Contacts of the helix formed by residues 99 - 114 (chain B) in PDB entry 1SA4


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 SER 99 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  ALA*     6.1     1.2    -      -       -      +
     96B  LEU*     2.9    25.0    +      -       -      +
     98B  ALA*     1.3    83.0    +      -       -      +
    100B  ARG*     1.3    64.7    +      -       -      +
    101B  PRO*     3.3     5.6    -      -       -      -
    102B  TRP*     3.1    43.0    +      -       -      +
    103B  LEU*     3.3     8.4    +      -       -      +
    106B  TRP*     5.4     0.4    -      -       -      -
    142B  GLY*     4.2     0.9    -      -       -      -
    152B  PRO*     5.5     0.9    -      -       -      -
    441B  JAN      3.8    17.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  GLN*     3.1    22.4    -      -       -      +
     82A  ASP*     2.8    35.1    +      -       -      +
     87A  VAL      3.1    24.4    +      -       -      -
     88A  VAL*     3.1    22.7    +      -       +      +
     89A  GLN*     3.8     7.1    -      -       -      +
     90A  ILE*     4.3    10.5    -      -       +      +
     92A  TYR*     3.8     3.1    +      -       -      -
     96B  LEU      3.8    12.8    -      -       -      +
     97B  ASP*     4.0    21.1    -      -       -      +
     99B  SER*     1.3    74.5    -      -       -      +
    101B  PRO*     1.3    71.1    -      -       +      +
    103B  LEU*     3.0    22.5    +      -       +      +
    104B  CYS*     3.1    14.7    +      -       -      -
    129B  PHE*     3.3    37.3    -      -       +      -
    142B  GLY      3.0    12.0    +      -       -      +
    143B  GLY*     4.8     1.8    -      -       -      -
    144B  PRO*     3.8     4.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  SER      3.6     2.9    -      -       -      -
    100B  ARG*     1.3    91.9    -      -       +      +
    102B  TRP*     1.3    60.9    +      -       -      +
    104B  CYS*     3.2     4.9    +      -       +      +
    105B  TYR*     3.0    19.6    +      -       -      +
    130B  LEU*     4.1    22.2    -      -       +      -
    133B  CYS*     4.1    16.4    -      -       +      -
    140B  PHE*     5.2     0.4    -      -       +      -
    141B  GLY      3.3    19.3    -      -       -      +
    142B  GLY*     3.3    19.3    -      -       -      +
    152B  PRO*     3.6    27.8    -      -       +      +
    155B  ALA*     3.6    10.0    -      -       +      +
    156B  ALA*     4.2     6.7    -      -       +      +
    159B  ALA*     5.1     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  SER*     3.1    36.3    +      -       -      +
    100B  ARG      3.1     0.2    -      -       -      -
    101B  PRO*     1.3    80.2    -      -       -      +
    103B  LEU*     1.3    56.0    +      -       -      +
    105B  TYR*     3.2     9.9    +      +       -      +
    106B  TRP*     2.8    81.1    +      +       +      -
    151B  ALA*     3.5    41.4    -      -       +      +
    152B  PRO*     4.7     9.0    -      -       +      -
    154B  TYR*     3.5    34.5    -      +       -      -
    155B  ALA*     3.7    11.4    -      -       +      +
    206B  CYS*     5.6     0.2    -      -       -      -
    303B  TRP*     5.7     0.2    -      +       -      -
    365B  TYR*     3.9    12.3    -      -       -      -
    440B  FPP      4.0    25.4    -      -       +      -
    441B  JAN      3.7    23.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with LEU 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  VAL*     3.7    19.7    -      -       +      +
     90A  ILE*     5.3     2.7    -      -       +      -
     89B  LEU*     3.6    26.0    -      -       +      -
     93B  TYR*     4.2     4.3    -      -       +      -
     96B  LEU*     4.1    32.3    -      -       +      -
     99B  SER      3.3     6.5    +      -       -      +
    100B  ARG*     3.0    27.0    +      -       +      +
    102B  TRP*     1.3    79.8    -      -       -      +
    104B  CYS*     1.3    62.8    +      -       -      +
    106B  TRP*     4.0    17.9    -      -       +      -
    107B  ILE*     3.0    32.5    +      -       +      +
    360B  PHE*     3.9    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 104 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  VAL*     4.3     4.5    -      -       -      -
     88A  VAL*     3.9    17.7    -      -       -      -
