Contacts of the helix formed by residues 374 - 392 (chain A) in PDB entry 3ISL


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 374 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  GLU*     2.7    30.5    +      -       -      -
    296A  ARG*     5.6     0.2    -      -       -      +
    300A  HIS*     3.8    13.0    -      -       -      +
    371A  TYR*     2.9    51.5    +      -       -      +
    372A  SER      2.9     6.9    +      -       -      -
    373A  CYS*     1.3    75.1    -      -       -      +
    375A  LYS*     1.3    65.5    +      -       -      +
    376A  GLU*     3.5    29.8    +      -       -      +
    377A  ASN*     3.1    33.1    +      -       +      +
    378A  VAL*     3.0    21.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 375 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300A  HIS*     3.2    12.7    -      -       +      -
    374A  ARG*     1.3    73.1    -      -       -      +
    376A  GLU*     1.3    78.3    +      -       +      +
    378A  VAL*     3.3     0.9    +      -       -      +
    379A  LEU*     2.9    51.8    +      -       +      +
    406A  LEU*     5.4     2.9    -      -       -      +
    409A  TYR*     3.2    58.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 376 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374A  ARG*     3.1    33.1    +      -       -      +
    375A  LYS*     1.3    92.0    +      -       +      +
    377A  ASN*     1.3    60.4    +      -       -      +
    379A  LEU*     3.8     7.8    -      -       +      +
    380A  PHE*     2.9    30.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 377 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  THR*     3.8    19.6    +      -       -      +
     17A  MET*     3.5    17.3    -      -       -      +
     23A  GLU*     2.9    25.3    +      -       -      +
    372A  SER*     3.4    27.6    -      -       -      +
    374A  ARG*     3.1    35.7    +      -       +      +
    376A  GLU*     1.3    76.2    -      -       -      +
    378A  VAL*     1.3    61.4    +      -       -      +
    380A  PHE*     4.0     4.5    -      -       -      +
    381A  VAL*     2.9    34.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 378 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  MET*     4.0    15.0    -      -       +      -
    300A  HIS*     4.0    22.4    -      -       +      +
    303A  ALA*     4.3     0.9    -      -       +      -
    304A  LEU*     3.9    29.8    -      -       +      +
    368A  THR*     4.2     9.0    -      -       +      -
    374A  ARG      3.0    13.7    +      -       -      +
    375A  LYS      3.7     2.2    -      -       -      +
    377A  ASN*     1.3    80.1    -      -       -      +
    379A  LEU*     1.3    64.5    +      -       -      +
    381A  VAL*     3.3    18.5    -      -       -      +
    382A  LEU*     3.3    17.0    +      -       +      +
    405A  ALA*     4.8     0.7    -      -       +      -
    409A  TYR*     3.3    33.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 379 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375A  LYS*     2.9    41.8    +      -       +      +
    376A  GLU*     3.8     7.2    -      -       +      +
    378A  VAL*     1.3    77.4    -      -       -      +
    380A  PHE*     1.3    56.7    +      -       -      +
    382A  LEU*     3.4     1.8    +      -       -      -
    383A  ALA*     3.0    28.6    +      -       -      +
    402A  LEU*     3.7    19.8    -      -       +      +
    405A  ALA*     3.8    28.0    -      -       +      -
    406A  LEU*     4.1    28.3    -      -       +      -
    409A  TYR*     3.9    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 380 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  THR*     3.4    29.8    -      -       +      -
    348A  PHE*     3.6    52.7    -      +       +      -
    350A  ILE*     3.2    16.5    -      -       +      +
    376A  GLU      2.9    22.1    +      -       -      +
    377A  ASN*     3.3     5.8    +      -       -      +
    379A  LEU*     1.3    70.0    -      -       -      +
    381A  VAL*     1.3    60.8    +      -       -      +
    383A  ALA*     4.4    10.1    -      -       +      -
