Contacts of the strand formed by residues 1219 - 1222 (chain A) in PDB entry 4YOC


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 MET1219 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1139A  LEU*     4.1    19.5    -      -       +      -
   1140A  ARG      2.9     5.1    +      -       -      +
   1141A  THR*     3.3    29.8    -      -       +      +
   1142A  LEU      2.9    27.0    +      -       -      -
   1155A  PHE*     4.0    27.4    -      -       +      -
   1160A  ILE*     4.4     8.3    -      -       -      -
   1161A  SER*     4.6     2.7    -      -       -      -
   1217A  VAL*     3.6     6.6    -      -       -      +
   1218A  GLU*     1.3    80.2    -      -       -      +
   1220A  LEU*     1.3    67.0    +      -       -      +
   1221A  CYS      4.8     0.2    -      -       -      +
   1262A  PHE*     3.6    29.4    -      -       +      +
   1263A  PHE      5.0     0.9    -      -       -      +
   1264A  LEU*     5.5     4.0    -      -       +      -
   1592A  ILE*     3.5    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1142A  LEU*     3.6    41.5    -      -       +      +
   1144A  VAL*     3.8    14.6    -      -       +      -
   1217A  VAL*     4.6     3.8    -      -       +      -
   1219A  MET*     1.3    75.6    -      -       -      +
   1221A  CYS*     1.3    60.7    +      -       -      +
   1251A  PHE*     3.6    17.3    -      -       +      +
   1254A  TYR*     4.0     7.9    -      -       +      +
   1255A  CYS*     3.6    36.8    -      -       -      +
   1258A  TYR*     5.7     0.9    -      -       +      -
   1260A  PRO*     3.6    17.6    -      -       +      +
   1262A  PHE      3.0     8.1    +      -       -      +
   1263A  PHE*     3.2    20.8    -      -       +      -
   1264A  LEU*     2.9    25.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS1221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1141A  THR*     3.7    24.0    -      -       +      -
   1142A  LEU      3.0     9.0    +      -       -      +
   1143A  ASP*     3.3    30.9    -      -       -      +
   1144A  VAL      2.9    24.4    +      -       -      -
   1151A  LEU*     3.8    16.6    -      -       +      -
   1152A  SER*     4.7     2.0    -      -       -      -
   1155A  PHE*     4.0    23.8    -      -       +      -
   1219A  MET*     5.0     1.6    -      -       +      -
   1220A  LEU*     1.3    75.4    -      -       -      +
   1222A  GLY*     1.3    58.6    +      -       -      +
   1251A  PHE*     3.5     7.1    -      -       -      -
   1264A  LEU*     3.3    12.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY1222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1143A  ASP*     4.2     3.8    -      -       -      -
   1144A  VAL      3.2    13.0    -      -       -      -
   1145A  PHE*     4.8     0.4    -      -       -      -
   1151A  LEU*     4.2     6.0    -      -       -      +
   1221A  CYS*     1.3    78.7    -      -       -      +
   1223A  GLY*     1.3    57.8    +      -       -      -
   1224A  PRO*     3.7     6.1    -      -       -      +
   1251A  PHE*     3.4     9.8    -      -       -      -
   1264A  LEU*     2.9     8.1    +      -       -      +
   1265A  LEU*     3.4     5.5    -      -       -      -
   1266A  GLU*     2.9    32.0    +      -       -      +
----------------------------------------------------------
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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