Contacts of the helix formed by residues 612 - 627 (chain A) in PDB entry 1Q2L


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 ARG 612 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    394A  ASN*     6.1     0.4    -      -       -      +
    505A  PRO      3.5    19.2    +      -       -      +
    506A  TYR*     3.9    31.4    -      -       +      +
    507A  ILE      3.0    27.1    +      -       -      +
    508A  PRO*     4.3     7.6    -      -       +      +
    509A  ASP*     3.3    27.9    +      -       -      -
    592A  ILE*     4.3     8.1    -      -       +      -
    609A  TYR*     4.4     1.8    +      -       -      +
    610A  THR      3.3     0.4    -      -       -      -
    611A  GLN*     1.3   101.9    +      -       -      +
    613A  LEU*     1.3    66.3    +      -       -      +
    614A  PRO*     3.4     2.7    -      -       -      -
    615A  GLN*     3.2    18.8    +      -       -      +
    616A  LEU*     2.9    20.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 613 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    548A  ALA*     3.8    32.8    -      -       +      +
    550A  VAL*     3.7    28.9    -      -       +      +
    592A  ILE*     4.0    27.3    -      -       +      +
    606A  ALA*     4.1    29.2    -      -       +      -
    607A  ASN      4.7     0.7    -      -       -      +
    608A  GLY      4.2     7.0    -      -       -      +
    609A  TYR      3.7     9.8    +      -       -      +
    610A  THR*     3.2    10.7    +      -       -      +
    612A  ARG*     1.3    76.2    -      -       -      +
    614A  PRO*     1.3    73.8    -      -       +      +
    616A  LEU*     3.0     4.4    +      -       +      +
    617A  PHE*     2.7    27.5    +      -       +      +
    708A  MET*     4.2     6.5    -      -       -      -
    716A  LEU*     5.6     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 614 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    610A  THR*     3.4    11.4    -      -       -      +
    611A  GLN      4.1     5.6    -      -       -      +
    612A  ARG      3.6     2.7    -      -       -      -
    613A  LEU*     1.3    94.2    -      -       +      +
    615A  GLN*     1.3    62.3    +      -       -      +
    617A  PHE*     3.2     1.7    +      -       -      +
    618A  GLN*     3.0    35.7    +      -       -      +
    708A  MET*     4.2    22.9    -      -       +      -
    712A  GLN*     5.9     2.7    -      -       +      +
    716A  LEU*     3.8    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 615 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    505A  PRO*     4.2    26.0    -      -       -      +
    506A  TYR*     3.7    26.3    +      -       +      +
    612A  ARG*     3.2    20.2    +      -       -      +
    614A  PRO*     1.3    79.6    -      -       -      +
    616A  LEU*     1.3    61.8    +      -       -      +
    618A  GLN*     3.4     9.4    +      -       -      +
    619A  ALA*     3.0    23.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 616 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    506A  TYR*     3.6    20.6    -      -       +      -
    583A  LEU*     3.7    34.5    -      -       +      -
    587A  ALA*     4.0    17.3    -      -       +      -
    592A  ILE*     3.8    35.9    -      -       +      -
    594A  PHE*     3.9    16.4    -      -       +      -
    606A  ALA*     4.4    12.6    -      -       +      -
    612A  ARG      2.9    12.7    +      -       -      +
    613A  LEU*     3.5     8.3    -      -       +      +
    615A  GLN*     1.3    75.4    -      -       -      +
    617A  PHE*     1.3    70.6    +      -       -      +
    619A  ALA      3.2     1.2    +      -       -      -
    620A  LEU*     2.9    24.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 617 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    550A  VAL*     3.6    45.1    -      -       +      -
    552A  LEU*     3.7    33.0    -      -       +      -
    604A  VAL*     3.9    24.2    -      -       +      -
    606A  ALA*     3.7    25.1    -      -       +      -
    613A  LEU*     2.7    20.6    +      -       +      +
    614A  PRO      3.6     4.0    -      -       -      +
    616A  LEU*     1.3    77.2    -      -       +      +
    618A  GLN*     1.3    61.7    +      -       -      +
    620A  LEU*     3.3     5.4    -      -       +      +
    621A  LEU*     3.1    45.1    +      -       +      +
    702A  PHE*     4.2     7.2    -      +       -      -
    716A  LEU*     4.3    13.7    -      -       +      -
    720A  VAL*     4.1    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 618 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    614A  PRO*     3.0    25.4    +      -       -      +
    615A  GLN*     3.9     7.3    -      -       -      +
    616A  LEU      3.2     0.2    -      -       -      -
    617A  PHE*     1.3    75.9    -      -       -      +
    619A  ALA*     1.3    58.7    +      -       -      +
    621A  LEU*     3.6     1.2    +      -       -      -
    622A  GLU*     3.0    13.5    +      -       -      +
    716A  LEU*     4.0    16.2    -      -       +      +
    719A  ASP*     3.7    37.9    +      -       -      +
    720A  VAL*     4.5     3.6    -      -       +      -
    722A  LYS*     5.4     2.9    +      -       -      -
    723A  GLN*     2.7    47.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 619 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    506A  TYR*     3.3    26.9    -      -       -      +
    580A  LEU*     4.3     0.2    -      -       -      +
    583A  LEU*     3.9    16.9    -      -       +      +
    615A  GLN*     3.0    12.5    +      -       +      +
    616A  LEU      3.8     3.1    -      -       -      +
    618A  GLN*     1.3    74.5    -      -       -      +
    620A  LEU*     1.3    61.4    +      -       -      +
