Contacts of the helix formed by residues 17 - 30 (chain A) in PDB entry 4L57


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 ASP 17 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  GLY*     5.0     0.4    -      -       -      +
     16A  ALA*     1.3    69.1    -      -       -      +
     18A  PHE*     1.3    61.3    +      -       -      +
     19A  GLU*     3.5     7.1    +      -       -      +
     20A  ALA*     3.0    35.8    +      -       +      +
     21A  GLY*     3.1    15.9    +      -       -      -
     24A  ARG*     5.3     0.3    +      -       -      -
     38A  LEU*     5.9     0.5    -      -       -      +
     74A  LEU*     3.6    12.0    -      -       -      +
     75A  GLU*     2.8    27.1    +      -       +      +
     76A  PRO      4.7     4.6    -      -       -      +
     77A  ILE*     3.7    26.2    -      -       +      +
     78A  PRO*     5.4     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 18 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  ASP*     3.8    33.9    -      -       +      +
     13A  GLY*     4.5     4.5    -      -       -      +
     16A  ALA      3.0     7.4    +      -       -      +
     17A  ASP*     1.3    73.2    -      -       -      +
     19A  GLU*     1.3    63.1    +      -       -      +
     21A  GLY*     3.2     1.6    +      -       -      -
     22A  LEU*     2.8    46.4    +      -       +      +
     65A  TYR*     4.0    27.6    -      +       +      -
     70A  PHE*     3.6    27.3    -      +       -      -
     71A  PHE*     3.9    18.4    -      +       -      -
     74A  LEU*     3.9     8.9    -      -       +      +
    102A  LEU*     5.0     6.3    -      -       +      -
    204A  GOL      3.5    39.7    -      -       -      +
    207A  GOL      3.6    21.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  GLY*     6.2     1.1    -      -       -      -
     17A  ASP*     3.4     5.9    +      -       -      +
     18A  PHE*     1.3    81.0    -      -       +      +
     20A  ALA*     1.3    62.7    +      -       -      +
     22A  LEU*     3.4     7.6    +      -       -      +
     23A  LEU*     3.1    18.9    +      -       -      +
     38A  LEU*     3.7    15.8    -      -       +      +
     41A  ARG*     2.8    50.4    +      -       -      +
     46A  ALA*     4.5     3.6    -      -       -      +
    165A  CYS*     4.2    13.9    -      -       -      -
    166A  CYS*     3.8    25.8    -      -       -      -
    167A  HIS*     3.7     2.0    -      -       -      -
    204A  GOL      2.5    32.4    +      -       -      +
    207A  GOL      3.8     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  ASP*     3.0    33.7    +      -       +      +
     19A  GLU*     1.3    77.4    -      -       -      +
     21A  GLY*     1.3    57.0    +      -       -      +
     23A  LEU*     3.4     2.3    +      -       -      +
     24A  ARG*     3.0    44.6    +      -       -      +
     38A  LEU*     4.3    21.2    -      -       +      +
     75A  GLU*     5.7     2.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  ASP      3.1    14.6    +      -       -      -
     18A  PHE      3.6     2.7    -      -       -      -
     20A  ALA*     1.3    78.2    -      -       -      +
     22A  LEU*     1.3    61.7    +      -       -      +
     24A  ARG*     3.5    22.9    +      -       -      +
     25A  GLY*     2.9    20.1    +      -       -      -
     70A  PHE*     3.6    12.8    -      -       -      -
     74A  LEU*     3.9    11.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  PHE*     2.8    32.3    +      -       +      +
     19A  GLU*     3.7    10.3    -      -       -      +
     21A  GLY*     1.3    78.5    -      -       -      +
     23A  LEU*     1.3    56.9    +      -       -      +
     25A  GLY*     3.3     0.7    +      -       -      -
     26A  PHE*     2.9    30.7    +      -       -      +
     46A  ALA*     3.7    30.5    -      -       +      -
     50A  TYR*     5.2     4.7    -      -       +      +
     61A  VAL*     3.6    32.8    -      -       +      +
     64A  VAL*     3.7    13.4    -      -       +      +
     65A  TYR*     3.6    26.9    -      -       +      -
     70A  PHE*     3.6     8.7    -      -       +      -
    207A  GOL      4.2     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  GLU      3.1    16.5    +      -       -      +