    384A  GLY      2.8    26.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 381 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  THR*     5.3     0.8    -      -       +      +
     17A  MET*     3.9    22.4    -      -       +      -
    304A  LEU*     3.9    23.8    -      -       +      -
    344A  LEU*     4.8     2.2    -      -       +      +
    350A  ILE*     3.8    21.8    -      -       +      +
    352A  ILE*     3.7    29.4    -      -       +      -
    366A  ILE*     4.4    11.2    -      -       +      -
    377A  ASN      2.9    15.6    +      -       -      +
    378A  VAL*     3.3    14.8    -      -       -      +
    380A  PHE*     1.3    76.6    -      -       -      +
    382A  LEU*     1.3    63.0    +      -       +      +
    384A  GLY      3.9     0.2    -      -       -      -
    385A  LEU*     2.9    33.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 382 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  ALA      4.5     2.0    -      -       -      +
    304A  LEU*     3.8    15.0    -      -       +      -
    307A  GLY*     3.8    12.6    -      -       -      +
    308A  ILE*     3.7    45.1    -      -       +      +
    311A  MET*     4.7     5.6    -      -       -      +
    378A  VAL*     3.3    25.9    +      -       +      +
    379A  LEU*     3.9     3.1    -      -       -      +
    380A  PHE      3.2     0.6    -      -       -      -
    381A  VAL*     1.3    79.9    -      -       +      +
    383A  ALA*     1.3    61.3    +      -       -      +
    385A  LEU*     4.2     3.3    -      -       +      +
    386A  GLU*     2.8    31.8    +      -       -      +
    401A  ALA*     4.5    10.3    -      -       +      +
    402A  LEU*     4.1    14.1    -      -       +      -
    405A  ALA*     3.7    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 383 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348A  PHE*     5.0     3.1    -      -       +      -
    379A  LEU      3.0    17.4    +      -       -      +
    380A  PHE*     3.3    13.0    +      -       +      +
    382A  LEU*     1.3    78.2    -      -       -      +
    384A  GLY*     1.3    62.5    +      -       -      +
    386A  GLU*     3.4     7.0    +      -       -      +
    387A  ALA*     3.1    23.7    +      -       -      +
    402A  LEU*     4.1    23.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 384 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344A  LEU*     3.4    16.8    -      -       -      -
    348A  PHE*     3.9    21.9    -      -       -      -
    350A  ILE*     3.9     4.7    -      -       -      -
    380A  PHE      2.8    19.7    +      -       -      -
    383A  ALA*     1.3    73.1    -      -       -      +
    385A  LEU*     1.3    57.6    +      -       -      +
    387A  ALA*     3.3     1.9    +      -       -      +
    388A  VAL*     2.9    34.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 385 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    308A  ILE*     3.9    28.3    -      -       +      -
    311A  MET*     3.6    11.0    -      -       +      -
    313A  LEU*     4.2     7.9    -      -       +      -
    329A  VAL*     5.3     3.1    -      -       +      -
    340A  VAL*     3.9    24.7    -      -       +      -
    344A  LEU*     3.7    13.5    -      -       +      +
    352A  ILE*     4.2    18.4    -      -       +      -
    364A  TRP*     4.7     9.0    -      -       +      -
    366A  ILE*     4.3    15.3    -      -       +      -
    381A  VAL*     2.9    21.2    +      -       +      +
    382A  LEU*     4.2     2.7    -      -       -      +
    384A  GLY*     1.3    72.7    -      -       -      +
    386A  GLU*     1.3    65.5    +      -       -      +
    388A  VAL*     3.5     1.0    +      -       -      +
    389A  LEU*     3.0    46.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 386 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311A  MET*     3.4    21.4    -      -       +      +
    382A  LEU      2.8    20.0    +      -       -      +
    383A  ALA*     3.6     6.9    -      -       -      +
    385A  LEU*     1.3    76.5    -      -       -      +
    387A  ALA*     1.3    58.2    +      -       -      +
    389A  LEU*     3.2     1.6    +      -       -      -
