Contacts of the helix formed by residues 89 - 101 (chain A) in PDB entry 5O67


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 ALA 89 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  PRO*     1.3    78.7    -      -       -      +
     90A  GLN*     1.3    65.2    +      -       -      +
     91A  SER*     3.9    10.3    -      -       -      +
     92A  VAL*     3.6    25.1    +      -       +      +
     93A  SER*     3.2    19.9    +      -       -      -
    329A  GLU*     3.3    22.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  PRO      4.6     0.2    -      -       -      -
     89A  ALA*     1.3    70.5    -      -       -      +
     91A  SER*     1.3    67.1    +      -       -      +
     92A  VAL      3.1     1.5    +      -       -      -
     93A  SER*     3.3     8.2    +      -       -      -
     94A  ASN*     3.1    35.5    +      -       -      +
    329A  GLU*     3.7    22.3    +      -       -      +
    330A  ARG*     4.3    10.7    -      -       -      -
    374A  ALA*     3.6    25.9    -      -       +      +
    376A  SER      3.3    24.3    +      -       -      +
    377A  GLU*     3.4    24.4    +      -       -      +
    379A  LEU      4.9     2.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  ALA*     3.9     9.9    -      -       -      +
     90A  GLN*     1.3    74.4    -      -       -      +
     92A  VAL*     1.3    58.3    +      -       -      +
     94A  ASN*     3.6     6.9    +      -       -      +
     95A  LEU*     3.1    28.2    +      -       -      +
    326A  ALA*     3.7    15.5    -      -       -      +
    328A  ASN      2.8    28.6    +      -       -      -
    329A  GLU      2.9    13.8    +      -       -      -
    330A  ARG*     4.4     6.7    -      -       -      +
    331A  MET      3.6    21.3    -      -       -      -
    332A  SER*     4.1     6.6    -      -       -      -
    372A  THR*     5.1     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  PRO*     5.1     7.4    -      -       +      -
     89A  ALA*     3.6    31.4    +      -       +      +
     90A  GLN      3.1     0.6    -      -       -      -
     91A  SER*     1.3    79.6    -      -       -      +
     93A  SER*     1.3    66.1    +      -       -      +
     95A  LEU*     3.2     6.7    +      -       -      +
     96A  TYR*     3.2    41.6    +      -       +      -
    276A  THR*     6.0     0.2    -      -       -      +
    326A  ALA*     4.4    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  PRO*     4.4    14.6    +      -       -      +
     89A  ALA      3.2    11.7    +      -       -      -
     90A  GLN*     3.3    13.2    +      -       -      -
     92A  VAL*     1.3    79.5    -      -       -      +
     94A  ASN*     1.3    60.6    +      -       -      +
     96A  TYR*     3.6     5.8    +      -       -      +
     97A  ASN*     3.1    38.2    +      -       -      +
    105A  ASN*     4.7    16.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  GLN*     3.1    29.8    +      -       -      +
     91A  SER*     4.0     1.4    -      -       -      +
     93A  SER*     1.3    79.2    -      -       -      +
     95A  LEU*     1.4    64.3    +      -       -      +
     97A  ASN*     3.3    13.3    +      -       -      +
     98A  GLU*     3.0    26.5    +      -       -      +
    330A  ARG      4.8     0.4    +      -       -      -
    372A  THR*     3.4    28.2    +      -       +      +
    374A  ALA*     4.2    16.4    -      -       -      +
    380A  THR*     3.7    34.2    +      -       +      +
    405A  TYR*     5.3     4.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  SER      3.1    17.7    +      -       -      +
     92A  VAL*     3.2     7.6    +      -       -      +
     94A  ASN*     1.4    73.7    -      -       -      +
     96A  TYR*     1.3    62.6    +      -       +      +
     98A  GLU*     3.4     3.7    +      -       -      +
     99A  ALA*     3.0    32.7    +      -       -      +
    281A  VAL*     5.4    10.5    -      -       +      -
    324A  ALA*     4.8    17.0    -      -       +      -
