Contacts of the strand formed by residues 46 - 52 (chain H) in PDB entry 1YYL


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 GLU 46 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37H  VAL*     3.4     6.9    -      -       -      +
     38H  ARG*     2.8    78.5    +      -       +      +
     44H  GLY      4.9     1.3    -      -       -      +
     45H  LEU*     1.3    75.3    -      -       -      +
     47H  TRP*     1.3    73.9    +      -       -      +
     48H  MET*     3.4     3.5    +      -       -      +
     63H  LEU*     4.9     6.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 47 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35H  THR*     3.5    26.1    +      -       +      +
     36H  TRP      4.3     1.8    -      -       -      -
     37H  VAL*     4.8     0.7    -      -       -      +
     46H  GLU*     1.3    81.5    -      -       -      +
     48H  MET*     1.3    65.1    +      -       -      +
     49H  GLY*     3.8    12.3    -      -       -      -
     50H  ARG*     3.8    24.7    -      -       +      -
     58H  HIS*     4.1     7.4    -      -       +      -
     59H  TYR      3.9     4.3    -      -       -      -
     60H  ALA*     3.6    43.8    -      -       +      +
     63H  LEU*     5.5     0.2    -      -       -      +
    100H  LEU*     5.2     0.6    -      -       +      +
     89L  GLN*     4.0    13.3    -      -       -      +
     95L  ARG*     4.2    23.8    -      -       -      -
     96L  TYR*     3.3    79.9    -      +       +      +
     97L  THR*     4.6     1.1    -      -       -      -
     98L  PHE*     3.7    24.0    -      +       +      +
----------------------------------------------------------
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Residues in contact with MET 48 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36H  TRP*     3.0    28.5    +      -       +      +
     38H  ARG*     3.7    48.5    -      -       +      +
     46H  GLU*     3.8     4.3    -      -       -      +
     47H  TRP*     1.3    80.2    -      -       -      +
     49H  GLY*     1.3    61.8    +      -       -      +
     59H  TYR*     3.3     6.6    -      -       -      +
     60H  ALA*     2.8    26.7    +      -       -      +
     63H  LEU*     3.8    30.9    -      -       +      +
     67H  VAL*     4.4    17.3    -      -       +      -
     69H  ILE*     5.0     0.7    -      -       -      -
     80H  LEU*     4.5    10.5    -      -       +      -
     82H  LEU*     4.5     8.7    -      -       +      -
     90H  TYR*     3.8    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 49 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35H  THR*     3.1     5.7    -      -       -      +
     36H  TRP      2.9    26.1    +      -       -      -
     47H  TRP*     3.8    12.7    -      -       -      -
     48H  MET*     1.3    82.9    -      -       -      +
     50H  ARG*     1.3    61.2    +      -       -      -
     58H  HIS      3.1    14.1    -      -       -      -
     59H  TYR*     4.1     0.4    -      -       -      -
     69H  ILE*     3.3    17.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 50 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  SER*     3.2    15.9    +      -       -      +
     34H  PHE      3.4    10.3    -      -       -      +
     35H  THR*     3.6    19.0    +      -       -      +
     47H  TRP*     3.8    14.9    -      -       +      +
     49H  GLY*     1.3    74.4    -      -       -      +
     51H  ILE*     1.3    69.4    +      -       -      +
     52H  ILE*     4.1    12.6    -      -       -      +
     56H  VAL      4.2     0.2    -      -       -      +
     57H  ALA*     3.3     1.7    -      -       -      +
     58H  HIS*     2.9    37.8    +      -       +      +
     69H  ILE*     3.6     3.3    -      -       -      +
     97H  GLU*     2.8    30.7    +      -       -      -
    100H  GLY*     2.5    69.2    +      -       -      +
     94L  TRP*     4.2    11.3    -      -       -      -
     95L  PRO*     5.7     4.3    -      -       -      -
     96L  TYR*     4.5    16.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 51 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  SER*     3.5     5.9    -      -       -      -
     34H  PHE*     2.9    45.4    +      -       +      +
     50H  ARG*     1.3    77.0    -      -       -      +
     52H  ILE*     1.3    83.1    +      -       +      +
     55H  ASP*     4.5    16.8    -      -       -      +
     56H  VAL      3.3    17.9    -      -       -      +
     57H  ALA*     4.0     4.0    -      -       +      +
     69H  ILE*     3.7    29.4    -      -       +      +
     70H  THR*     4.0    13.9    -      -       -      -
     71H  ALA*     3.8    27.6    -      -       +      +
     78H  VAL*     4.4     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 52 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120G  VAL*     4.2    17.3    -      -       +      -
    434G  MET*     4.1    17.7    -      -       +      -
     33H  SER*     4.6     0.9    -      -       -      -
     50H  ARG*     4.1    17.5    -      -       -      +
     51H  ILE*     1.3    69.3    -      -       -      +
     52H  THR*     1.3    52.5    +      -       -      +
     53H  ILE*     3.3    12.6    -      -       +      -
     54H  LEU*     2.9    20.8    +      -       +      -
     55H  ASP      2.8    30.0    +      -       -      -
     56H  VAL*     2.8    19.9    +      -       +      +
     58H  HIS*     4.5     9.6    -      -       +      +
    100H  TYR*     3.2    49.4    -      -       +      +
     94L  TRP*     4.3     8.5    -      -       +      -
----------------------------------------------------------
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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