Contacts of the strand formed by residues 218 - 226 (chain A) in PDB entry 3HO5


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 CYS 218 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217A  PHE*     1.3    80.1    -      -       -      +
    219A  ILE*     1.3    63.0    +      -       -      +
    537A  LEU*     4.4     1.6    -      -       -      +
    538A  GLY      4.2     2.7    -      -       -      -
    540A  SER*     3.8    15.9    -      -       -      -
    543A  CYS*     2.0    59.0    -      -       -      -
    544A  ARG      4.0     4.0    -      -       -      -
    582A  ILE*     3.4     2.6    -      -       -      +
    583A  VAL*     2.5    48.5    +      -       +      +
    585A  PRO*     3.8    14.1    -      -       +      -
    589B  LEU*     4.9     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  CYS*     1.3    78.4    -      -       -      +
    220A  GLN*     1.3    61.9    +      -       -      +
    518A  PHE*     5.8     1.8    -      -       +      -
    537A  LEU*     3.8    26.7    -      -       +      -
    542A  SER      4.7     0.5    -      -       -      +
    543A  CYS*     3.7     2.5    -      -       -      -
    544A  ARG*     2.9    53.4    +      -       -      +
    545A  GLY      3.7     4.5    -      -       -      -
    546A  TYR*     3.2    41.5    -      -       -      +
    547A  PHE*     4.0    12.8    -      -       +      -
    564A  ILE*     4.9    12.1    -      -       +      -
    580A  TYR*     4.7    11.4    -      -       +      -
    581A  LYS      3.4     4.7    -      -       -      +
    582A  ILE*     3.9    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  ILE*     1.3    74.6    -      -       -      +
    221A  GLU*     1.3    69.3    +      -       -      +
    222A  VAL*     3.3     2.1    +      -       -      +
    542A  SER*     3.1    36.9    +      -       -      -
    543A  CYS*     3.1    23.0    +      -       -      +
    580A  TYR*     3.2     5.3    -      -       -      -
    581A  LYS*     2.7    42.6    +      -       +      +
    583A  VAL*     4.3    14.1    -      -       +      +
    589A  LEU*     6.2     0.5    -      -       -      +
    220B  GLN*     3.5    31.6    -      -       -      +
    221B  GLU      4.7     4.6    +      -       -      -
    542B  SER*     3.7    22.4    -      -       -      +
    589B  LEU*     4.7     5.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  GLN*     1.3    83.7    +      -       -      +
    222A  VAL*     1.3    61.6    +      -       -      +
    223A  VAL      4.4     6.2    -      -       -      +
    224A  SER*     3.7    21.1    +      -       -      -
    578A  LYS*     3.6    32.3    -      -       +      +
    579A  LEU      4.2     4.3    -      -       -      +
    580A  TYR*     3.5    28.8    +      -       +      -
    220B  GLN*     4.9     4.5    +      -       -      -
    542B  SER*     4.8     2.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  GLN      3.9     0.7    -      -       -      +
    221A  GLU*     1.3    78.2    -      -       -      +
    223A  VAL*     1.3    62.0    +      -       +      +
    254A  LEU*     3.8    28.7    -      -       +      -
    258A  GLY      5.7     0.9    -      -       -      +
    563A  TYR*     3.8    14.4    -      -       +      -
    579A  LEU*     2.7    21.1    +      -       +      +
    581A  LYS*     3.7    35.4    -      -       +      +
    542B  SER*     3.9    15.0    -      -       -      -
    544B  ARG*     3.8    26.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 223 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  GLU*     4.4     5.3    -      -       -      +
    222A  VAL*     1.3    85.1    -      -       +      +
    224A  SER*     1.3    76.1    +      -       -      +
    226A  LEU*     3.9    19.7    -      -       +      -
    244A  ILE*     6.3     0.4    -      -       +      -
    254A  LEU*     3.8    39.0    -      -       +      -
    258A  GLY      5.1     2.9    -      -       -      +
    260A  ILE*     4.0    25.1    -      -       +      -
    578A  LYS*     3.3     4.0    -      -       -      +
    579A  LEU*     2.6    42.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 224 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  GLU*     3.7    18.8    +      -       -      -
    223A  VAL*     1.3    86.8    -      -       -      +
    225A  GLY*     1.3    66.1    +      -       -      +
    226A  LEU*     3.2     4.9    +      -       -      +
    576A  ASN*     3.6    12.1    -      -       -      -
    577A  GLY      3.4     7.2    -      -       -      -
    578A  LYS*     3.8    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 225 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224A  SER*     1.3    77.8    +      -       -      +
    226A  LEU*     1.3    60.3    +      -       -      +
    227A  ARG*     4.2     1.2    +      -       -      +
    252A  LYS*     4.5     7.6    +      -       -      -
    575A  HIS*     3.2    24.5    -      -       -      +
    576A  ASN*     3.2    11.4    +      -       -      -
    577A  GLY      3.2     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  VAL*     3.9    26.5    -      -       +      -
    224A  SER      4.8     0.4    -      -       -      +
    225A  GLY*     1.3    79.4    -      -       -      +
    227A  ARG*     1.3    63.0    +      -       -      +
    228A  GLN      3.9     0.2    +      -       -      -
    229A  PRO*     4.7     5.8    -      -       +      -
    244A  ILE*     3.2    43.3    -      -       +      -
    246A  GLU*     3.7    13.5    -      -       -      +
    252A  LYS*     4.1    17.3    -      -       +      +
    260A  ILE*     4.8     5.2    -      -       +      -
    575A  HIS*     3.2    12.2    -      -       -      -
    577A  GLY*     2.7    43.8    +      -       -      +
    578A  LYS      3.9     4.0    -      -       -      +
    579A  LEU*     3.9    23.1    -      -       +      +
----------------------------------------------------------
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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