  GLU*     5.2     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 79 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8D  ILE*     4.0    23.1    -      -       +      -
      9D  ALA      3.4     5.2    -      -       -      -
     10D  ILE*     3.6    36.1    -      -       +      -
     45D  PHE*     3.0    11.0    -      -       -      +
     46D  GLU*     2.8    52.6    +      -       +      +
     48D  LEU*     3.7    23.3    -      -       +      +
     77D  PHE*     4.6     2.7    -      -       +      -
     78D  GLN*     1.3    73.1    -      -       -      +
     80D  THR*     1.3    60.9    +      -       -      +
     81D  VAL*     4.7     4.3    -      -       +      -
    162D  ILE*     3.5    18.6    -      -       +      +
    197D  MET*     4.2    11.7    -      -       +      -
    199D  MET*     3.5    15.6    -      -       +      +
    256D  HIS*     2.9    37.7    +      +       -      -
    308D  TRP*     4.9     3.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR 80 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8D  ILE*     3.6     1.6    -      -       -      -
      9D  ALA*     2.8    45.6    +      -       -      +
     33D  CSS      4.3    13.9    -      -       -      -
     36D  THR*     4.3     8.5    -      -       +      +
     42D  PHE*     4.1    16.2    -      -       +      -
     44D  GLY      3.5     3.1    -      -       -      -
     45D  PHE*     4.2     5.8    -      -       +      -
     78D  GLN*     3.6     8.6    +      -       +      +
     79D  TYR*     1.3    79.1    -      -       -      +
     81D  VAL*     1.3    61.6    +      -       -      +
     82D  TRP*     2.9    31.9    +      -       +      -
     88D  HIS*     3.9     6.8    +      -       -      -
    116D  GLU*     4.1     4.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 81 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6D  PRO*     3.6    31.6    -      -       +      -
      7D  ILE      3.4     7.4    -      -       -      +
      8D  ILE*     4.2    19.3    -      -       +      -
     42D  PHE*     3.8     1.9    -      -       -      -
     43D  LEU*     2.8    31.8    +      -       +      -
     44D  GLY      2.8    19.2    +      -       -      +
     45D  PHE      4.8     0.2    -      -       -      +
     79D  TYR*     4.7     6.1    -      -       +      -
     80D  THR*     1.3    76.6    -      -       -      +
     82D  TRP*     1.3    64.9    +      -       -      +
    308D  TRP*     3.7    50.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 82 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6D  PRO*     3.4     4.5    -      -       -      +
      7D  ILE*     2.9    38.4    +      -       +      +
      9D  ALA*     4.4     5.6    -      -       +      -
     36D  THR*     3.4    35.4    -      -       +      -
     39D  HIS*     4.0     6.5    -      -       +      -
     41D  GLY      3.3    22.7    -      -       -      -
     42D  PHE*     3.7    22.4    -      +       +      -
     43D  LEU*     3.6     6.3    -      -       -      -
     80D  THR*     2.9    44.6    +      -       +      -
     81D  VAL*     1.3    74.8    -      -       -      +
     83D  LYS*     1.3    62.3    +      -       -      +
     84D  ASP      3.2    19.2    +      -       -      +
     87D  SER*     3.8    23.6    -      -       -      -
     88D  HIS*     3.2    38.5    -      +       +      -
     91D  MET*     3.6    24.7    -      -       +      -
    118D  TYR*     5.6     1.1    -      +       -      -
----------------------------------------------------------
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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