Contacts of the strand formed by residues 77 - 87 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76B  ALA*     1.3    77.1    -      -       -      +
     78B  GLY*     1.3    61.8    +      -       -      +
    114B  SER*     2.9    19.4    -      -       -      -
    115B  THR*     3.0    26.5    +      -       -      +
    118B  GLY      4.0     2.6    +      -       -      +
    119B  GLU      3.7     8.0    +      -       -      +
    120B  SER*     3.7    16.6    -      -       -      +
    122B  SER*     3.2    39.9    +      -       -      +
    123B  ALA      5.6     0.4    -      -       -      +
    124B  ASP*     3.0    25.1    +      -       -      +
    258B  PRO      3.0    22.6    +      -       -      -
    259B  ASP*     2.6    30.4    +      -       -      +
    262B  ILE*     3.9    12.1    -      -       +      -
    170C  ARG*     4.4     5.8    -      -       -      +
    175C  HIS*     5.7     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 78 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76B  ALA      3.4     5.3    +      -       -      -
     77B  LYS*     1.3    79.2    -      -       -      +
     79B  ALA*     1.3    59.2    -      -       -      +
    112B  ARG*     3.9    10.6    -      -       -      +
    113B  PHE      2.9    14.8    -      -       -      -
    114B  SER*     3.6     4.9    -      -       -      -
    124B  ASP*     5.6     2.0    -      -       -      -
    209B  HIS*     5.5     2.0    -      -       -      -
    262B  ILE*     4.1    13.4    -      -       -      +
    325B  TYR*     2.7    28.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 79 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78B  GLY*     1.3    76.1    -      -       -      +
     80B  GLY*     1.3    59.3    +      -       -      +
    112B  ARG*     3.1     9.8    -      -       -      +
    113B  PHE*     2.8    31.7    +      -       -      -
    209B  HIS*     4.2    16.5    +      -       +      +
    262B  ILE*     4.0    26.7    -      -       +      +
    265B  LEU*     4.1    18.8    -      -       +      -
    325B  TYR*     4.5     7.4    -      -       +      -
    329B  VAL*     4.3     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 80 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  ALA*     1.3    76.9    -      -       -      +
     81B  ALA*     1.3    65.7    +      -       -      +
     82B  PHE*     6.1     0.2    -      -       -      -
    111B  VAL      3.2    10.5    -      -       -      -
    112B  ARG*     4.3     2.2    -      -       -      -
    113B  PHE*     5.6     0.4    -      -       -      -
    265B  LEU*     4.0     9.5    -      -       -      +
    321B  ASN*     4.7     1.9    +      -       -      -
    322B  PRO*     3.5    21.6    -      -       -      +
    325B  TYR*     4.7     1.4    -      -       -      -
    329B  VAL*     3.7    24.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 81 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  GLY*     1.3    75.7    -      -       -      +
     82B  PHE*     1.3    76.2    +      -       -      +
    111B  VAL*     3.0    32.5    +      -       -      +
    113B  PHE*     5.4     0.7    -      -       +      -
    265B  LEU*     4.2    10.3    -      -       +      -
    269B  ILE*     3.8    26.9    -      -       +      -
    318B  LEU*     4.2    19.7    -      -       +      -
    320B  ARG      3.6     5.8    -      -       -      +
    321B  ASN*     4.7     1.6    -      -       -      +
    322B  PRO*     4.5     2.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 82 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  ALA*     1.3    82.5    -      -       -      +
     83B  GLY*     1.3    59.9    +      -       -      +
    109B  ILE      3.8     7.6    -      -       -      +
    110B  ALA*     3.7    32.1    -      -       +      -
    137B  TYR*     4.6     5.8    -      +       -      -
    318B  LEU*     3.5     8.3    -      -       -      -
    319B  ASN*     2.9    21.4    +      -       -      -
    320B  ARG*     2.7    66.1    +      -       -      +
    321B  ASN      4.2     0.9    -      -       -      -
    322B  PRO*     3.9    18.6    -      -       +      -
    328B  GLU*     3.6    48.2    -      -       +      -
    329B  VAL*     5.4     0.7    -      -       +      -
    332B  ILE*     4.8     0.9    -      -       +      -
    375B  VAL*     4.2    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 83 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  PHE*     1.3    77.9    -      -       -      +
     84B  TYR*     1.3    68.1    +      -       -      +
    108B  PRO*     3.7     5.9    -      -       -      +
    109B  ILE*     3.3    22.1    +      -       -      +
    317B  VAL      3.1    14.6    -      -       -      -
    318B  LEU*     4.1     2.2    -      -       -      +
    319B  ASN*     3.5    16.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 84 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  GLY*     1.3    78.8    -      -       -      +
     85B  PHE*     1.3    64.0    +      -       -      +
     86B  GLU*     4.0    22.2    +      -       +      -
    106B  LYS*     3.7    38.5    +      -       +      -
    107B  THR      3.3    19.7    -      -       -      +
    108B  PRO*     4.3     2.0    -      -       +      -
    109B  ILE*     3.2    13.1    -      -       -      +
    315B  LYS      4.1     0.2    -      -       -      +
    316B  LEU*     4.1     0.5    -      -       -      -
    317B  VAL*     3.1    65.7    +      -       +      +
    319B  ASN*     4.0    18.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  TYR*     1.3    78.2    -      -       -      +
     86B  GLU*     1.3    75.5    +      -       -      +
     87B  VAL*     3.7    25.6    -      -       +      -
     99B  VAL*     4.1    21.1    -      -       +      -
    100B  PHE*     4.5    17.5    -      +       -      -
    105B  LYS      3.3     2.3    -      -       -      +
    106B  LYS*     3.2     4.7    -      -       -      -
    107B  THR*     2.8    37.0    +      -       -      +
    109B  ILE*     3.8     6.5    -      -       +      -
    136B  PHE*     3.5    31.4    -      +       +      -
    143B  TRP*     6.4     0.2    -      +       -      -
    279B  PHE*     4.0    28.3    -      +       +      -
    313B  VAL*     4.5     7.6    -      -       +      -
    314B  GLY*     4.1     6.7    -      -       -      -
    315B  LYS      3.3    19.3    -      -       -      -
    316B  LEU*     3.5    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  TYR*     4.0    22.8    +      -       +      -
     85B  PHE*     1.3    78.3    -      -       -      +
     87B  VAL*     1.3    74.9    +      -       -      +
     88B  THR*     3.6    10.1    +      -       +      +
    104B  GLY*     4.4    10.9    -      -       -      -
    105B  LYS      3.5     4.9    -      -       -      +
    106B  LYS*     3.4    30.1    +      -       +      -
    314B  GLY*     3.0     5.9    -      -       -      -
    315B  LYS*     2.8    46.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85B  PHE*     3.7    15.3    -      -       +      -
     86B  GLU*     1.3    77.0    -      -       -      +
     88B  THR*     1.3    58.3    +      -       -      +
     89B  HIS      3.2    25.8    -      -       -      +
     90B  ASP*     5.2     0.7    -      -       -      -
     91B  ILE*     6.3     0.2    -      -       +      -
     99B  VAL      3.4    25.8    -      -       -      +
    100B  PHE*     4.1    16.6    -      -       +      +
    102B  HIS      3.5    19.7    -      -       -      +
    103B  ILE*     3.7    17.6    -      -       -      +
    104B  GLY*     2.8    27.7    +      -       -      -
    105B  LYS*     3.2    14.5    +      -       +      +
    313B  VAL*     3.8     7.0    -      -       +      +
    314B  GLY*     4.2     0.4    -      -       -      -
----------------------------------------------------------
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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