    622A  GLU*     3.6     7.3    -      -       -      +
    623A  GLY*     2.9    26.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 620 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    580A  LEU*     3.6    19.9    -      -       +      +
    583A  LEU*     3.5    12.1    -      -       +      +
    594A  PHE*     3.6    53.8    -      -       +      -
    596A  THR*     4.5    11.2    -      -       +      -
    604A  VAL*     3.5    31.6    -      -       +      -
    605A  ASN      4.8     0.2    -      -       -      +
    616A  LEU*     2.9    18.7    +      -       +      +
    617A  PHE*     3.3    15.3    -      -       +      +
    618A  GLN      3.2     0.2    -      -       -      -
    619A  ALA*     1.3    78.6    -      -       -      +
    621A  LEU*     1.3    67.3    +      -       +      +
    623A  GLY      3.2     0.2    +      -       -      -
    624A  TYR*     3.0    21.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 621 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552A  LEU*     4.0    17.0    -      -       +      -
    554A  LEU*     4.8     0.4    -      -       +      -
    602A  LEU*     4.3     2.2    -      -       +      -
    604A  VAL*     3.9    35.2    -      -       +      -
    617A  PHE*     3.1    42.2    +      -       +      +
    618A  GLN      4.1     3.4    -      -       -      +
    620A  LEU*     1.3    80.6    -      -       +      +
    622A  GLU*     1.3    61.7    +      -       -      +
    624A  TYR*     4.2     4.5    -      -       +      -
    625A  PHE*     3.1    53.2    +      -       +      +
    720A  VAL*     4.5     9.9    -      -       +      -
    723A  GLN*     4.0    10.8    -      -       -      +
    724A  LEU*     4.2    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 622 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    618A  GLN      3.0    20.0    +      -       -      +
    619A  ALA*     3.6     8.5    -      -       -      +
    621A  LEU*     1.3    79.3    -      -       -      +
    623A  GLY*     1.3    62.0    +      -       -      +
    625A  PHE*     3.5     1.8    +      -       -      +
    626A  SER*     2.5    61.6    +      -       -      +
    723A  GLN*     3.2    15.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 623 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    576A  ALA*     4.9     0.2    -      -       -      +
    579A  ALA*     4.6     4.8    -      -       -      +
    580A  LEU*     3.9    16.5    -      -       -      +
    619A  ALA      2.9    16.4    +      -       -      -
    620A  LEU      3.8     1.1    -      -       -      -
    622A  GLU*     1.3    82.6    +      -       -      +
    624A  TYR*     1.3    61.7    +      -       -      +
    626A  SER*     4.3     1.6    -      -       -      -
    627A  TYR*     3.3    29.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 624 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    569A  PHE*     4.1     8.5    +      -       -      -
    572A  ASN*     3.5    21.3    +      -       -      -
    573A  ASP*     2.8    40.6    +      -       -      +
    576A  ALA*     3.4    27.4    -      -       +      -
    580A  LEU*     4.0     9.3    -      -       +      +
    596A  THR*     3.8    25.8    -      -       +      -
    602A  LEU*     3.4    31.5    -      -       +      +
    604A  VAL*     5.9     0.7    -      -       +      -
    620A  LEU*     3.0    16.8    +      -       +      +
    621A  LEU*     3.6     9.9    -      -       +      +
    622A  GLU      3.2     0.2    -      -       -      -
    623A  GLY*     1.3    78.3    -      -       -      +
    625A  PHE*     1.3    76.9    +      +       +      +
    627A  TYR*     3.2    20.1    -      -       -      -
    691A  ARG*     3.5     6.4    -      -       -      -
    694A  LEU*     4.2     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 625 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    554A  LEU*     3.9     6.5    -      -       +      -
    602A  LEU*     3.6    33.0    -      -       +      -
    621A  LEU*     3.1    39.3    +      -       +      +
    622A  GLU*     3.9     1.8    -      -       -      +
    624A  TYR*     1.3    88.1    -      +       -      +
    626A  SER*     1.3    59.8    +      -       -      +
    691A  ARG*     3.4    56.3    +      -       +      +
    692A  ASP*     5.0     3.7    -      -       -      +
    694A  LEU*     4.0    15.9    -      -       +      -
    695A  LYS*     3.6    44.0    -      -       +      -
    724A  LEU*     3.7    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 626 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    622A  GLU*     2.5    39.2    +      -       -      -
    623A  GLY*     4.2     1.7    -      -       -      -
    625A  PHE*     1.3    80.1    -      -       -      +
    627A  TYR*     1.3    70.0    +      -       -      +
    628A  THR*     4.4     4.0    +      -       -      -
    691A  ARG*     3.9     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 627 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572A  ASN*     2.7    40.6    +      -       -      -
    575A  LEU*     3.5    50.1    -      -       +      +
    576A  ALA*     3.9     9.9    -      -       -      -
    579A  ALA*     3.5    22.4    -      -       +      -
    623A  GLY*     3.3    16.4    +      -       -      +
    624A  TYR      3.2    20.2    -      -       -      -
    626A  SER*     1.3    82.4    -      -       -      +
    628A  THR*     1.3    73.5    +      -       -      +
    629A  ALA*     4.0    10.1    -      -       +      -
    687A  VAL*     4.0     5.2    -      -       -      +
    688A  LEU*     4.5    10.5    -      -       +      +
    691A  ARG*     2.8    43.3    +      -       -      +
----------------------------------------------------------
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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