Contacts of the helix formed by residues 214 - 235 (chain C) in PDB entry 6NHW
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 ILE 214 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C SER 4.9 6.3 - - - +
211C LEU* 3.6 19.9 + - + +
213C GLY* 1.4 73.2 - - - +
215C ILE* 1.4 62.7 + - + +
216C ILE 3.3 3.6 - - - -
217C GLY* 3.0 23.7 + - - -
218C VAL* 4.1 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ILE* 4.1 27.6 - - + -
219B THR* 6.2 1.8 - - + -
220B VAL* 6.1 4.3 - - + -
211C LEU 4.5 1.5 + - - +
212C SER* 3.5 23.5 + - - +
214C ILE* 1.4 81.8 - - + +
216C ILE* 1.4 66.0 + - + +
217C GLY 3.4 0.3 + - - -
218C VAL* 3.6 29.4 - - + +
219C THR* 3.4 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ILE* 5.2 16.2 - - + -
212C SER 5.6 1.1 - - - +
213C GLY* 3.4 20.6 - - - +
215C ILE* 1.4 81.4 - - + +
217C GLY* 1.4 66.6 + - - +
219C THR* 3.3 21.1 + - + -
220C VAL* 3.4 18.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C ILE 3.0 12.9 + - - -
216C ILE* 1.4 84.0 - - - +
218C VAL* 1.4 60.6 + - - +
220C VAL* 3.3 22.0 - - - +
221C ALA* 3.4 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B THR* 4.5 13.7 + - + +
220B VAL* 5.3 9.2 - - + -
223B VAL* 5.2 16.0 - - + +
214C ILE 4.6 6.7 - - - +
215C ILE* 3.6 30.0 + - + +
216C ILE 3.4 0.6 - - - -
217C GLY* 1.4 73.6 - - - +
219C THR* 1.4 74.3 + - - +
221C ALA* 3.5 18.5 + - - +
222C ALA* 3.9 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ILE* 4.1 14.8 - - + +
218A VAL* 4.0 31.1 - - + +
219A THR* 4.3 6.3 - - + -
216B ILE* 5.8 2.1 - - - +
219B THR* 3.6 36.8 + - + +
215C ILE* 3.4 15.1 + - - +
216C ILE* 3.3 16.5 + - + -
218C VAL* 1.4 81.2 - - - +
220C VAL* 1.4 60.4 + - - +
222C ALA* 3.8 13.9 + - - +
223C VAL* 4.6 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A VAL* 5.1 7.0 - - + -
216C ILE* 3.4 15.8 + - + +
217C GLY* 3.3 21.5 - - - +
219C THR* 1.4 74.4 - - - +
221C ALA* 1.4 65.0 + - - +
222C ALA 3.2 3.9 + - - -
223C VAL* 3.2 27.8 + - + +
224C VAL* 3.5 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B VAL* 5.6 9.0 - - + -
217C GLY 3.4 11.4 + - - +
218C VAL* 3.5 15.5 - - - +
219C THR 3.4 0.8 - - - -
220C VAL* 1.4 83.3 - - - +
222C ALA* 1.4 60.6 + - - +
224C VAL* 3.4 9.5 - - - +
225C LEU* 3.2 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ALA* 4.5 9.4 - - + -
219B THR* 5.3 4.3 - - - +
222B ALA* 4.3 24.0 - - + -
223B VAL* 4.8 12.9 - - + +
226B ILE* 4.6 12.1 - - + -
218C VAL 3.9 6.0 + - - +
219C THR 3.8 11.8 + - - +
220C VAL 3.2 1.0 + - - -
221C ALA* 1.4 79.1 - - - +
223C VAL* 1.4 62.4 + - + +
225C LEU* 4.1 0.9 - - - +
226C ILE* 3.5 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A VAL* 3.7 44.4 - - + +
219A THR* 5.7 0.2 - - - -
221A ALA* 4.6 7.6 - - + -
222A ALA* 4.1 20.9 - - + +
219C THR 4.9 2.0 - - - +
220C VAL* 3.2 26.4 - - + +
222C ALA* 1.4 77.7 - - + +
224C VAL* 1.4 61.6 + - + +
226C ILE* 3.4 22.5 - - + +
227C VAL* 3.5 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C VAL* 3.5 18.8 - - + +
