Contacts of the strand formed by residues 162 - 165 (chain H) in PDB entry 2YMX


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 THR 162 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160H  PRO*     5.1    10.8    -      -       +      -
    161H  VAL*     1.3    76.7    -      -       -      +
    163H  VAL*     1.3    64.8    +      -       -      +
    164H  THR*     5.9     3.2    -      -       -      +
    207H  ASN      3.7     0.7    -      -       -      +
    208H  VAL*     3.3     4.5    -      -       -      -
    209H  ALA*     2.8    48.5    +      -       -      +
    211H  PRO*     5.7     5.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 163 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151H  CYS*     5.3     1.8    -      -       +      -
    153H  VAL*     4.5     1.6    -      -       +      -
    161H  VAL*     4.1     9.2    -      -       +      -
    162H  THR*     1.3    80.6    -      -       -      +
    164H  THR*     1.3    81.3    +      -       -      +
    165H  TRP*     4.2     6.5    -      -       +      +
    176H  THR*     4.2    21.9    +      -       +      +
    188H  LEU*     3.6    31.9    -      -       +      -
    190H  SER*     3.8    25.4    -      -       -      +
    206H  CYS*     4.6     9.9    -      -       +      -
    207H  ASN      3.2     5.8    -      -       -      +
    208H  VAL*     4.3    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 164 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162H  THR*     5.8     3.4    -      -       -      +
    163H  VAL*     1.3    82.3    -      -       -      +
    165H  TRP*     1.3    67.1    -      -       -      +
    167H  SER*     4.0     3.3    -      -       -      -
    168H  GLY*     3.6    23.7    +      -       -      +
    206H  CYS*     3.4     4.9    -      -       -      -
    207H  ASN*     2.8    57.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 165 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149H  LEU*     5.0     0.2    -      -       +      -
    150H  GLY*     3.4    31.2    -      -       -      -
    151H  CYS*     3.6     5.4    -      -       +      -
    163H  VAL*     4.2     3.1    -      -       +      +
    164H  THR*     1.3    77.9    -      -       -      +
    166H  ASN*     1.3    68.8    +      -       -      +
    167H  SER      3.2     0.9    -      -       -      -
    168H  GLY*     3.1     8.7    +      -       -      +
    170H  LEU*     3.1    44.2    +      -       +      +
    174H  VAL*     3.7    29.7    -      -       +      +
    176H  THR*     5.1     0.2    -      -       -      -
    190H  SER*     2.9    43.8    +      -       -      -
    191H  SER      4.1     0.4    +      -       -      -
    192H  VAL*     3.7    20.0    -      -       +      +
    204H  VAL*     3.6    27.6    -      -       +      -
    205H  THR      3.4    17.7    -      -       -      -
    206H  CYS*     3.5    29.8    -      -       +      -
    221H  ILE*     3.8    11.0    -      -       +      -
----------------------------------------------------------
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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