Contacts of the strand formed by residues 1099 - 1104 (chain I) in PDB entry 2X4Y


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 TYR1099 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1090I  TRP*     4.1     2.7    -      -       -      -
   1091I  ALA*     2.9    33.5    +      -       -      +
   1097I  PRO*     3.9     7.0    -      -       +      +
   1098I  SER*     1.3    76.6    -      -       -      +
   1100I  PRO*     1.3    86.6    -      -       +      +
   1101I  ALA      3.5     0.3    +      -       -      -
   1147I  PHE*     3.7    23.7    -      +       +      -
   1149I  ASP*     3.3    41.8    -      -       +      +
   1150I  ASN      4.9     0.2    +      -       -      -
   1184I  ILE*     4.5     5.2    -      -       +      -
   1187I  SER*     2.8    35.7    +      -       -      -
   1188I  VAL*     3.7    23.6    -      -       +      -
   1191I  ALA*     3.3    22.8    -      -       +      +
   1194I  ARG*     5.1     1.4    +      -       -      -
     36J  M3L      3.8    30.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO1100 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1089I  VAL      3.5     7.4    -      -       -      +
   1090I  TRP*     3.7    22.7    -      -       +      -
   1099I  TYR*     1.3   103.4    -      -       +      +
   1101I  ALA*     1.3    61.1    +      -       -      +
   1147I  PHE*     3.5     0.7    -      -       -      -
   1148I  PHE*     3.0    23.4    +      -       +      -
   1165I  LEU*     3.6    15.9    -      -       +      -
   1188I  VAL*     3.8     9.2    -      -       +      +
   1191I  ALA*     3.7    24.5    -      -       +      +
   1192I  TYR*     3.5    26.2    -      -       -      +
   1195I  ALA*     4.2     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA1101 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1088I  LEU*     3.6     5.2    -      -       -      +
   1089I  VAL*     2.9    31.6    +      -       +      -
   1091I  ALA*     4.1     9.0    -      -       +      -
   1099I  TYR      4.1     3.1    -      -       -      +
   1100I  PRO*     1.3    76.9    -      -       -      +
   1102I  LEU*     1.3    61.1    +      -       -      +
   1145I  VAL*     3.9    19.7    -      -       +      -
   1146I  LEU      3.3    13.5    -      -       -      +
   1147I  PHE*     3.8    17.3    -      -       +      -
   1148I  PHE*     3.6    13.9    -      -       -      -
   1165I  LEU*     4.8     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1102 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1086I  LEU*     3.3    41.3    -      -       +      +
   1087I  ASP      3.6     4.5    -      -       -      +
   1088I  LEU*     3.8    15.5    -      -       +      -
   1101I  ALA*     1.3    74.1    -      -       -      +
   1103I  ILE*     1.3    71.2    +      -       -      +
   1104I  ILE*     3.5    21.4    +      -       +      +
   1120I  ILE*     4.8     6.1    -      -       +      -
   1121I  PRO*     5.6     2.2    -      -       +      -
   1145I  VAL*     3.3     4.1    -      -       -      -
   1146I  LEU*     2.8    38.7    +      -       +      +
   1148I  PHE*     4.1    11.9    -      -       +      -
   1152I  ARG*     5.0     8.7    -      -       -      +
   1198I  HIS*     3.9    32.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1103 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1083I  LEU*     3.6    42.4    -      -       +      -
   1084I  ASP      3.6    20.4    -      -       -      +
   1085I  ALA*     3.9     8.7    -      -       -      +
   1086I  LEU*     2.6    30.5    +      -       -      +
   1087I  ASP*     3.0    17.9    +      -       +      +
   1089I  VAL*     3.8    20.6    -      -       +      -
   1102I  LEU*     1.3    71.6    -      -       -      +
   1104I  ILE*     1.3    71.5    +      -       -      +
   1143I  TYR*     4.1    26.7    -      -       +      -
   1144I  LEU      3.4    11.2    -      -       -      +
   1145I  VAL*     4.3     5.8    -      -       +      -
   1162I  LEU*     4.5     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1104 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1085I  ALA*     4.5     0.4    -      -       -      -
   1086I  LEU*     4.2     3.6    -      -       +      -
   1102I  LEU*     3.7    30.1    -      -       +      +
   1103I  ILE*     1.3    88.0    -      -       -      +
   1105I  ASP*     1.3    73.4    +      -       -      +
   1106I  PRO*     3.3     9.7    -      -       -      +
   1108I  MET*     3.9    19.5    -      -       -      -
   1120I  ILE*     3.6    25.6    -      -       +      -
   1121I  PRO      4.4     1.8    -      -       -      +
   1123I  PRO*     4.0    16.2    -      -       +      -
   1144I  LEU*     2.9    25.5    +      -       +      +
   1146I  LEU*     4.0    12.6    -      -       +      +
   1154I  TRP*     3.8    25.4    -      -       +      -
----------------------------------------------------------
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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