Contacts of the helix formed by residues 230 - 242 (chain D) in PDB entry 5TWV
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.
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 TYR 230 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D SER* 5.9 9.6 - - - -
228D GLY* 4.4 9.9 - - - +
229D THR* 1.3 76.7 - - - +
231D TRP* 1.3 69.0 + - + +
232D TRP* 3.4 1.5 - - - -
233D MET* 3.8 3.4 + - - +
234D ASN* 3.4 30.1 + - + +
1247D TRP* 4.7 15.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D TRP* 5.2 15.0 - + + -
219D GLN 5.5 0.2 - - - -
220D PRO* 4.1 20.2 - - + -
221D PHE* 3.5 24.7 - - - -
222D VAL* 3.7 25.3 + - + -
225D LEU* 3.2 31.2 - - + +
226D SER* 5.1 3.4 - - - -
227D LYS 5.9 0.2 - - - -
230D TYR* 1.3 84.2 - - + +
232D TRP* 1.3 96.4 + + - +
233D MET 3.0 6.7 + - - -
234D ASN* 3.4 13.6 + - - +
235D ALA* 3.4 28.5 + - + +
236D PHE* 6.5 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D PHE* 3.2 40.6 - - + -
222D VAL 3.2 26.6 + - - -
223D ASN* 3.6 11.9 + - + +
225D LEU* 4.4 5.0 - - + +
227D LYS* 5.9 3.9 - - - +
229D THR* 4.5 24.0 - - - -
230D TYR 3.4 0.8 - - - -
231D TRP* 1.3 116.1 - + - +
233D MET* 1.3 57.7 + - + +
235D ALA* 4.6 1.7 - - - +
236D PHE* 3.4 38.1 - + - -
378D TYR* 3.4 33.7 - + - -
1239D LEU* 5.7 10.1 - - + -
1243D ALA* 4.9 18.6 - - + +
1246D ARG* 6.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D THR 4.3 3.1 - - - +
230D TYR 3.8 5.5 + - - +
231D TRP 3.0 0.4 - - - -
232D TRP* 1.3 80.7 - - - +
234D ASN* 1.3 50.6 + - - +
235D ALA 3.3 2.5 - - - -
236D PHE* 4.5 3.3 - - - +
237D ILE* 2.4 41.6 + - - +
1247D TRP* 3.5 55.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D TYR* 3.4 26.6 + - + +
231D TRP* 3.4 8.3 + - - +
233D MET* 1.3 77.3 - - - +
235D ALA* 1.3 59.9 + - - +
237D ILE* 3.7 6.5 - - - -
238D LYS* 3.2 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 235 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D GLN* 6.4 1.8 - - + -
220D PRO* 6.3 0.9 - - + -
231D TRP* 3.4 37.0 + - + +
232D TRP 5.0 1.6 - - - +
233D MET 3.3 0.2 - - - -
234D ASN* 1.3 78.5 - - - +
236D PHE* 1.3 74.6 + - + +
238D LYS* 4.2 3.3 - - - +
239D THR* 4.2 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D GLN* 4.3 23.6 - - + -
221D PHE* 5.7 8.3 - - + -
231D TRP* 6.5 0.4 - + - -
232D TRP* 3.4 29.1 + + - +
233D MET* 4.0 4.3 + - - +
235D ALA* 1.3 86.8 - - + +
237D ILE* 1.3 58.5 + - - +
239D THR* 3.4 8.2 + - - -
240D ALA* 2.9 28.0 + - - +
1185D ALA* 5.3 6.9 - - + +
1240D PHE* 3.7 38.6 - + + -
1243D ALA* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D MET 2.4 32.3 + - - +
234D ASN* 3.7 6.5 - - - -
235D ALA 3.3 0.2 - - - -
236D PHE* 1.3 75.6 - - - +
238D LYS* 1.3 60.6 + - - +
240D ALA* 3.2 8.7 + - - +
241D HIS* 2.9 30.0 + - - +
1177D PHE* 6.3 3.4 - - + -
1181D TYR* 5.1 7.5 - - + -
1185D ALA* 5.9 1.1 - - - -
1247D TRP* 6.1 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D ASN 3.2 17.2 + - - +
235D ALA* 4.7 4.0 - - - +
236D PHE 3.4 0.6 - - - -
237D ILE* 1.3 76.6 - - - +
239D THR* 1.3 63.4 + - - +
241D HIS* 3.2 8.2 + - - +
242D LYS* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D ALA 4.2 9.5 + - - -
236D PHE* 3.4 10.6 + - - -
237D ILE 3.2 0.2 - - - -
238D LYS* 1.3 77.9 - - - +
240D ALA* 1.3 63.1 + - - +
242D LYS* 3.0 20.0 + - - +
245D ILE* 4.3 12.6 - - - -
246D ASP* 3.5 12.9 + - - -
249D ALA* 4.4 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D PHE 2.9 16.7 + - - +
237D ILE* 3.2 9.1 + - - +
239D THR* 1.3 77.6 - - - +
241D HIS* 1.3 62.1 + - - +
242D LYS 3.2 7.4 - - - +
243D LYS* 5.2 0.5 - - - -
246D ASP* 3.8 14.2 - - - +
1181D TYR* 4.4 17.8 - - + +
1184D VAL* 4.8 8.8 - - + +
1185D ALA* 3.8 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D ILE 2.9 17.1 + - - +
238D LYS* 3.5 8.1 - - - +
240D ALA* 1.3 75.7 - - - +
242D LYS* 1.3 65.1 + - - +
243D LYS* 3.4 3.3 + - - +
1181D TYR* 3.5 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D LYS 3.0 13.7 + - - +
239D THR* 3.0 15.9 + - - +
240D ALA 3.2 0.9 - - - +
241D HIS* 1.3 76.9 - - - +
243D LYS* 1.3 60.3 + - - +
244D PRO* 4.7 3.6 - - + -
245D ILE* 3.4 27.8 - - + +
246D ASP* 3.2 14.9 + - - +
----------------------------------------------------------
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