Contacts of the helix formed by residues 38 - 53 (chain A) in PDB entry 1SL0


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 38 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  SER      4.5     2.7    -      -       -      +
     34A  TYR*     3.6    21.2    -      -       +      -
     35A  ARG*     2.4    54.5    +      -       -      +
     37A  SER*     1.3    79.4    +      -       -      +
     39A  PHE*     1.3    64.7    +      -       -      -
     40A  GLY      3.2     2.5    -      -       -      -
     41A  ALA*     2.6    22.8    +      -       +      +
     42A  TYR      2.7    11.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  PHE*     3.2    54.1    -      +       +      -
     35A  ARG      3.1     4.8    +      -       -      -
     36A  PRO      3.7    11.0    -      -       -      +
     37A  SER      3.2     1.8    -      -       -      -
     38A  ASP*     1.3    75.0    -      -       -      +
     40A  GLY*     1.3    66.0    +      -       -      +
     42A  TYR*     2.7    18.1    +      +       -      +
     43A  LEU*     2.8    32.7    +      -       +      +
     69A  LEU*     3.7    16.2    -      -       +      -
     72A  LEU*     3.9    34.5    -      -       +      -
     73A  ALA      4.2     4.7    -      -       -      -
     76A  GLN*     3.6    25.8    -      -       +      +
     77A  LEU*     3.6    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  SER      4.4     4.2    +      -       -      -
     38A  ASP      3.2     0.8    -      -       -      -
     39A  PHE*     1.3    78.5    -      -       -      +
     41A  ALA*     1.3    56.2    +      -       -      +
     43A  LEU*     3.4     3.0    +      -       -      +
     44A  ASP*     3.0    32.7    +      -       -      +
     77A  LEU*     3.8    24.7    -      -       -      +
     79A  ARG*     3.4    10.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  TYR*     3.6    18.9    -      -       +      -
     37A  SER      5.3     0.2    +      -       -      -
     38A  ASP*     2.6    26.9    +      -       +      +
     40A  GLY*     1.3    69.7    -      -       -      +
     42A  TYR*     1.3    52.6    +      -       -      +
     44A  ASP*     2.8    13.6    +      -       -      +
     45A  ALA*     2.8    34.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  SER*     2.7    30.0    +      -       -      -
      6A  ILE*     2.9    27.0    -      -       +      +
     18A  PHE*     4.0    14.4    -      +       +      -
     21A  GLY*     3.8    18.4    -      -       -      -
     23A  ILE*     3.8    13.0    -      -       +      -
     34A  TYR*     3.3    38.9    -      +       +      -
     38A  ASP      2.7    11.1    +      -       -      +
     39A  PHE*     2.7    20.2    +      +       -      +
     41A  ALA*     1.3    73.7    -      -       -      +
     43A  LEU*     1.3    66.6    +      -       -      +
     45A  ALA*     3.1     9.7    +      -       -      +
     46A  LEU*     3.3    25.0    +      -       +      +
     58A  PHE*     3.4    15.6    -      -       -      -
     69A  LEU*     3.5    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  PHE*     2.8    37.1    +      -       +      +
     40A  GLY*     3.4     7.2    -      -       -      +
     42A  TYR*     1.3    79.4    -      -       +      +
     44A  ASP*     1.3    56.5    +      -       -      +
     46A  LEU*     3.5     1.6    +      -       -      -
     47A  GLU*     3.0    31.2    +      -       -      +
     69A  LEU*     4.5    11.7    -      -       +      -
     73A  ALA*     4.0     8.3    -      -       +      -
     77A  LEU*     3.9    21.5    -      -       +      -
     79A  ARG*     3.5    40.2    -      -       -      +
     81A  PHE*     3.3    42.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  GLY      3.0    15.2    +      -       -      +
     41A  ALA*     2.8    15.0    +      -       -      +
     43A  LEU*     1.3    77.2    -      -       -      +
     45A  ALA*     1.3    55.9    +      -       -      +
     47A  GLU*     3.3    10.1    +      -       -      +
     48A  ALA*     2.9    28.4    +      -       -      +
     79A  ARG*     2.5    33.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ILE*     4.8     2.2    -      -       -      +
     23A  ILE*     3.8    17.7    -      -       +      -
     34A  TYR*     3.5    26.2    -      -       +      +
     41A  ALA      2.8    10.6    +      -       -      +
     42A  TYR      3.4    10.3    -      -       -      +
     44A  ASP*     1.3    73.1    -      -       -      +
     46A  LEU*     1.3    57.0    +      -       -      +
     48A  ALA*     2.8    27.2    +      -       -      +
     49A  GLU*     3.4     6.8    +      -       -      +
     52A  ARG*     4.8     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ILE*     4.0    19.1    -      -       +      -