     86B  LEU*     4.7     6.7    -      -       -      -
    100B  ARG      3.1    15.9    +      -       -      -
    101B  PRO*     3.2     9.2    +      -       +      +
    103B  LEU*     1.3    76.3    -      -       -      +
    105B  TYR*     1.3    57.1    +      -       -      +
    107B  ILE*     4.1     0.5    -      -       -      +
    108B  LEU*     2.9    37.6    +      -       +      +
    126B  VAL*     4.3    20.4    -      -       +      -
    129B  PHE*     3.9    28.0    -      -       -      -
    130B  LEU*     4.2     8.3    -      -       +      -
    159B  ALA*     4.4    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  PRO      3.0    10.2    +      -       -      +
    102B  TRP*     3.7    20.4    -      +       -      +
    104B  CYS*     1.3    74.0    -      -       -      +
    106B  TRP*     1.3    77.1    +      +       -      +
    108B  LEU*     4.7     0.4    -      -       -      -
    109B  HIS*     2.8    51.0    +      +       +      +
    154B  TYR*     4.3     5.0    +      +       -      -
    155B  ALA*     3.6    22.9    -      -       +      +
    158B  ASN*     3.5    38.8    +      -       +      -
    159B  ALA*     4.1     8.9    -      -       -      +
    162B  ILE*     3.9     8.1    -      -       +      -
    364B  CYS*     4.2     3.1    -      -       -      -
    365B  TYR*     3.6    20.5    +      -       -      -
    402B  ASN*     2.7    49.1    +      -       -      +
    403B  ILE*     4.0     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  LEU*     5.3     0.4    -      -       -      -
     96B  LEU*     4.7     4.5    -      -       +      -
     99B  SER*     5.1     0.9    -      -       -      -
    102B  TRP*     2.8    63.5    +      +       +      +
    103B  LEU*     4.0    25.1    -      -       +      +
    105B  TYR*     1.3    87.1    -      +       -      +
    107B  ILE*     1.3    58.5    +      -       -      +
    109B  HIS      4.1     0.2    -      -       -      -
    110B  SER*     2.7    33.7    +      -       -      -
    360B  PHE*     3.5    20.2    -      -       +      +
    361B  TYR*     3.6    22.4    -      +       +      -
    364B  CYS*     3.7    23.2    -      -       +      +
    365B  TYR*     3.4    19.3    +      +       -      -
    441B  JAN      3.5    63.9    -      +       +      -
----------------------------------------------------------
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Residues in contact with ILE 107 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  VAL*     4.4     4.9    -      -       +      -
     82B  LEU*     3.6    28.0    -      -       +      +
     85B  GLY      3.5    31.6    -      -       -      +
     86B  LEU*     3.6    22.7    -      -       +      +
    103B  LEU*     3.0    25.0    +      -       +      +
    104B  CYS      4.1     1.1    -      -       -      +
    106B  TRP*     1.3    74.1    -      -       -      +
    108B  LEU*     1.3    65.3    +      -       -      +
    110B  SER*     3.3     3.3    +      -       -      -
    111B  LEU*     3.0    34.7    +      -       +      +
    360B  PHE*     3.7    40.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 108 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86B  LEU*     4.2    24.9    -      -       +      -
    104B  CYS*     2.9    25.5    +      -       +      +
    105B  TYR*     4.0     1.6    -      -       -      +
    107B  ILE*     1.3    76.0    -      -       -      +
    109B  HIS*     1.3    58.6    +      -       -      +
    111B  LEU*     3.4     5.6    +      -       +      +
    112B  GLU*     2.9    29.6    +      -       -      +
    118B  ILE*     3.9    36.1    -      -       +      +
    126B  VAL*     4.1    23.3    -      -       +      -
    159B  ALA*     4.1    30.1    -      -       +      +
    162B  ILE*     4.1    18.2    -      -       +      +
    163B  ILE*     4.1    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 109 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105B  TYR*     2.8    24.9    +      -       +      +
    106B  TRP      4.1     2.5    -      -       -      +
    108B  LEU*     1.3    74.6    -      -       -      +
    110B  SER*     1.3    61.5    +      -       -      +
    112B  GLU*     2.7    27.7    +      -       -      +
    113B  LEU*     2.8    54.0    +      -       +      +
    162B  ILE*     3.7    12.9    -      -       +      +
    364B  CYS*     3.8    16.2    -      -       -      -
