Contacts of the helix formed by residues 982 - 995 (chain A) in PDB entry 5IYB


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 ASN 982 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    902A  GLU*     2.8    40.2    +      -       -      +
    903A  PHE      4.9     3.2    +      -       -      -
    904A  GLN*     3.8    23.2    -      -       -      +
    980A  PRO      3.9     0.2    -      -       -      -
    981A  CYS*     1.3    67.4    -      -       -      +
    983A  LEU*     1.3    60.5    +      -       -      +
    984A  LEU*     3.5    16.8    +      -       -      +
    985A  ARG*     3.3    35.2    +      -       -      +
    986A  MET*     2.8    35.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 983 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    904A  GLN*     3.6     5.4    +      -       -      +
    981A  CYS*     2.9    21.5    +      -       +      +
    982A  ASN*     1.3    71.2    +      -       -      +
    984A  LEU*     1.3    61.5    +      -       -      +
    986A  MET*     3.9     3.7    -      -       -      +
    987A  ILE*     2.9    37.1    +      -       +      +
   1041A  PHE*     4.8     6.3    -      -       +      -
   1044A  HIS*     3.7    34.1    -      -       +      +
   1045A  LEU*     3.6    32.8    -      -       +      -
   1048A  THR*     4.3    17.0    -      -       +      +
   1049A  LEU*     4.5     5.8    -      -       +      -
   1068A  LEU*     6.3     0.2    -      -       -      -
   1072A  ILE*     3.7    40.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 984 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    904A  GLN*     5.0     2.0    +      -       -      +
    905A  ASN*     5.8    10.5    -      -       +      +
    982A  ASN*     3.4     8.4    +      -       -      +
    983A  LEU*     1.3    77.8    -      -       -      +
    985A  ARG*     1.3    57.4    +      -       -      +
    987A  ILE*     3.4     4.7    +      -       -      +
    988A  TRP*     2.8    31.7    +      -       -      +
   1044A  HIS*     6.3     3.4    -      -       +      +
   1048A  THR*     4.1    21.8    -      -       +      -
   1053A  ARG*     5.0     5.6    -      -       -      +
   1058A  PHE*     4.2    20.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 985 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    601A  ASN*     4.8    16.8    -      -       +      +
    602A  CYS*     5.2     1.1    -      -       -      +
    655A  ILE*     3.7    44.4    +      -       -      +
    658A  LEU*     4.3    16.2    -      -       -      +
    659A  GLU*     2.9    33.1    +      -       -      +
    902A  GLU*     3.0    26.3    +      -       -      -
    982A  ASN*     3.3    34.5    +      -       -      +
    984A  LEU*     1.3    76.2    -      -       -      +
    986A  MET*     1.3    62.3    +      -       -      +
    988A  TRP*     3.6     7.7    -      -       +      +
    989A  ASN*     2.7    45.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 986 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    659A  GLU*     5.3     5.4    -      -       -      +
    981A  CYS*     4.1    26.5    -      -       +      +
    982A  ASN*     2.8    26.9    +      -       +      +
    983A  LEU*     3.9     5.2    -      -       -      +
    985A  ARG*     1.3    80.0    -      -       -      +
    987A  ILE*     1.3    59.4    +      -       -      +
    989A  ASN*     3.0    16.6    +      -       -      +
    990A  ALA*     2.8    28.2    +      -       -      +
   1067A  TRP*     4.2     2.6    -      -       +      -
   1068A  LEU*     3.9    17.3    -      -       +      +
   1071A  GLU*     3.9    21.8    -      -       +      +
   1072A  ILE*     4.3    17.9    -      -       +      -
   1075A  LYS*     3.7    42.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 987 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    983A  LEU*     2.9    28.6    +      -       -      +
    984A  LEU*     3.7     5.2    -      -       -      +
    986A  MET*     1.3    72.5    -      -       -      +
    988A  TRP*     1.3    63.9    +      -       -      +
    990A  ALA*     3.2     6.2    +      -       -      +
    991A  GLN*     3.2    24.0    +      -       +      +
   1048A  THR*     4.1     7.0    -      -       +      -
   1049A  LEU*     3.8    23.8    -      -       +      -
   1054A  MET*     4.1     2.7    -      -       +      -
   1058A  PHE*     3.4    64.2    -      -       +      -
   1060A  LEU*     4.1     8.5    -      -       +      -
   1068A  LEU*     3.9    26.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 988 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    601A  ASN*     3.0    48.2    -      -       +      -
    603A  ILE*     3.1    35.6    -      -       +      +
    629A  VAL*     6.2     1.3    -      -       +      -
    630A  VAL      3.9     4.9    -      -       -      -