    325A  PHE      5.6     2.7    -      -       -      +
    326A  ALA*     5.9     1.6    -      -       +      +
    332A  SER*     4.2    18.8    -      -       -      +
    372A  THR*     4.5     1.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  VAL*     3.2    35.4    +      -       +      +
     93A  SER*     3.8     9.6    -      -       -      +
     95A  LEU*     1.3    81.0    -      -       +      +
     97A  ASN*     1.3    54.4    +      -       -      +
     99A  ALA*     4.5     3.6    -      -       -      -
    100A  SER*     2.6    46.6    +      -       -      +
    102A  PHE      5.8     0.2    -      -       -      +
    217A  GLU*     2.6    27.5    +      -       -      -
    223A  ASP*     4.0    21.3    -      -       +      -
    274A  VAL*     3.3    31.9    -      -       +      +
    276A  THR*     2.6    31.7    +      -       -      -
    281A  VAL*     4.3    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  SER*     3.1    26.5    +      -       -      +
     94A  ASN*     3.3    14.5    +      -       -      +
     96A  TYR*     1.3    78.4    -      -       -      +
     98A  GLU*     1.3    63.1    +      -       -      +
    101A  GLY*     3.1    23.7    +      -       -      -
    102A  PHE      3.1    25.1    +      -       -      +
    103A  ALA*     3.9    14.0    -      -       +      -
    104A  GLY*     3.5    10.7    -      -       -      +
    105A  ASN*     5.0     5.8    +      -       -      +
    405A  TYR*     3.6    21.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ASN      3.0    16.0    +      -       -      +
     95A  LEU*     3.9     4.9    -      -       -      +
     97A  ASN*     1.3    77.8    -      -       -      +
     99A  ALA*     1.3    63.5    +      -       -      +
    101A  GLY*     4.1     2.8    +      -       -      -
    334A  SER*     6.1     4.5    -      -       -      +
    372A  THR*     4.6     8.7    -      -       -      +
    382A  VAL*     3.7    26.3    -      -       +      +
    384A  ASN*     4.7    13.3    -      -       -      +
    401A  LYS*     3.1    31.5    +      -       -      -
    501A  LDA      4.2    10.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  LEU      3.0    19.1    +      -       -      +
     96A  TYR*     3.9     3.1    -      -       -      +
     98A  GLU*     1.3    79.7    -      -       -      +
    100A  SER*     1.3    57.9    +      -       -      +
    272A  SER*     4.5     1.4    +      -       -      -
    274A  VAL*     4.4    11.0    -      -       +      +
    281A  VAL*     6.0     1.6    -      -       +      -
    283A  PHE*     3.9    48.5    -      -       +      +
    284A  GLY      5.7     0.7    -      -       -      +
    501A  LDA      3.3    22.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  TYR*     2.6    33.1    +      -       -      +
     99A  ALA*     1.3    73.2    -      -       -      +
    101A  GLY*     1.3    61.6    +      -       -      +
    102A  PHE*     3.3    26.6    +      -       -      +
    213A  LYS*     6.1     0.6    -      -       -      -
    223A  ASP*     5.7     4.5    -      -       -      -
    225A  VAL*     4.8    11.5    -      -       -      +
    272A  SER*     3.4    32.7    +      -       -      -
    274A  VAL*     4.0    12.6    -      -       -      -
    501A  LDA      4.1    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  ASN      3.1    14.9    +      -       -      -
     98A  GLU      4.8     0.2    -      -       -      -
     99A  ALA      3.5     2.2    +      -       -      -
    100A  SER*     1.3    76.8    -      -       -      +
    102A  PHE*     1.3    58.1    +      -       -      +
    103A  ALA      4.1     1.0    +      -       -      -
    157A  ARG*     4.9     8.8    +      -       -      -
    165A  GLN*     3.3    18.4    +      -       -      -
    225A  VAL*     6.2     0.2    -      -       -      -
    501A  LDA      4.0    19.5    -      -       -      -
----------------------------------------------------------
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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