     20A  ALA*     4.0     3.4    -      -       -      +
     22A  LEU*     1.3    76.4    -      -       -      +
     24A  ARG*     1.3    63.8    +      -       -      +
     26A  PHE*     3.3     4.1    +      -       +      +
     27A  ARG*     2.9    43.7    +      -       +      +
     35A  HIS*     3.6    32.3    -      -       +      +
     36A  VAL      3.8    11.7    -      -       -      +
     37A  PRO*     4.5     1.1    -      -       +      -
     38A  LEU*     3.8    34.1    -      -       +      +
     50A  TYR*     3.6    20.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  ASP      5.3     0.4    +      -       -      -
     20A  ALA*     3.0    41.3    +      -       -      +
     21A  GLY*     3.5    22.7    +      -       -      +
     23A  LEU*     1.3    78.7    -      -       -      +
     25A  GLY*     1.3    57.3    +      -       -      +
     27A  ARG*     3.4     3.7    +      -       -      +
     28A  ARG*     3.0    31.0    +      -       +      +
     73A  ASP      4.6     6.3    +      -       -      -
     74A  LEU*     4.9     1.4    -      -       -      +
     75A  GLU*     3.9    42.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  GLY      2.9    16.9    +      -       -      -
     22A  LEU      3.8     0.7    -      -       -      -
     24A  ARG*     1.3    78.8    -      -       -      +
     26A  PHE*     1.3    57.9    +      -       -      +
     28A  ARG*     3.3    17.6    +      -       -      +
     29A  ARG*     3.0    33.3    +      -       -      +
     64A  VAL*     3.9    16.8    -      -       -      +
     70A  PHE*     6.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  LEU      2.9    18.2    +      -       -      +
     23A  LEU*     3.7     6.1    -      -       -      +
     25A  GLY*     1.3    77.7    -      -       -      +
     27A  ARG*     1.3    62.7    +      -       +      +
     30A  PHE*     2.8    61.1    +      +       +      +
     33A  GLU*     3.9    22.9    -      -       +      -
     34A  PRO      3.3    27.1    -      -       -      -
     35A  HIS*     4.0    17.7    -      -       +      -
     50A  TYR*     3.8    24.7    -      +       -      +
     57A  LEU*     4.2     9.2    -      -       +      -
     60A  LYS*     4.1     6.1    -      -       +      -
     61A  VAL*     3.9    37.2    -      -       +      -
     64A  VAL*     3.9    10.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LEU*     2.9    47.4    +      -       +      +
     24A  ARG*     4.2     4.5    -      -       -      +
     26A  PHE*     1.3    78.6    -      -       +      +
     28A  ARG*     1.3    62.0    +      -       -      +
     30A  PHE      4.5     4.3    -      -       -      -
     31A  PRO*     3.3    24.6    -      -       +      +
     35A  HIS*     3.5    41.6    +      -       +      +
     78B  PRO*     5.9     6.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  ARG*     3.0    20.8    +      -       +      +
     25A  GLY*     3.6    15.8    +      -       -      +
     27A  ARG*     1.3    77.2    -      -       -      +
     29A  ARG*     1.3    82.5    +      -       -      +
     31A  PRO*     3.5    12.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  GLY      3.0    15.5    +      -       -      +
     28A  ARG*     1.3    94.1    -      -       -      +
     30A  PHE*     1.3    90.5    +      -       +      +
     31A  PRO*     3.3     9.2    -      -       -      +
     63A  SER*     3.2    47.9    +      -       -      -
     64A  VAL*     4.2     7.3    -      -       -      +
     67A  ALA*     4.4    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  PHE*     2.8    49.0    +      +       +      +
     27A  ARG*     4.5     1.4    -      -       -      -
     29A  ARG*     1.3   111.7    -      -       +      +
     31A  PRO*     1.3    64.4    -      -       -      +
     32A  GLU      3.2     4.4    +      -       -      -
     33A  GLU*     3.2    36.2    +      -       -      +
     60A  LYS*     3.3    53.6    -      -       +      -
     63A  SER*     3.6    17.5    -      -       -      -
     64A  VAL*     4.0     4.9    -      -       +      -
----------------------------------------------------------
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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