Contacts of the strand formed by residues 12 - 22 (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 VAL 12 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  LEU      3.6    23.3    -      -       -      +
      8A  PHE*     4.5     6.1    -      -       +      -
     10A  GLY      3.7    12.3    -      -       -      +
     11A  VAL*     1.3    78.6    -      -       -      +
     13A  PRO*     1.3    81.5    -      -       +      +
     14A  ILE*     3.8     0.9    -      -       -      +
     34A  GLU*     3.2     4.6    -      -       -      -
     35A  GLY      2.9    31.0    +      -       -      -
     71A  PHE*     3.7    29.2    -      -       +      -
    114A  PHE*     3.8    25.6    -      -       +      -
    117A  ASP      3.9     3.6    -      -       -      +
    119A  LEU*     4.1     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 13 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  VAL*     4.2     5.1    -      -       +      +
     12A  VAL*     1.3    87.4    -      -       -      +
     14A  ILE*     1.3    60.7    +      -       -      +
     15A  LEU*     6.2     0.4    -      -       +      -
     33A  GLY      3.6     8.5    -      -       -      +
     34A  GLU*     4.3     3.8    -      -       +      -
    117A  ASP*     3.6    17.9    -      -       +      +
    118A  THR*     3.5    23.2    -      -       +      +
    119A  LEU      2.9    24.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 14 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  VAL      3.8     2.9    -      -       -      +
     13A  PRO*     1.3    79.9    -      -       -      +
     15A  LEU*     1.3    70.8    +      -       -      +
     16A  VAL*     4.0    15.3    -      -       +      -
     32A  GLU*     3.5     5.1    -      -       -      -
     33A  GLY      2.9    32.8    +      -       -      +
     34A  GLU      3.5     7.6    -      -       -      +
     35A  GLY      3.4    19.3    -      -       -      +
     42A  LEU*     3.6    18.6    -      -       +      -
     44A  LEU*     3.8    21.8    -      -       +      -
     68A  VAL*     4.6    15.0    -      -       +      -
     71A  PHE*     3.4    35.0    -      -       +      -
    119A  LEU*     3.3    10.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 15 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  PRO*     6.4     0.4    -      -       +      -
     14A  ILE*     1.3    81.1    -      -       -      +
     16A  VAL*     1.3    64.5    +      -       -      +
     17A  GLU*     4.3     7.9    -      -       +      +
     31A  GLY      3.5     3.4    -      -       -      +
     32A  GLU*     4.0    24.2    -      -       +      -
    118A  THR*     3.6    23.8    -      -       +      -
    119A  LEU      3.0     6.3    +      -       -      +
    120A  VAL*     3.2    23.6    -      -       +      +
    121A  ASN*     2.8    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 16 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ILE*     4.0    17.9    -      -       +      -
     15A  LEU*     1.3    79.2    -      -       -      +
     17A  GLU*     1.3    71.7    +      -       -      +
     18A  LEU      5.0     0.2    -      -       -      +
     29A  VAL      4.5     0.4    -      -       -      +
     30A  SER*     3.4     1.9    -      -       -      -
     31A  GLY      2.8    35.0    +      -       -      +
     44A  LEU*     4.4     7.4    -      -       +      -
     46A  PHE*     3.9    22.0    -      -       +      -
     64A  LEU*     3.8    35.7    -      -       +      +
     68A  VAL*     5.1     1.6    -      -       +      -
    121A  ASN*     3.2    11.9    -      -       +      +
    123A  ILE*     3.7    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 17 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  LEU*     4.3     7.8    -      -       +      +
     16A  VAL*     1.3    79.4    -      -       -      +
     18A  LEU*     1.3    56.0    +      -       -      +
     28A  SER*     6.1     0.7    -      -       -      -
     29A  VAL      3.5     2.9    -      -       -      +
     30A  SER*     2.6    35.7    +      -       -      -
     31A  GLY      4.6     2.6    +      -       -      +
    120A  VAL*     5.9     3.1    -      -       +      -
    121A  ASN      2.9    11.6    +      -       -      +
    122A  ARG*     3.4    15.8    -      -       +      +
    123A  ILE*     2.8    33.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 18 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  VAL      4.3     0.2    -      -       -      -
     17A  GLU*     1.3    75.6    +      -       -      +
     19A  ASP*     1.3    82.5    +      -       -      +
     20A  GLY*     3.6     2.5    -      -       -      +
     27A  PHE*     3.5    33.7    -      -       +      -
     28A  SER*     3.1     7.1    -      -       -      -
     29A  VAL*     2.8    43.3    +      -       +      +
     60A  LEU*     4.9     6.5    -      -       +      -
     63A  THR*     3.7    30.3    -      -       +      -
     64A  LEU*     4.0    22.4    -      -       +      -
    123A  ILE*     3.4    20.6    -      -       +      +
    125A  LEU*     4.4    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  LEU*     1.3    79.7    -      -       -      +
     20A  GLY*     1.3    58.8    -      -       -      +
     27A  PHE      3.6     2.9    -      -       -      +
     28A  SER*     2.7    27.5    +      -       -      -
    122A  ARG*     5.9     0.9    +      -       -      -
    123A  ILE      3.0     9.3    +      -       -      +
    124A  GLU*     3.4    13.8    -      -       +      +
    125A  LEU      2.9    24.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  LEU*     3.6     4.6    -      -       -      +
     19A  ASP*     1.3    75.1    -      -       -      +
     21A  ASP*     1.3    61.3    +      -       -      +
     26A  LYS*     3.3     6.4    -      -       -      +
     27A  PHE*     2.7    59.3    +      -       -      +
    125A  LEU*     3.4     9.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  GLY*     1.3    75.2    -      -       -      +
     22A  VAL*     1.3    56.3    +      -       -      +
     23A  ASN      3.9     0.5    +      -       -      -
     24A  GLY*     2.9    33.0    +      -       -      -
     25A  HIS      3.4     4.7    -      -       -      -
     26A  LYS*     4.1    25.3    -      -       +      +
     27A  PHE*     4.0     0.6    -      -       -      -
    125A  LEU*     3.1     9.5    +      -       -      +
    126A  LYS*     3.4    30.0    +      -       +      +
    127A  GLY      2.7    31.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  ASP*     1.3    77.4    +      -       -      +
     23A  ASN*     1.3    67.0    +      -       -      +
     25A  HIS*     2.8    39.8    +      -       +      +
     27A  PHE*     3.9    14.8    -      -       +      -
     54A  PRO*     5.5     0.4    -      -       +      -
     55A  VAL*     3.9    25.8    -      -       +      -
    106A  TYR*     3.8    12.8    -      -       +      -
    125A  LEU*     3.5    26.0    -      -       +      -
    127A  GLY*     3.4     4.5    -      -       -      -
    130A  PHE*     3.7    29.6    -      -       +      -
    137A  LEU*     4.3    11.9    -      -       +      -
----------------------------------------------------------
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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