Contacts of the strand formed by residues 1233 - 1239 (chain B) in PDB entry 4Z4Q


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 LYS1233 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1227B  LYS*     3.5     8.0    -      -       -      +
   1228B  ALA*     3.1    15.1    +      -       -      -
   1231B  THR*     2.9    20.7    +      -       -      +
   1232B  GLY*     1.3    82.1    -      -       -      +
   1234B  GLY*     1.3    59.0    +      -       -      +
   1327B  PHE      3.3     8.3    -      -       -      +
   1328B  ASN*     3.3    32.2    +      -       +      +
   1339B  GLN*     3.3    31.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY1234 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1224B  GLU*     3.6    15.9    -      -       -      -
   1227B  LYS*     4.9     2.7    -      -       -      -
   1228B  ALA*     3.7    13.2    -      -       -      +
   1233B  LYS*     1.3    75.7    -      -       -      +
   1235B  ARG*     1.3    59.8    +      -       -      -
   1326B  ASN*     3.5     5.7    -      -       -      +
   1327B  PHE*     2.8    35.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG1235 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1224B  GLU*     2.8    43.4    +      -       -      +
   1234B  GLY*     1.3    73.2    -      -       -      -
   1236B  VAL*     1.3    64.4    +      -       -      +
   1237B  VAL*     6.1     1.8    -      -       -      -
   1324B  ASN*     3.4    42.4    -      -       +      +
   1325B  TYR      3.7     2.7    -      -       -      -
   1326B  ASN*     3.3    34.7    +      -       -      +
   1327B  PHE*     5.4     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1236 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1211B  PRO*     5.9     1.1    -      -       +      -
   1213B  PHE*     5.5     2.0    -      -       +      -
   1219B  ILE*     3.5    29.4    -      -       +      -
   1220B  GLN      2.9    26.5    -      -       -      +
   1221B  GLY*     4.1     4.7    -      -       -      +
   1224B  GLU*     4.7     0.9    -      -       +      -
   1225B  ILE*     3.9    20.0    -      -       +      -
   1234B  GLY      4.2     0.4    -      -       -      -
   1235B  ARG*     1.3    76.0    -      -       -      +
   1237B  VAL*     1.3    64.6    +      -       -      +
   1238B  VAL*     4.4     2.7    -      -       +      -
   1324B  ASN*     3.4     8.8    -      -       -      +
   1325B  TYR*     3.0    51.1    +      -       +      +
   1327B  PHE*     4.3    20.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1237 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1218B  ILE      3.6     0.9    -      -       -      +
   1219B  ILE*     3.4     4.7    -      -       -      +
   1220B  GLN*     2.8    68.8    +      -       +      +
   1235B  ARG*     6.1     1.8    -      -       -      -
   1236B  VAL*     1.3    76.8    -      -       -      +
   1238B  VAL*     1.3    66.6    +      -       -      +
   1239B  ARG*     4.6     1.3    -      -       +      +
   1322B  GLN*     3.8    33.4    -      -       +      +
   1323B  ILE      3.6     3.1    -      -       -      +
   1324B  ASN*     3.9    17.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1238 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1213B  PHE*     3.5    34.8    -      -       +      -
   1217B  ALA*     3.9    16.2    -      -       +      -
   1218B  ILE      3.4    11.0    -      -       -      +
   1219B  ILE*     4.7     2.0    -      -       +      -
   1236B  VAL*     4.4     4.9    -      -       +      -
   1237B  VAL*     1.3    77.2    -      -       -      +
   1239B  ARG*     1.3    62.6    +      -       -      +
   1260B  PRO*     3.7    29.2    -      -       +      +
   1261B  TYR*     4.7     1.3    -      -       +      +
   1322B  GLN*     3.2     4.2    -      -       -      +
   1323B  ILE*     2.8    46.2    +      -       +      -
   1325B  TYR*     4.0    21.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG1239 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1217B  ALA*     3.3     4.7    -      -       -      +
   1218B  ILE*     2.9    52.9    +      -       +      +
   1220B  GLN*     3.6    31.4    +      -       -      +
   1237B  VAL*     4.7     4.0    -      -       +      -
   1238B  VAL*     1.3    75.9    -      -       -      +
   1240B  SER*     1.3    68.6    +      -       -      +
   1260B  PRO*     4.6     1.3    -      -       -      -
   1313B  ASN*     5.2     2.8    +      -       -      -
   1316B  PHE*     2.6    61.9    -      -       +      +
   1321B  LEU      3.8     3.8    -      -       -      -
   1322B  GLN*     2.8    31.1    +      -       +      -
----------------------------------------------------------
 Back to top of page


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