Contacts of the helix formed by residues 28 - 37 (chain S) in PDB entry 6Y5D


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 VAL 28 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18S  ARG*     3.6    43.3    -      -       +      +
     19S  SER*     3.7    12.6    +      -       -      +
     22S  ALA*     4.2     4.0    -      -       +      -
     24S  LEU*     4.1    24.2    -      -       +      -
     26S  PHE      4.1     0.4    -      -       -      +
     27S  PRO*     1.3    76.5    -      -       -      +
     29S  GLY*     1.3    63.6    +      -       -      +
     30S  ARG      3.1     1.6    -      -       -      -
     31S  VAL*     3.1     5.7    +      -       -      +
     32S  HIS*     2.9    25.1    +      -       -      +
     49S  PRO*     3.6    14.9    -      -       +      +
     50S  VAL*     3.6    28.9    -      -       +      +
     53S  ALA*     4.2     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 29 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18S  ARG*     3.7    28.7    -      -       -      +
     28S  VAL*     1.3    78.6    -      -       -      +
     30S  ARG*     1.3    56.3    +      -       -      +
     32S  HIS*     3.3     3.3    +      -       -      +
     33S  ARG*     3.0    27.9    +      -       -      +
     33V    G      5.2    11.2    +      -       -      -
     34V    A      4.4     9.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 30 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27S  PRO*     3.8    25.5    -      -       +      +
     28S  VAL      3.1     0.6    -      -       -      +
     29S  GLY*     1.3    74.3    -      -       -      +
     31S  VAL*     1.3    60.3    +      -       -      +
     33S  ARG*     3.2    24.3    +      -       -      +
     34S  LEU*     2.8    41.8    +      -       +      +
     36T  GLU*     3.9    23.5    +      -       -      +
     37T  SER*     2.6    34.8    +      -       -      +
     38T  TYR*     4.0    20.6    -      -       -      +
     40T  VAL*     5.9     0.2    -      -       -      +
     41T  TYR*     3.5    29.3    +      -       -      -
    125U    G      4.9     4.4    +      -       -      -
    126U    C      3.3    24.5    +      -       -      -
     33V    G      4.7    11.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 31 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26S  PHE*     5.7     0.2    -      -       +      -
     27S  PRO*     3.1    26.5    -      -       +      +
     28S  VAL      3.1     8.1    +      -       -      +
     30S  ARG*     1.3    77.0    -      -       -      +
     32S  HIS*     1.3    54.2    +      -       -      +
     34S  LEU*     3.1     7.7    +      -       +      +
     35S  LEU*     2.7    34.4    +      -       +      +
     49S  PRO*     3.5    26.0    -      -       +      +
     52S  MET*     3.5    31.2    -      -       +      -
     53S  ALA*     4.3     8.7    -      -       +      -
     56S  LEU*     4.5    12.8    -      -       +      -
     38T  TYR*     4.5    15.0    -      -       +      +
     71T  PHE*     4.4     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 32 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18S  ARG*     3.0    33.9    +      -       -      +
     28S  VAL      2.9     6.0    +      -       -      +
     29S  GLY      3.4     9.4    -      -       -      +
     31S  VAL*     1.3    75.3    -      -       -      +
     33S  ARG*     1.3    62.9    +      -       -      +
     35S  LEU*     3.2     2.7    +      -       -      +
     36S  ARG*     3.1    49.7    +      -       -      +
     44S  VAL*     3.1    40.3    +      -       +      +
     45S  GLY      4.1     3.1    +      -       -      -
     46S  ALA*     4.7     8.7    -      -       +      -
     49S  PRO*     3.3    32.0    -      -       +      +
    116U    A      4.8     4.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 33 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29S  GLY      3.0    14.2    +      -       -      +
     30S  ARG*     3.3    25.0    +      -       -      +
     32S  HIS*     1.3    77.4    -      -       -      +
     34S  LEU*     1.3    67.0    +      -       -      +
     36S  ARG*     3.1    21.7    -      -       -      +
     37S  LYS*     3.0    65.1    +      -       -      +
     36T  GLU*     2.8    33.1    +      -       -      -
     32V    G      4.7     5.9    -      -       -      -
     33V    G      3.9    30.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 34 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30S  ARG*     2.8    31.9    +      -       +      +
     31S  VAL*     3.6     4.3    -      -       -      +
     33S  ARG*     1.3    88.8    -      -       -      +
     35S  LEU*     1.3    60.4    +      -       -      +
     37S  LYS*     2.8    49.4    -      -       -      +
     40S  TYR*     3.6     6.1    -      -       -      -
     38T  TYR*     2.9    32.1    -      -       +      +
     68T  ASN*     5.4     2.7    -      -       -      +
     71T  PHE*     3.4    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 35 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31S  VAL*     2.7    22.7    +      -       +      +
     32S  HIS      3.2     4.2    +      -       -      +
     34S  LEU*     1.3    72.7    -      -       -      +
     36S  ARG*     1.3    62.2    +      -       -      +
     37S  LYS      3.1     7.3    -      -       -      +
     40S  TYR*     3.3    22.6    +      -       +      +
     41S  ALA      4.3     1.0    +      -       -      -
     44S  VAL*     3.8    26.4    -      -       +      +
     48S  ALA*     3.8    11.2    -      -       +      +
     49S  PRO*     3.6    37.0    -      -       +      -
     52S  MET*     3.7    31.4    -      -       +      -
     71T  PHE*     4.2     1.1    -      -       +      -
     75T  ALA*     3.9    17.7    -      -       +      -
     90T  ILE*     4.6     8.2    -      -       +      +
     95T  ILE*     4.1    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 36 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18S  ARG*     5.6     1.0    -      -       -      +
     32S  HIS*     3.1    55.3    +      -       -      +
     33S  ARG*     3.1    26.0    -      -       -      +
     35S  LEU*     1.3    76.0    -      -       -      +
     37S  LYS*     1.3    63.6    +      -       +      +
     39S  ASN*     4.1     7.1    +      -       -      +
     41S  ALA      3.9    16.4    -      -       -      +
     42S  GLU      5.8     2.7    -      -       -      +
     43S  ARG      5.7     0.4    -      -       -      -
     44S  VAL*     3.6    18.6    -      -       +      +
    116U    A      4.4    19.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 37 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83P  HIS*     5.6     0.9    -      -       -      -
     33S  ARG*     3.0    50.9    +      -       -      +
     34S  LEU*     2.8    36.9    -      -       +      +
     35S  LEU      3.1     0.5    -      -       -      +
     36S  ARG*     1.3    80.0    -      -       +      +
     38S  GLY*     1.3    59.9    +      -       -      +
     39S  ASN      2.9     9.5    +      -       -      +
     40S  TYR*     2.9    14.6    -      -       -      -
    702S  PTD      1.3    82.1    -      -       +      +
----------------------------------------------------------
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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