    631A  GLU*     3.2    51.6    -      -       +      -
    984A  LEU      2.8    18.2    +      -       -      +
    985A  ARG*     3.6     8.5    -      -       +      +
    987A  ILE*     1.3    79.5    -      -       -      +
    989A  ASN*     1.3    60.4    +      -       -      +
    991A  GLN*     3.5    21.6    +      -       -      +
    992A  LYS*     3.2    24.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 989 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    599A  HIS*     5.7     4.0    -      -       +      -
    601A  ASN*     2.2    47.7    +      -       -      +
    659A  GLU*     2.8    30.0    +      -       -      +
    985A  ARG*     2.7    34.0    +      -       -      +
    986A  MET*     3.0    21.4    +      -       -      +
    988A  TRP*     1.3    71.8    -      -       -      +
    990A  ALA*     1.3    61.8    +      -       -      +
    992A  LYS*     3.5     3.1    +      -       -      +
    993A  ILE*     3.2    30.9    +      -       +      +
   1067A  TRP*     4.4    15.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 990 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    986A  MET      2.8    14.9    +      -       -      +
    987A  ILE*     3.5     9.2    -      -       -      +
    989A  ASN*     1.3    70.8    -      -       -      +
    991A  GLN*     1.3    64.9    +      -       -      +
    993A  ILE*     3.4     0.4    +      -       -      -
    994A  PHE*     3.2    35.9    +      -       +      +
   1060A  LEU*     3.8    24.9    -      -       +      -
   1064A  ALA*     4.4     9.6    -      -       +      +
   1067A  TRP*     4.0    24.3    -      -       +      -
   1068A  LEU*     4.7     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 991 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    987A  ILE*     3.2     9.2    +      -       -      +
    988A  TRP*     3.8    27.9    +      -       -      +
    989A  ASN      3.4     0.2    -      -       -      -
    990A  ALA*     1.3    78.4    -      -       -      +
    992A  LYS*     1.3    61.4    +      -       -      +
    995A  HIS*     3.2    17.8    +      -       -      -
    996A  ILE*     3.3    28.7    +      -       +      +
    998A  PRO*     5.5     8.7    -      -       -      +
   1057A  GLU      4.2     5.1    +      -       -      -
   1058A  PHE*     2.7    38.0    +      -       -      +
   1059A  ARG*     4.8     2.8    -      -       -      +
   1060A  LEU*     3.5    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 992 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    598A  GLY      4.5     0.8    +      -       -      -
    599A  HIS*     2.9    51.6    +      -       -      +
    601A  ASN*     3.3    24.3    +      -       -      +
    631A  GLU*     5.2     5.8    -      -       +      +
    632A  ASN*     3.3    40.9    +      -       +      +
    988A  TRP*     3.2    20.6    +      -       +      +
    989A  ASN*     3.7     8.5    -      -       -      +
    990A  ALA      3.2     0.2    -      -       -      -
    991A  GLN*     1.3    79.7    -      -       -      +
    993A  ILE*     1.3    77.2    +      -       -      +
    995A  HIS*     3.0    26.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 993 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    599A  HIS*     4.1    22.9    -      -       +      +
    989A  ASN*     3.2    18.4    +      -       +      +
    990A  ALA      3.4     0.2    +      -       -      -
    992A  LYS*     1.3    88.6    -      -       -      +
    994A  PHE*     1.3    80.4    +      -       +      +
    995A  HIS*     3.1    24.0    +      -       -      -
   1067A  TRP*     4.1    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 994 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    990A  ALA      3.2    20.5    +      -       -      +
    993A  ILE*     1.3    92.2    -      -       +      +
    995A  HIS*     1.3    71.0    +      -       -      +
    996A  ILE*     3.6    23.4    +      -       +      +
   1061A  SER*     4.6     1.6    -      -       -      -
   1063A  GLU*     3.9    25.1    -      -       +      -
   1064A  ALA*     3.6    41.1    -      -       +      -
   1067A  TRP*     3.6    41.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with HIS 995 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    632A  ASN*     6.0     2.9    -      -       -      -
    991A  GLN      3.2     7.9    +      -       -      -
    992A  LYS      3.0    18.3    +      -       -      -
    993A  ILE*     3.1    15.9    +      -       -      -
    994A  PHE*     1.3    80.7    -      -       -      +
    996A  ILE*     1.3    62.6    +      -       -      +
    997A  ASN*     3.5     3.5    +      -       -      +
    138H  ASP*     5.4    10.6    +      -       -      -
----------------------------------------------------------
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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