Contacts of the strand formed by residues 1191 - 1197 (chain Q) 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 VAL1191 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1149Q  LYS      3.7     0.9    -      -       -      +
   1150Q  VAL*     3.5     3.3    -      -       -      +
   1151Q  ASP*     2.8    73.7    +      -       -      +
   1152Q  ASN*     5.4     4.0    -      -       -      +
   1190Q  LYS*     1.3    76.6    -      -       +      +
   1192Q  TYR*     1.3    62.2    +      -       -      +
   1193Q  ALA*     5.1     3.8    -      -       +      +
   1208Q  SER*     4.4    16.6    -      -       -      +
   1209Q  PHE      3.2     6.7    -      -       -      +
   1210Q  ASN*     3.0    26.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR1192 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1117Q  ILE*     3.6     5.2    -      -       -      +
   1132Q  VAL*     4.7     8.7    -      -       +      -
   1148Q  TRP*     5.0     3.4    -      +       +      -
   1149Q  LYS      3.9     2.0    -      -       -      -
   1150Q  VAL*     3.4    32.8    -      -       +      -
   1179Q  LEU*     4.3    11.0    -      -       +      -
   1181Q  LEU*     4.0    11.9    -      -       +      -
   1185Q  ASP      3.8     1.2    +      -       -      -
   1186Q  TYR*     2.6    69.8    +      +       -      -
   1189Q  HIS*     3.3    17.8    -      -       +      +
   1190Q  LYS      4.0    14.4    -      -       -      -
   1191Q  VAL*     1.3    72.7    -      -       -      +
   1193Q  ALA*     1.3    60.4    +      -       -      +
   1208Q  SER*     2.9    18.2    -      -       -      -
   1209Q  PHE*     2.8    44.0    +      +       +      -
   1211Q  ARG*     4.0    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA1193 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1148Q  TRP*     3.3    14.8    -      -       -      -
   1149Q  LYS*     3.0    52.8    +      -       +      +
   1191Q  VAL*     5.2     5.2    -      -       +      -
   1192Q  TYR*     1.3    72.8    -      -       -      +
   1194Q  CYS*     1.3    60.1    +      -       -      +
   1195Q  GLU      4.1     0.2    -      -       -      -
   1206Q  THR*     4.1    14.8    -      -       +      -
   1207Q  LYS      3.5     0.9    -      -       -      +
   1208Q  SER*     3.3    20.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS1194 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1115Q  VAL*     4.8     0.6    -      -       -      +
   1117Q  ILE*     4.3    10.3    -      -       +      +
   1134Q  CYS*     2.0    53.4    -      -       +      -
   1146Q  VAL*     3.9    12.3    -      -       -      -
   1147Q  GLN      3.8     2.5    -      -       -      -
   1148Q  TRP*     4.4     8.1    -      -       +      -
   1193Q  ALA*     1.3    73.1    -      -       -      +
   1195Q  GLU*     1.3    59.5    +      -       -      +
   1196Q  VAL*     3.9    15.4    +      -       -      +
   1205Q  VAL      3.7     1.9    -      -       -      +
   1206Q  THR*     3.1    23.6    -      -       -      -
   1207Q  LYS*     2.8    20.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU1195 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1145Q  LYS      3.7     0.7    -      -       -      +
   1146Q  VAL*     3.3     4.3    -      -       -      +
   1147Q  GLN*     2.8    69.8    +      -       +      +
   1149Q  LYS*     3.0    29.7    +      -       +      +
   1193Q  ALA      4.1     0.6    -      -       -      -
   1194Q  CYS*     1.3    71.3    -      -       -      +
   1196Q  VAL*     1.3    60.0    +      -       -      +
   1197Q  THR*     4.4     6.9    -      -       +      +
   1204Q  PRO*     2.8    36.7    -      -       +      +
   1205Q  VAL      4.3     0.2    -      -       -      +
   1206Q  THR*     2.6    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1196 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1113Q  PRO*     4.5     8.3    -      -       +      -
   1115Q  VAL*     4.1    16.8    -      -       +      -
   1136Q  LEU*     3.6    47.3    -      -       +      -
   1145Q  LYS      3.3     7.9    -      -       -      +
   1146Q  VAL*     4.3     5.2    -      -       +      -
   1194Q  CYS*     3.9    17.7    -      -       -      +
   1195Q  GLU*     1.3    79.1    -      -       -      +
   1197Q  THR*     1.3    74.0    +      -       -      +
   1198Q  HIS*     4.8     1.6    -      -       +      -
   1201Q  LEU*     3.5    14.4    -      -       +      +
   1204Q  PRO*     3.5     1.0    -      -       -      +
   1205Q  VAL      2.9    38.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR1197 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1144Q  ALA*     4.1     0.5    -      -       -      -
   1145Q  LYS*     3.1    54.2    +      -       +      +
   1147Q  GLN*     5.9     1.8    -      -       -      +
   1195Q  GLU*     4.4     8.7    -      -       +      +
   1196Q  VAL*     1.3    78.0    -      -       -      +
   1198Q  HIS*     1.3    62.7    +      -       -      +
   1201Q  LEU*     4.4     1.3    -      -       -      -
   1204Q  PRO*     3.5    35.2    -      -       +      -
----------------------------------------------------------
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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