      4A  SER*     4.2     7.2    -      -       -      -
     23A  ILE*     3.6    27.4    -      -       +      -
     42A  TYR*     3.3    45.3    +      -       +      +
     43A  LEU      3.9     2.9    -      -       -      +
     45A  ALA*     1.3    73.5    -      -       -      +
     47A  GLU*     1.3    63.9    +      -       -      +
     48A  ALA      2.8     6.8    +      -       -      -
     49A  GLU*     3.1    13.7    +      -       -      +
     50A  VAL*     3.2    15.8    +      -       -      +
     56A  ILE*     3.8    13.7    -      -       +      +
     58A  PHE*     4.3     4.3    -      -       +      -
     69A  LEU*     3.8    15.5    -      -       +      -
     81A  PHE*     3.9    18.2    -      -       +      -
     83A  LEU*     4.1     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  LEU      3.0    17.5    +      -       -      +
     44A  ASP*     3.5    10.5    -      -       -      +
     46A  LEU*     1.3    76.5    -      -       -      +
     48A  ALA*     1.3    60.1    +      -       -      +
     50A  VAL*     3.7    13.9    -      -       +      +
     51A  ALA*     3.5    17.0    +      -       -      +
     79A  ARG*     3.2    27.1    +      -       -      +
     80A  GLU      4.6     8.8    -      -       -      +
     81A  PHE*     3.7    19.4    -      -       +      -
     82A  HIS      5.4     0.7    +      -       -      -
     83A  LEU*     5.0     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  ASP      2.9    11.3    +      -       -      +
     45A  ALA*     2.8    18.8    -      -       -      +
     46A  LEU      2.8     1.4    -      -       -      -
     47A  GLU*     1.3    76.9    -      -       -      +
     49A  GLU*     1.3    63.7    +      -       -      +
     50A  VAL      3.2     1.6    -      -       -      -
     51A  ALA*     2.9    22.9    +      -       -      +
     52A  ARG*     3.1    28.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET      3.5    17.8    +      -       -      +
      2A  ILE*     3.3    45.6    -      -       +      +
     25A  ASP*     4.2     3.5    -      -       -      +
     27A  SER*     5.6     0.5    +      -       -      -
     45A  ALA      3.4     1.9    +      -       -      +
     46A  LEU      3.1     9.5    +      -       -      +
     48A  ALA*     1.3    77.5    -      -       -      +
     50A  VAL*     1.3    58.5    +      -       -      +
     52A  ARG*     2.8    37.0    +      -       -      +
     53A  GLY      2.8     9.2    +      -       -      -
     54A  GLY*     2.8    34.5    +      -       -      -
     55A  LEU      2.7    34.4    +      -       -      +
     56A  ILE*     4.2     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  LEU      3.2    17.3    -      -       -      +
     47A  GLU*     3.7    12.8    -      -       +      +
     48A  ALA      3.2     0.2    -      -       -      -
     49A  GLU*     1.3    74.7    -      -       -      +
     51A  ALA*     1.3    61.1    +      -       -      +
     53A  GLY*     3.1    11.6    +      -       -      -
     56A  ILE*     4.1     6.3    -      -       +      -
     83A  LEU*     3.5    27.1    -      -       +      -
     84A  PRO*     3.8    29.2    -      -       +      -
     86A  GLU*     5.7     0.4    -      -       -      +
     87A  ASN*     3.9    20.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  GLU      3.5    10.0    +      -       -      +
     48A  ALA*     2.9    15.6    +      -       -      +
     50A  VAL*     1.3    76.7    -      -       -      +
     52A  ARG*     1.3    63.1    +      -       +      +
     53A  GLY*     3.0     2.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ILE*     5.1     0.6    -      -       -      +
     25A  ASP*     4.6    14.6    +      -       -      -
     27A  SER*     5.7     1.8    -      -       -      -
     45A  ALA      4.8     1.0    +      -       -      -
     48A  ALA*     3.5    25.3    -      -       -      +
     49A  GLU*     2.8    57.2    +      -       -      +
     51A  ALA*     1.3    77.2    -      -       +      +
     53A  GLY*     1.3    61.5    +      -       -      +
     54A  GLY*     4.1     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  GLU      2.8     2.0    +      -       -      -
     50A  VAL      3.1    10.0    +      -       -      -
     51A  ALA      3.0     5.1    -      -       -      -
     52A  ARG*     1.3    81.2    -      -       -      +
     54A  GLY*     1.3    63.4    +      -       -      +
     87A  ASN*     4.2     1.6    -      -       -      -
    202A  GLY*     3.7     7.4    -      -       -      -
    203A  TYR*     3.4    39.6    +      -       -      -
----------------------------------------------------------
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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