Contacts of the strand formed by residues 1016 - 1020 (chain S) 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 LEU1016 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1007S  GLN      5.9     0.4    -      -       -      -
   1010S  CYS*     3.6     3.2    -      -       -      +
   1015S  LEU*     1.3    82.8    -      -       -      +
   1017S  GLY*     1.3    61.5    +      -       -      +
   1026S  CYS*     3.2     7.6    -      -       -      -
   1027S  VLM      3.0    37.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY1017 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1003S  LEU*     4.2     7.6    -      -       -      +
   1006S  CYS*     4.1    11.0    -      -       -      -
   1007S  GLN*     3.6    33.0    +      -       -      +
   1010S  CYS*     4.0    11.7    -      -       -      +
   1016S  LEU*     1.3    80.1    -      -       -      +
   1018S  LYS*     1.3    61.5    +      -       -      +
   1025S  ALA      3.4     9.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS1018 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1281P  ALA*     4.7    22.6    +      -       -      +
   1455P  THR*     5.7     7.3    -      -       -      +
   1001S  MPT      4.6     2.9    -      -       -      -
   1003S  LEU*     4.9     5.6    -      -       +      -
   1006S  CYS*     4.1     1.7    -      -       -      -
   1017S  GLY*     1.3    75.6    -      -       -      -
   1019S  CYS*     1.3    79.6    +      -       -      +
   1020S  ALA*     5.2     3.4    -      -       -      -
   1025S  ALA*     3.2    37.6    +      -       +      +
   1027S  VLM      3.4    30.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS1019 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1001S  MPT      2.0    63.5    -      -       +      -
   1003S  LEU*     3.9    21.7    -      -       +      +
   1018S  LYS*     1.3    95.4    -      -       -      +
   1020S  ALA*     1.3    59.8    +      -       -      +
   1021S  GLY      4.0     9.0    -      -       -      +
   1023S  BIF      3.6     0.7    -      -       -      -
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Residues in contact with ALA1020 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1371P  ILE*     4.4     5.6    -      -       +      -
   1472P  GLY      3.8    20.2    -      -       -      +
   1473P  GLY*     3.1    17.5    -      -       -      -
   1474P  ASP*     3.7     3.6    -      -       -      +
   1018S  LYS*     5.1     3.8    -      -       +      +
   1019S  CYS*     1.3    77.2    -      -       -      +
   1021S  GLY*     1.3    62.8    +      -       -      +
   1023S  BIF      3.1    23.2    +      -       +      +
   1025S  ALA*     4.2    20.6    -      -       +      -
----------------------------------------------------------
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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