    390A  LEU*     2.9    50.3    +      -       +      +
    396A  ILE*     3.8    10.4    -      -       +      +
    397A  GLU      4.6     0.3    -      -       -      +
    398A  ALA      2.0    36.9    -      -       -      +
    399A  GLY*     3.8     7.7    +      -       -      -
    401A  ALA*     3.9    16.5    -      -       +      +
    402A  LEU*     4.8     5.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 387 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348A  PHE*     3.8    23.8    -      -       +      -
    383A  ALA      3.1    15.3    +      -       -      +
    386A  GLU*     1.3    77.6    -      -       -      +
    388A  VAL*     1.3    58.3    +      -       -      +
    390A  LEU*     3.6    10.6    +      -       -      +
    391A  ARG*     2.9    27.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 388 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340A  VAL*     3.7    31.4    -      -       +      +
    343A  MET*     3.8    23.3    -      -       +      -
    344A  LEU*     3.9    17.0    -      -       +      +
    348A  PHE*     3.9    21.1    -      -       +      -
    384A  GLY      2.9    19.6    +      -       -      +
    385A  LEU      4.1     2.5    -      -       -      +
    387A  ALA*     1.3    73.2    -      -       -      +
    389A  LEU*     1.3    65.9    +      -       -      +
    391A  ARG*     3.1     6.0    +      -       -      +
    392A  HIS*     2.8    49.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 389 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311A  MET*     3.1    30.5    -      -       +      -
    313A  LEU*     3.8    20.2    -      -       +      -
    332A  PRO*     5.1     2.0    -      -       +      -
    335A  ILE*     4.2    19.7    -      -       +      -
    340A  VAL*     3.8    25.1    -      -       +      -
    364A  TRP*     3.8    17.3    -      -       +      -
    385A  LEU*     3.0    34.1    +      -       +      +
    386A  GLU      3.8     2.2    -      -       -      +
    388A  VAL*     1.3    75.7    -      -       -      +
    390A  LEU*     1.3    57.3    +      -       -      +
    392A  HIS*     3.0     5.6    +      -       +      +
    393A  ASN      3.0     9.0    +      -       -      -
    394A  ALA*     2.5    28.8    +      -       +      +
    396A  ILE*     4.0    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 390 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    386A  GLU*     2.9    45.2    +      -       +      +
    387A  ALA*     3.8     7.6    -      -       -      +
    389A  LEU*     1.3    75.5    -      -       -      +
    391A  ARG*     1.4    61.3    +      -       -      +
    393A  ASN*     3.0    16.5    +      -       -      -
    394A  ALA*     3.0    23.0    -      -       +      +
    396A  ILE*     3.8    31.2    -      -       +      +
    398A  ALA*     5.3     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 391 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  MET*     3.8    34.8    -      -       +      +
    387A  ALA      2.9    16.2    +      -       -      +
    388A  VAL*     3.1     8.9    +      -       -      +
    390A  LEU*     1.4    74.8    -      -       -      +
    392A  HIS*     1.3    59.3    +      -       +      +
    393A  ASN*     3.3     3.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 392 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334A  GLY      5.2     1.9    -      -       -      +
    335A  ILE*     4.4    19.1    -      -       +      +
    336A  ASP*     4.5     5.1    +      -       -      +
    339A  SER*     2.4    46.9    +      -       -      -
    340A  VAL*     3.7    16.5    -      -       +      +
    343A  MET*     3.6    25.1    -      -       +      +
    388A  VAL*     2.8    44.2    +      -       +      +
    389A  LEU*     3.0     8.0    +      -       -      +
    391A  ARG*     1.3    77.5    -      -       -      +
    393A  ASN*     1.3    71.6    +      -       -      +
    394A  ALA      3.8     0.2    +      -       -      -
----------------------------------------------------------
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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