Contacts of the helix formed by residues 92 - 105 (chain L) in PDB entry 5DST


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 92 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88L  GLU      3.2    12.3    +      -       -      +
     89L  MET      3.3    12.3    -      -       -      +
     90L  LEU      3.1     2.1    -      -       -      -
     91L  LYS*     1.3    73.5    -      -       -      +
     93L  GLU*     1.3    56.3    +      -       -      +
     94L  VAL*     3.2    12.1    +      -       -      +
     95L  ARG*     3.1    25.0    +      -       +      +
     96L  THR*     3.0    30.0    +      -       -      -
    332L  TYR*     4.0    10.3    -      -       +      +
    333L  THR*     3.5    13.0    -      -       -      -
    334L  HIS*     2.9    48.1    +      -       +      +
    335L  TRP*     3.9     0.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 93 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243K  TYR*     3.4    23.6    -      -       +      +
     91L  LYS*     2.8    17.4    +      -       -      +
     92L  ASP*     1.3    68.8    +      -       -      +
     94L  VAL*     1.3    60.7    +      -       +      +
     97L  LEU*     2.7    56.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 94 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92L  ASP*     3.2     7.9    +      -       -      +
     93L  GLU*     1.3    78.4    -      -       +      +
     95L  ARG*     1.3    65.0    +      -       -      +
     97L  LEU*     4.6     1.1    -      -       -      +
     98L  THR*     2.8    30.0    +      -       -      +
    324L  PHE*     3.5    31.2    -      -       +      -
    325L  SER      5.1     2.0    -      -       -      +
    331L  PRO*     4.4    24.0    -      -       +      +
    332L  TYR      3.6    20.6    -      -       -      +
    333L  THR*     4.1    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 95 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89L  MET*     2.9    38.1    +      -       -      +
     90L  LEU*     4.0     8.7    -      -       -      +
     92L  ASP*     3.1    19.3    +      -       -      +
     94L  VAL*     1.3    84.2    -      -       -      +
     96L  THR*     1.3    86.1    +      -       -      +
     98L  THR*     3.6     1.9    -      -       -      -
     99L  TYR*     3.0    40.5    +      -       +      -
    124L  ILE*     4.7     1.6    -      -       -      +
    125L  LEU*     5.5     2.1    -      -       -      +
    185L  GLU*     3.0    25.8    +      -       -      +
    324L  PHE*     4.4    11.4    -      -       +      -
    334L  HIS*     3.6    15.5    -      -       -      -
    335L  TRP*     3.5    33.9    -      -       +      -
    401L  SAH      2.9    37.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 96 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243K  TYR*     3.3    42.0    -      -       +      -
     89L  MET      3.1    17.2    +      -       -      -
     90L  LEU*     3.3     5.9    +      -       +      -
     92L  ASP      3.0    11.2    +      -       -      -
     95L  ARG*     1.3    92.1    +      -       -      +
     97L  LEU*     1.3    64.4    +      -       -      +
     99L  TYR*     3.2     7.5    +      -       -      +
    100L  ARG*     2.9    20.8    +      -       -      +
    124L  ILE*     4.5     7.4    -      -       +      -
    125L  LEU*     5.6     1.3    -      -       +      -
    128L  PHE*     3.8    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 97 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243K  TYR*     3.7    25.1    -      -       +      -
     93L  GLU*     2.7    46.3    +      -       +      +
     94L  VAL*     4.6     1.1    -      -       -      +
     96L  THR*     1.3    73.5    -      -       -      +
     98L  THR*     1.3    55.7    +      -       -      +
    100L  ARG*     3.5    38.5    -      -       -      +
    101L  ASN*     2.8    41.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 98 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94L  VAL*     2.8    25.3    +      -       -      +
     95L  ARG      3.6     3.4    -      -       -      -
     97L  LEU*     1.3    79.7    -      -       -      +
     99L  TYR*     1.3    64.2    +      -       -      +
    101L  ASN*     3.7     5.3    -      -       -      +
    102L  SER*     2.9    22.4    +      -       -      -
    315L  PHE*     3.5    30.5    -      -       +      -
    322L  MET*     3.9    11.3    -      -       +      +
    323L  GLY      3.9    23.5    +      -       -      +
    324L  PHE*     3.9    18.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 99 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95L  ARG*     3.0    37.9    +      -       +      +
     96L  THR*     3.2     9.2    +      -       -      +
     98L  THR*     1.3    76.2    -      -       -      +
    100L  ARG*     1.3    60.5    +      -       -      +
