Contacts of the strand formed by residues 77 - 87 (chain D) in PDB entry 1QQW


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 LYS 77 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  ARG*     4.3     9.0    -      -       -      +
    175A  HIS*     5.8     1.8    -      -       +      -
     75D  HIS      3.6     0.2    -      -       -      -
     76D  ALA*     1.3    76.7    -      -       -      +
     78D  GLY*     1.3    61.2    +      -       -      +
    114D  SER*     3.3     3.2    -      -       -      -
    115D  THR*     3.3    34.6    +      -       +      +
    118D  GLY      3.9     2.4    +      -       -      -
    119D  GLU      3.6     5.8    -      -       -      +
    120D  SER*     3.3    27.4    -      -       -      +
    122D  SER*     3.1    36.8    +      -       -      +
    123D  ALA      5.6     0.2    -      -       -      +
    124D  ASP*     3.2    22.1    +      -       -      +
    258D  PRO*     3.0    22.6    +      -       -      +
    259D  ASP*     2.5    34.3    +      -       -      +
    262D  ILE*     4.1    12.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 78 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76D  ALA      3.3     5.9    +      -       -      -
     77D  LYS*     1.3    76.8    -      -       -      +
     79D  ALA*     1.3    59.9    +      -       -      +
    112D  ARG*     3.9    11.9    -      -       -      +
    113D  PHE      2.9    14.6    -      -       -      -
    114D  SER*     3.8     4.3    -      -       -      -
    124D  ASP*     5.7     1.8    -      -       -      -
    209D  HIS*     5.5     1.6    -      -       -      -
    262D  ILE*     3.9    15.8    -      -       -      +
    325D  TYR*     2.7    27.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 79 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78D  GLY*     1.3    74.9    -      -       -      +
     80D  GLY*     1.3    61.0    +      -       -      +
    112D  ARG*     3.0    10.3    -      -       -      +
    113D  PHE*     2.7    31.6    +      -       -      -
    209D  HIS*     4.1    23.8    -      -       +      +
    262D  ILE*     3.9    28.5    -      -       +      +
    265D  LEU*     4.4     9.4    -      -       +      -
    325D  TYR*     4.4     7.0    -      -       -      -
    329D  VAL*     4.3     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 80 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79D  ALA*     1.3    76.8    -      -       -      +
     81D  ALA*     1.3    65.3    +      -       -      +
    111D  VAL      3.2    10.1    -      -       -      -
    112D  ARG*     4.2     1.8    -      -       -      -
    113D  PHE*     5.3     0.4    -      -       -      -
    265D  LEU*     3.9    10.0    -      -       -      +
    321D  ASN*     5.0     1.6    +      -       -      -
    322D  PRO*     3.6    21.0    -      -       -      +
    325D  TYR*     4.7     1.6    -      -       -      -
    329D  VAL*     3.7    24.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 81 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80D  GLY*     1.3    76.6    -      -       -      +
     82D  PHE*     1.3    75.8    +      -       -      +
    111D  VAL*     3.0    31.4    +      -       -      +
    113D  PHE*     4.9     0.9    -      -       +      -
    265D  LEU*     4.0    12.1    -      -       +      -
    269D  ILE*     3.7    27.4    -      -       +      -
    318D  LEU*     4.0    18.8    -      -       +      -
    320D  ARG      3.7     5.2    -      -       -      -
    321D  ASN*     5.0     0.2    -      -       -      +
    322D  PRO*     4.6     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 82 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81D  ALA*     1.3    82.7    -      -       -      +
     83D  GLY*     1.3    59.4    +      -       -      +
    109D  ILE      3.8    15.7    -      -       -      +
    110D  ALA*     3.8    20.6    -      -       +      -
    137D  TYR*     4.5     5.2    -      +       -      -
    318D  LEU*     3.1    12.2    -      -       -      +
    319D  ASN*     2.8    21.0    +      -       -      -
    320D  ARG*     2.8    63.6    +      -       -      +
    321D  ASN      4.2     2.7    -      -       -      -
    322D  PRO*     3.9    18.2    -      -       +      -
    328D  GLU*     3.6    47.1    -      -       +      -
    329D  VAL*     5.5     1.1    -      -       +      -
    332D  ILE*     5.1     0.9    -      -       +      -
    375D  VAL*     4.1    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 83 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82D  PHE*     1.3    78.6    -      -       -      +
     84D  TYR*     1.3    66.4    +      -       -      +
    108D  PRO*     3.8     5.5    -      -       -      +
    109D  ILE*     3.3    23.8    +      -       -      +
    317D  VAL      3.0    14.4    -      -       -      -
    319D  ASN*     3.4    18.2    -      -       -      -
    320D  ARG*     5.0     2.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 84 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83D  GLY*     1.3    79.1    -      -       -      +
     85D  PHE*     1.3    62.7    +      -       -      +
     86D  GLU*     3.6    23.9    +      -       +      -
    106D  LYS*     3.4    45.5    +      -       +      -
    107D  THR      3.4    15.0    -      -       -      +
    108D  PRO*     4.4     1.8    -      -       +      -
    109D  ILE*     3.2    15.3    -      -       -      +
    315D  LYS      4.1     0.5    -      -       -      +
    316D  LEU*     4.0     0.5    -      -       -      -
    317D  VAL*     3.0    67.5    +      -       +      +
    319D  ASN*     4.4    17.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 85 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84D  TYR*     1.3    75.1    -      -       -      +
     86D  GLU*     1.3    70.9    +      -       -      +
     87D  VAL*     3.9    21.8    -      -       +      -
     99D  VAL*     3.9    21.8    -      -       +      -
    100D  PHE*     3.9    29.8    -      +       -      -
    105D  LYS      3.4     2.6    -      -       -      +
    106D  LYS*     3.1     6.2    -      -       -      -
    107D  THR*     2.8    39.7    +      -       -      +
    109D  ILE*     3.8     3.1    -      -       +      -
    136D  PHE*     3.6    26.5    -      +       +      -
    279D  PHE*     4.0    29.2    -      +       +      -
    313D  VAL*     4.3    12.3    -      -       +      -
    314D  GLY*     4.4     1.8    -      -       -      -
    315D  LYS      3.2    24.5    -      -       -      -
    316D  LEU*     3.4    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 86 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84D  TYR*     3.6    22.8    +      -       +      -
     85D  PHE*     1.3    78.8    -      -       -      +
     87D  VAL*     1.3    71.9    +      -       -      +
     88D  THR*     3.5     7.8    +      -       +      +
    104D  GLY*     4.2    16.3    -      -       -      +
    105D  LYS      3.7     1.8    -      -       -      -
    106D  LYS*     3.2    35.0    +      -       +      +
    314D  GLY*     3.1     4.2    -      -       -      -
    315D  LYS*     2.8    48.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 87 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85D  PHE*     3.9    12.6    -      -       +      -
     86D  GLU*     1.3    75.6    -      -       -      +
     88D  THR*     1.3    59.6    +      -       -      +
     89D  HIS      3.3    24.5    -      -       -      +
     90D  ASP*     5.1     0.9    -      -       -      -
     99D  VAL      3.3    27.1    -      -       -      +
    100D  PHE*     3.9    23.8    -      -       +      +
    102D  HIS      3.6    22.2    -      -       -      +
    103D  ILE*     3.7     9.9    -      -       +      +
    104D  GLY*     2.7    28.6    +      -       -      +
    105D  LYS*     3.4    14.4    +      -       +      +
    313D  VAL*     3.8     8.3    -      -       +      +
    314D  GLY*     4.3     0.7    -      -       -      -
----------------------------------------------------------
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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