Contacts of the strand formed by residues 117 - 123 (chain B) in PDB entry 1QN7


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 ASN 117 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  ASN      4.0     0.3    -      -       -      +
     28B  ILE*     3.5     2.9    -      -       -      +
     29B  VAL*     2.9    38.5    +      -       +      +
    115B  ILE*     3.7     1.2    -      -       -      +
    116B  GLN*     1.3    80.9    -      -       -      +
    118B  ILE*     1.3    66.1    +      -       -      +
    119B  VAL*     3.7    10.0    -      -       -      +
    173B  THR*     3.4     2.2    +      -       -      -
    174B  GLY*     2.9    35.6    +      -       -      -
    175B  ALA      3.3     6.2    +      -       -      -
    206E    A      3.3    28.0    +      -       -      -
    207E    T      3.1    42.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  LEU*     3.9    25.6    -      -       +      -
     27B  ASN      3.7     3.1    -      -       -      -
     28B  ILE*     3.7    18.4    -      -       +      -
     87B  GLU*     3.9    16.2    -      -       +      +
    115B  ILE*     3.7    17.9    -      -       +      -
    117B  ASN*     1.3    77.9    +      -       -      +
    119B  VAL*     1.3    65.6    +      -       -      +
    172B  ILE      3.8     1.2    -      -       -      +
    173B  THR*     3.6     3.5    -      -       -      -
    174B  GLY      3.5    18.4    +      -       -      -
    175B  ALA*     2.8    25.1    +      -       +      +
    176B  LYS      3.9     3.6    -      -       -      +
    177B  MET*     3.6    14.1    -      -       -      +
    178B  ARG*     3.4    30.3    -      -       -      +
    181B  THR*     3.9     8.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  LEU*     3.6     4.3    -      -       -      +
     26B  GLN*     2.7    36.6    +      -       +      -
     27B  ASN*     2.9    25.3    +      -       +      +
     29B  VAL*     5.7     0.2    -      -       +      -
    117B  ASN*     3.7     9.9    -      -       -      +
    118B  ILE*     1.3    77.9    -      -       -      +
    120B  GLY*     1.3    56.6    +      -       -      +
    171B  VAL*     4.0    12.8    -      -       +      -
    172B  ILE      3.5     4.5    -      -       -      +
    173B  THR*     3.4    20.0    -      -       -      +
    206E    A      3.6     8.1    -      -       +      -
    223F    T      3.5    21.1    -      -       -      +
    224F    A      3.7    29.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  THR      3.0    17.3    -      -       -      -
     25B  LEU*     4.1     2.0    -      -       -      -
     26B  GLN*     4.1     3.4    -      -       -      -
    118B  ILE      4.2     0.2    -      -       -      -
    119B  VAL*     1.3    75.6    -      -       -      +
    121B  SER*     1.3    63.2    +      -       -      -
    171B  VAL*     3.4     7.4    -      -       -      +
    172B  ILE*     2.8    36.0    +      -       -      +
    181B  THR*     4.7    14.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  PRO*     3.3     2.1    -      -       -      +
     24B  THR*     2.8    32.9    +      -       -      +
     26B  GLN*     2.9    29.0    +      -       -      +
    120B  GLY*     1.3    75.9    -      -       -      -
    122B  CYS*     1.3    63.8    +      -       -      +
    170B  ILE      3.0    17.9    -      -       -      -
    171B  VAL*     4.2     1.1    -      -       -      +
    172B  ILE*     4.4     2.4    -      -       -      +
    224F    A      4.0    28.2    +      -       -      -
    225F    T      5.2     3.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  ILE*     4.2    11.4    -      -       +      -
     22B  VAL      4.6     2.0    -      -       -      +
     23B  PRO*     3.7    23.6    -      -       +      -
     24B  THR*     5.6     0.4    -      -       -      -
    121B  SER*     1.3    78.0    -      -       -      +
    123B  ASP*     1.3    63.5    +      -       -      +
    169B  LYS*     3.5     6.9    -      -       -      +
    170B  ILE*     2.8    36.2    +      -       -      +
    172B  ILE*     4.2     6.5    -      -       -      -
    185B  PHE*     3.5    41.5    -      -       -      -
    225F    T      5.8     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  ILE*     4.2    17.0    -      -       -      +
    122B  CYS*     1.3    81.3    -      -       -      +
    124B  VAL*     1.3    62.9    +      -       -      +
    125B  LYS*     2.8    62.7    +      -       -      +
    126B  PHE      4.5     0.2    +      -       -      -
    167B  SER      4.5     1.0    -      -       -      +
    168B  GLY*     3.3    16.6    -      -       -      +
    169B  LYS*     3.1    35.4    +      -       +      -
----------------------------------------------------------
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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