221C ALA* 3.4 18.8 - - - +
223C VAL* 1.4 82.8 - - + +
225C LEU* 1.4 63.5 + - + +
227C VAL* 3.3 21.9 - - + +
228C ALA* 3.5 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B VAL* 5.7 6.7 - - + -
226B ILE* 4.0 36.6 - - + -
227B VAL* 6.5 0.9 - - + -
221C ALA* 3.2 18.7 + - + +
222C ALA 4.1 3.4 - - - +
223C VAL 3.4 0.6 - - - -
224C VAL* 1.4 80.4 - - + +
226C ILE* 1.4 63.3 + - - +
228C ALA* 3.6 17.9 + - + +
229C VAL* 3.6 12.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA 5.1 0.9 - - - +
222A ALA* 4.2 25.6 - - + +
225A LEU* 4.0 42.3 - - + +
226A ILE* 5.8 8.1 - - + -
226B ILE* 3.6 29.4 - - + -
222C ALA 3.5 16.8 + - - +
223C VAL* 3.4 20.6 - - + +
225C LEU* 1.4 73.3 - - - +
227C VAL* 1.4 68.4 + - + +
229C VAL* 3.3 22.3 - - - +
230C PHE* 3.6 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 5.9 4.7 - - + -
223C VAL 3.5 13.7 - - - +
224C VAL* 3.3 20.6 - - + +
226C ILE* 1.4 82.2 - - + +
228C ALA* 1.4 66.7 + - - +
230C PHE* 3.4 9.7 + - + +
231C VAL* 3.3 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C VAL* 3.5 16.6 - - + +
225C LEU* 3.6 14.1 - - + +
226C ILE 3.4 0.4 - - - -
227C VAL* 1.4 81.9 - - - +
229C VAL* 1.4 59.7 + - - +
231C VAL* 3.3 13.3 - - - +
232C CYS* 3.0 27.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ILE* 6.5 0.9 - - + -
225C LEU* 3.6 10.9 + - + +
226C ILE* 3.3 21.5 - - - +
228C ALA* 1.4 76.4 - - - +
230C PHE* 1.4 64.3 + - + +
232C CYS* 3.5 8.4 + - + +
233C LYS* 3.2 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 6.2 4.7 - - + -
226C ILE 3.7 10.8 - - - +
227C VAL* 3.4 15.4 + - + +
229C VAL* 1.4 83.5 - - + +
231C VAL* 1.4 64.1 + - + +
233C LYS* 3.4 24.8 + - + +
234C SER* 3.7 8.2 + - - -
231D VAL* 5.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C VAL* 3.3 15.0 + - + +
228C ALA* 3.3 22.9 - - - +
230C PHE* 1.4 79.9 - - + +
232C CYS* 1.4 69.3 + - - +
234C SER* 3.3 21.0 + - - -
235C LEU* 3.9 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C ALA* 3.0 24.9 - - - +
229C VAL* 3.5 10.1 + - + +
230C PHE 3.4 0.2 - - - -
231C VAL* 1.4 81.0 - - - +
233C LYS* 1.4 60.5 + - - +
234C SER 3.4 0.2 - - - -
235C LEU* 3.5 14.7 - - - +
236C LEU* 3.4 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C VAL* 3.2 14.3 + - + +
230C PHE* 3.5 19.5 - - + +
231C VAL 3.2 0.6 - - - -
232C CYS* 1.4 73.6 - - - +
234C SER* 1.4 63.2 + - - +
235C LEU 3.2 2.2 - - - -
236C LEU* 3.3 24.9 + - + +
237C TRP 4.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C PHE* 3.7 7.2 + - - -
231C VAL* 3.3 16.9 + - - -
233C LYS* 1.4 78.2 - - - +
235C LEU* 1.4 56.9 + - - +
236C LEU 3.2 0.2 - - - -
237C TRP* 3.1 30.9 - - - +
238C LYS 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C VAL 3.9 4.4 + - - +
232C CYS* 3.5 19.7 + - - +
233C LYS 3.2 0.6 - - - -
234C SER* 1.4 77.2 - - - +
236C LEU* 1.4 65.7 + - + +
237C TRP 3.3 1.9 + - - -
238C LYS* 3.6 33.6 + - - +
----------------------------------------------------------
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