    368B  SER*     3.1    20.6    +      -       -      -
    397B  THR*     3.2    16.3    +      -       -      -
    402B  ASN*     2.9    45.1    +      -       -      -
    403B  ILE*     3.6     3.9    -      -       -      -
    404B  GLY      4.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 110 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  LEU*     3.6    29.0    -      -       -      +
    106B  TRP      2.7    22.0    +      -       -      -
    107B  ILE      3.6     0.7    -      -       -      -
    109B  HIS*     1.3    76.7    -      -       -      +
    111B  LEU*     1.3    62.8    +      -       -      +
    113B  LEU*     3.2     7.3    +      -       -      +
    114B  LEU*     3.0    28.2    +      -       -      +
    360B  PHE      4.8     0.2    +      -       -      -
    363B  THR*     3.8     4.5    -      -       -      +
    364B  CYS*     3.3    25.1    +      -       -      -
    367B  LEU*     3.9    14.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 111 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  PHE*     3.7    33.4    -      -       +      +
     82B  LEU*     3.9    25.6    -      -       +      -
     83B  LYS*     4.8     3.6    -      -       -      +
     86B  LEU*     4.3    13.9    -      -       +      -
    107B  ILE*     3.0    36.7    +      -       +      +
    108B  LEU*     3.6     5.4    -      -       -      +
    110B  SER*     1.3    75.6    -      -       -      +
    112B  GLU*     1.3    62.2    +      -       -      +
    114B  LEU*     3.2     3.5    +      -       -      -
    115B  ASP      3.0     4.5    +      -       -      -
    116B  GLU*     2.9    38.7    +      -       +      +
    117B  PRO      6.0     0.2    -      -       -      +
    118B  ILE*     3.7    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 112 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108B  LEU      2.9    16.4    +      -       -      +
    109B  HIS*     2.7    30.7    +      -       +      +
    111B  LEU*     1.3    77.3    -      -       -      +
    113B  LEU*     1.3    64.1    +      -       +      +
    115B  ASP*     3.0    12.5    +      -       -      +
    116B  GLU      5.0     2.9    -      -       -      +
    118B  ILE*     5.3     2.6    -      -       +      +
    162B  ILE*     3.7    25.8    -      -       +      +
    395B  GLN*     3.5    16.9    -      -       +      +
    396B  PRO      5.8     0.7    -      -       -      +
    404B  GLY*     2.9    31.3    +      -       -      -
    406B  ASP*     4.4     0.9    -      -       -      +
    407B  LYS*     3.2    27.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 113 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B  ARG*     5.0     0.2    +      -       -      -
    109B  HIS*     2.8    44.3    +      -       +      +
    110B  SER*     3.2     6.7    +      -       -      +
    112B  GLU*     1.3    77.6    -      -       +      +
    114B  LEU*     1.3    57.1    +      -       -      +
    115B  ASP*     3.1     4.0    +      -       -      +
    364B  CYS      4.2     2.0    -      -       -      +
    367B  LEU*     3.7    14.8    -      -       +      -
    368B  SER*     3.5    40.4    -      -       -      +
    371B  SER*     4.1     8.5    -      -       -      -
    394B  LEU*     3.5    18.6    -      -       +      +
    395B  GLN*     3.0    48.9    +      -       +      +
    396B  PRO      4.4     2.9    -      -       -      +
    397B  THR*     4.0    14.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73B  LEU*     4.0    13.5    -      -       +      -
     75B  ARG*     3.1    42.2    +      -       +      +
     78B  HIS*     4.0    17.7    -      -       +      -
     79B  PHE*     4.4     8.5    -      -       -      +
     82B  LEU*     3.7    25.6    -      -       +      -
    110B  SER      3.0    19.8    +      -       -      +
    111B  LEU*     3.7     4.9    -      -       -      +
    112B  GLU      3.2     0.2    -      -       -      -
    113B  LEU*     1.3    74.7    -      -       -      +
    115B  ASP*     1.3    71.0    +      -       -      +
    116B  GLU*     3.2    17.8    +      -       +      +
    367B  LEU*     4.3    15.0    -      -       +      -
    394B  LEU*     3.7    20.6    -      -       +      -
----------------------------------------------------------
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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