Contacts of the strand formed by residues 105 - 115 (chain A) in PDB entry 1QYF


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 105 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  THR*     4.9     5.2    -      -       +      -
     98A  ILE      3.1    15.9    -      -       -      +
     99A  SER*     4.3     9.2    -      -       -      +
    104A  GLY*     1.3    77.2    -      -       -      +
    106A  TYR*     1.3    60.0    +      -       -      +
    107A  LYS*     3.9    24.1    -      -       -      +
    126A  LYS      3.8     0.7    -      -       -      +
    127A  GLY*     3.2     4.2    -      -       -      -
    128A  ILE*     3.0    56.9    +      -       -      +
    129A  ASP*     5.0     4.6    +      -       -      +
    130A  PHE*     3.3     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  VAL*     3.8    17.5    -      -       +      -
     55A  VAL*     3.4    21.4    -      -       +      +
     59A  THR*     2.9    44.3    +      -       -      -
     60A  LEU*     4.1    11.2    -      -       +      -
     63A  THR*     5.0     0.2    -      -       -      -
     96A  ALA      3.9     0.3    -      -       -      +
     97A  THR*     3.4     5.2    -      -       -      +
     98A  ILE*     2.8    52.4    +      -       +      +
    100A  PHE*     3.8    20.9    -      +       -      -
    105A  ASN*     1.3    74.5    -      -       -      +
    107A  LYS*     1.3    64.2    +      -       -      +
    108A  THR*     4.2     2.5    -      -       +      -
    125A  LEU*     3.8    24.5    -      -       +      -
    126A  LYS      3.4     3.8    -      -       -      +
    127A  GLY*     3.9     7.9    -      -       -      -
    130A  PHE*     3.4    30.7    -      +       -      -
    136A  ILE*     3.9     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  ALA      3.4     5.2    -      -       -      +
     97A  THR*     2.9    35.9    +      -       +      +
    105A  ASN*     3.9    16.2    -      -       -      +
    106A  TYR*     1.3    78.5    -      -       -      +
    108A  THR*     1.3    62.0    +      -       -      +
    124A  GLU      4.0     0.5    -      -       -      +
    125A  LEU*     3.5     1.6    -      -       -      -
    126A  LYS*     2.8    39.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  THR*     3.7    33.5    +      -       +      +
     94A  GLN*     4.9     1.7    +      -       -      +
     95A  GLU*     3.3     7.2    -      -       -      +
     96A  ALA*     2.9    49.2    +      -       -      +
     98A  ILE*     4.9     3.6    -      -       +      -
    106A  TYR*     4.5     6.7    -      -       +      -
    107A  LYS*     1.3    81.0    -      -       -      +
    109A  ARG*     1.3    62.9    +      -       -      +
    110A  ALA*     6.1     0.4    -      -       -      -
    123A  ILE*     4.5     3.1    -      -       -      -
    124A  GLU      3.2     7.4    -      -       -      -
    125A  LEU*     3.8    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  VAL*     3.9    27.1    -      -       +      +
     94A  GLN      3.5     3.6    -      -       -      -
     95A  GLU*     4.2    19.3    +      -       +      +
    108A  THR*     1.3    76.2    -      -       -      +
    110A  ALA*     1.3    64.5    +      -       -      +
    111A  GLU*     3.0    33.9    +      -       -      +
    122A  ARG      4.0     0.2    -      -       -      +
    123A  ILE*     3.4     2.1    -      -       -      -
    124A  GLU*     2.8    50.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  THR      5.7     0.9    -      -       -      +
     93A  VAL*     3.2    10.2    -      -       -      +
     94A  GLN*     2.8    46.4    +      -       +      +
    108A  THR*     6.1     0.7    -      -       -      +
    109A  ARG*     1.3    78.3    -      -       -      +
    111A  GLU*     1.3    65.1    +      -       -      +
    112A  VAL*     4.6     1.6    -      -       +      -
    121A  ASN*     3.5    19.1    -      -       -      +
    122A  ARG      3.1    11.9    -      -       -      +
    123A  ILE*     3.8    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  TYR      3.6     3.4    -      -       -      +
     93A  VAL*     4.2    12.3    -      -       +      -
    109A  ARG*     3.0    32.2    +      -       -      +
    110A  ALA*     1.3    78.7    -      -       -      +
    112A  VAL*     1.3    61.8    -      -       -      +
    113A  LYS*     2.5    41.6    +      -       -      +
    120A  VAL      3.5     3.1    -      -       -      +
    121A  ASN*     3.6     0.5    -      -       -      -
    122A  ARG*     2.9    39.6    +      -       +      +
    188A  ILE*     4.3    11.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  CRO      3.8    14.1    -      -       -      +
     68A  VAL*     4.6     4.5    -      -       +      -
     70A  CYS*     4.6     2.5    -      -       -      -
     88A  MET*     3.8    15.6    -      -       +      +
     91A  GLY*     3.0     4.0    -      -       -      -
     92A  TYR*     2.8    63.9    +      -       +      +
     94A  GLN*     5.1     2.9    -      -       +      -
    110A  ALA*     4.6     6.3    -      -       +      -
    111A  GLU*     1.3    71.8    -      -       -      +
    113A  LYS*     1.3    62.8    +      -       -      +
    119A  LEU*     3.8    22.7    -      -       +      -
    120A  VAL      3.2     9.9    -      -       -      +
    121A  ASN*     3.4    23.8    -      -       -      +
    188A  ILE*     4.5     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  MET*     4.2     3.4    -      -       -      -
     89A  PRO      3.8     5.8    -      -       -      +
     90A  GLU      3.4    23.3    -      -       -      +
     91A  GLY*     4.0     2.5    -      -       -      -
    111A  GLU*     2.5    41.8    +      -       -      +
    112A  VAL*     1.3    77.7    -      -       -      +
    114A  PHE*     1.3    69.8    +      -       -      +
    115A  GLU*     3.4    26.1    +      -       +      +
    119A  LEU*     4.0     6.7    -      -       -      -
    120A  VAL*     2.9    36.5    +      -       +      +
    122A  ARG*     5.7     9.2    -      -       -      +
    188A  ILE*     4.8     6.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  LEU*     3.9    34.1    -      -       +      -
      8A  PHE*     3.6    36.8    -      +       -      -
     12A  VAL*     3.8    18.4    -      -       +      -
     88A  MET*     4.0     7.6    -      -       +      -
     89A  PRO*     3.2    40.4    +      -       +      +
    113A  LYS*     1.3    82.2    -      -       -      +
    115A  GLU*     1.3    63.9    +      -       -      +
    116A  GLY      3.7    19.8    +      -       -      +
    117A  ASP*     3.8    18.2    -      -       -      -
    118A  THR      3.3    14.8    -      -       -      -
    119A  LEU*     4.0    10.5    -      -       +      -
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Residues in contact with GLU 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  LYS*     3.4    29.0    +      -       +      +
    114A  PHE*     1.3    78.0    -      -       -      +
    116A  GLY*     1.3    63.9    +      -       -      +
    117A  ASP      3.3     0.9    +      -       -      -
    118A  THR*     2.8    26.8    +      -       -      +
    120A  VAL*     3.6    30.1    -      -       +      -
----------------------------------------------------------
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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