    102L  SER*     2.6    23.0    +      -       -      -
    103L  MET*     3.4    21.1    -      -       +      +
    125L  LEU*     3.8    34.1    -      -       +      -
    128L  PHE*     4.3     1.6    -      -       -      -
    183L  ILE*     5.5     0.4    -      -       +      -
    184L  SER      2.6    35.6    +      -       -      -
    185L  GLU*     3.2    23.9    -      -       +      +
    187L  MET*     3.4    18.3    -      -       +      +
    215L  PHE*     4.1     7.4    -      -       +      -
    216L  PRO*     3.4     9.2    -      -       -      +
    315L  PHE*     4.0    31.4    -      +       -      -
    324L  PHE*     4.6     6.1    -      +       -      -
----------------------------------------------------------
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Residues in contact with ARG 100 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243K  TYR*     4.3    24.9    +      -       -      +
     96L  THR      2.9    12.4    +      -       -      +
     97L  LEU*     3.5    31.1    -      -       +      +
     99L  TYR*     1.3    77.9    -      -       -      +
    101L  ASN*     1.3    75.2    +      -       -      +
    103L  MET*     3.1     3.3    +      -       -      +
    104L  TYR*     2.9    61.4    +      -       +      +
    128L  PHE*     3.5    49.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 101 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97L  LEU*     2.8    27.1    +      -       -      +
     98L  THR*     4.6     0.9    -      -       -      -
    100L  ARG*     1.3   102.4    -      -       -      +
    102L  SER*     1.3    63.6    +      -       -      +
    104L  TYR*     4.6     1.4    -      -       -      +
    105L  HIS*     2.9    64.6    +      -       +      +
    322L  MET*     3.7    24.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 102 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98L  THR      2.9    15.9    +      -       -      -
     99L  TYR*     2.6    22.7    +      -       -      -
    101L  ASN*     1.3    76.4    -      -       -      +
    103L  MET*     1.3    65.9    +      -       -      +
    106L  ASN*     2.9    21.2    -      -       -      +
    215L  PHE*     3.4    24.5    -      -       -      -
    315L  PHE*     3.8    28.3    -      -       -      -
    318L  CYS*     3.7    10.3    -      -       -      -
    322L  MET*     3.6    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 103 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99L  TYR*     3.4    20.2    -      -       +      +
    100L  ARG      3.1     4.4    +      -       -      +
    101L  ASN      3.0     0.2    -      -       -      -
    102L  SER*     1.3    86.7    -      -       -      +
    104L  TYR*     1.3    62.2    -      -       +      +
    105L  HIS      3.3     1.1    -      -       -      -
    106L  ASN      2.8    32.9    +      -       -      +
    107L  LYS*     3.2     4.3    +      -       -      -
    110L  PHE*     3.6    30.7    -      -       +      -
    125L  LEU*     3.9    17.0    -      -       +      +
    128L  PHE*     3.8    11.9    -      -       +      -
    129L  ALA*     3.6    31.6    -      -       -      -
    132L  ALA*     3.9    14.5    -      -       +      +
    183L  ILE*     3.9    31.9    -      -       +      -
    215L  PHE*     4.6     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 104 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243K  TYR      4.8     1.9    +      -       -      -
    245K  PHE*     3.5    29.1    -      -       -      -
    100L  ARG*     2.9    52.7    +      -       +      +
    101L  ASN*     4.6     1.1    -      -       -      +
    103L  MET*     1.3    79.3    -      -       +      +
    105L  HIS*     1.3    62.3    +      -       +      +
    106L  ASN      3.4     0.7    +      -       -      -
    107L  LYS*     3.1    32.5    +      -       -      +
    128L  PHE*     3.3    37.9    -      -       -      -
    131L  LYS*     3.5    19.3    -      -       +      +
    132L  ALA*     4.5     5.2    -      -       +      -
    345N  TYR*     2.7    24.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 105 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101L  ASN*     2.9    56.4    +      -       +      +
    104L  TYR*     1.3    81.8    -      -       +      +
    106L  ASN*     1.3    61.6    +      -       -      +
    107L  LYS      3.8     0.9    -      -       -      -
    108L  HIS*     4.8     0.9    +      -       -      -
    322L  MET*     4.7    10.3    -      -       +      +
    229N  ARG*     4.9    22.8    +      -       -      -
    303N  TYR*     2.5    49.7    +      +       +      +
    345N  TYR*     3.7    12.8    +      +       -      -
    347N  THR*     5.2     0.5    +      -       -      +
----------------------------------------------------------
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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