Contacts of the helix formed by residues 264 - 279 (chain C) in PDB entry 4HHM
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 ASP 264 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A SER* 6.0 2.6 - - - -
263A GLY 4.2 10.9 - - - +
264A ASP* 5.3 9.4 - - - +
265A LEU 5.6 0.3 + - - -
222C GLN* 3.5 27.4 - - - +
249C GLN 3.4 7.9 + - - +
250C SER* 5.1 0.4 - - - +
262C ALA 3.7 3.6 + - - +
263C GLY* 1.3 67.2 - - - -
265C LEU* 1.3 63.0 + - - +
266C ARG* 3.7 7.3 + - - +
267C ALA* 3.2 27.6 + - + +
268C ALA* 3.2 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ASP* 5.7 0.6 + - - +
265A LEU* 4.0 21.5 - - + +
266A ARG* 3.6 20.3 - - + +
380A MET* 3.8 18.6 - - + -
383A LEU* 3.5 32.5 - - + -
384A LEU* 3.8 15.7 - - + -
261C GLY* 3.5 27.8 - - - +
263C GLY 2.9 7.3 + - - -
264C ASP* 1.3 71.0 + - - +
266C ARG* 1.3 64.2 + - - +
268C ALA* 3.1 6.2 + - - +
269C PHE* 2.9 18.9 + - - +
309C ASN* 6.2 0.2 - - - -
313C LEU* 4.2 22.4 - - + -
383C LEU* 4.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG* 4.2 0.6 - - - +
262A ALA* 4.2 16.6 - - - +
263A GLY 4.6 11.5 + - - +
265A LEU* 4.0 21.1 - - + +
264C ASP* 3.5 7.4 + - - +
265C LEU* 1.3 77.7 - - - +
267C ALA* 1.3 62.9 + - - +
269C PHE* 3.0 11.8 + - - +
270C TRP* 2.9 47.7 + - + +
376C ASP* 2.6 52.4 + - - -
379C ALA* 4.2 6.1 - - - +
380C MET* 3.4 40.2 - - + +
383C LEU* 3.8 23.1 - - + -
144D GLU 5.8 0.4 + - - -
145D SER* 5.3 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C VAL* 6.2 0.7 - - + -
222C GLN* 3.8 11.9 - - - +
227C ASN* 6.4 0.4 - - - -
228C PHE* 5.7 1.1 - - + +
229C PRO* 3.5 23.1 - - + +
264C ASP* 3.2 37.1 + - + +
265C LEU 3.2 0.4 - - - -
266C ARG* 1.3 77.3 - - - +
268C ALA* 1.3 62.8 + - - +
270C TRP* 3.3 6.1 + - - +
271C LEU* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C VAL* 6.3 2.9 - - + -
260C PHE* 3.8 24.3 - - + -
261C GLY* 4.3 14.6 - - - +
262C ALA 5.7 0.4 - - - +
264C ASP 3.2 12.2 + - - +
265C LEU* 3.1 10.9 + - - +
267C ALA* 1.3 75.6 - - - +
269C PHE* 1.3 63.3 + - - +
271C LEU* 3.1 7.6 + - - +
272C VAL* 3.0 26.7 + - - +
313C LEU* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C LEU 2.9 12.2 + - - +
266C ARG* 3.2 14.8 - - - +
268C ALA* 1.3 76.6 - - - +
270C TRP* 1.3 106.0 + + - +
271C LEU 3.1 0.3 + - - -
272C VAL* 3.2 5.4 + - - +
273C ASP* 3.0 22.3 + - + +
313C LEU* 3.8 25.5 - - + +
316C ARG* 3.9 13.0 - - + -
317C ALA* 3.5 39.9 - - + +
320C PHE* 4.6 11.0 - + + -
379C ALA* 4.5 19.1 - - + -
383C LEU* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C PRO* 4.0 18.9 - - + +
266C ARG* 2.9 50.5 + - + +
267C ALA* 3.9 6.1 - - - +
269C PHE* 1.3 94.0 - + - +
271C LEU* 1.3 56.4 + - - +
273C ASP* 3.5 18.7 - - - +
274C LEU* 3.1 27.2 + - - +
320C PHE* 4.1 7.0 - + - -
321C ARG* 4.0 13.2 - - - -
376C ASP* 4.0 8.5 - - - -
379C ALA* 3.8 28.7 - - + -
146D GLY* 3.4 30.3 - - - +
147D ALA* 3.3 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C VAL* 4.2 2.5 - - + -
228C PHE* 3.8 20.6 - - + -
229C PRO* 3.9 11.6 - - + +
232C ILE* 3.9 32.1 - - + -
244C ILE* 4.3 1.8 - - + -
246C LEU* 3.6 29.8 - - + -
260C PHE* 3.8 19.7 - - + -
267C ALA 2.9 14.7 + - - +
268C ALA* 3.3 9.6 - - - +
269C PHE 3.1 0.2 - - - -
270C TRP* 1.3 75.0 - - - +
272C VAL* 1.3 59.9 + - - +
274C LEU* 3.2 3.6 + - + +
275C LEU* 2.9 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C PHE* 4.0 8.7 - - + -
268C ALA 3.0 14.1 + - - +
269C PHE 3.2 6.3 + - - +
271C LEU* 1.3 75.2 - - + +
273C ASP* 1.3 63.8 + - - +
275C LEU* 3.8 1.1 - - - +
276C GLU* 2.9 39.4 + - + +
310C TYR* 3.5 39.5 - - + -
313C LEU* 3.9 19.3 - - + +
314C LYS* 3.4 39.9 - - + +
317C ALA* 4.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C PHE* 3.0 15.4 + - + +
270C TRP* 3.5 28.3 - - + +
272C VAL* 1.3 76.8 - - - +
274C LEU* 1.3 59.1 + - - +
276C GLU* 4.1 2.3 - - - +
277C SER* 2.9 37.6 + - - -
317C ALA* 3.8 24.5 - - + +
320C PHE* 4.6 2.8 - - - -
321C ARG* 2.9 52.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C PRO* 3.3 33.2 - - + +
232C ILE* 3.5 23.6 - - + -
233C ALA* 3.6 19.3 - - + +
236C LEU* 4.0 17.3 - - + -
270C TRP 3.1 14.3 + - - +
271C LEU* 3.6 4.9 - - + +
273C ASP* 1.3 79.9 + - - +
275C LEU* 1.3 60.3 + - - +
277C SER* 3.3 8.0 + - - +
278C ALA* 2.9 39.1 + - + +
150D ASP* 5.7 4.7 - - - +
152D ARG* 4.9 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C ILE* 4.1 13.0 - - + -
236C LEU* 4.7 2.5 - - + -
241C LEU* 3.8 29.4 - - + -
244C ILE* 4.3 13.2 - - + -
246C LEU* 4.8 2.9 - - + -
271C LEU* 2.9 40.7 + - + +
272C VAL 3.9 2.5 - - - +
274C LEU* 1.3 77.2 - - - +
276C GLU* 1.3 63.4 + - - +
278C ALA* 3.9 1.5 - - - -
279C GLY* 3.2 17.2 + - - -
280C TRP* 3.2 36.0 + - + +
284C ARG* 4.1 19.0 + - + +
310C TYR* 4.0 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C VAL* 2.9 35.6 + - + +
273C ASP* 4.1 2.7 - - - +
275C LEU* 1.3 74.6 - - - +
277C SER* 1.3 64.3 + - - +
279C GLY* 3.2 13.1 + - - -
284C ARG* 2.8 16.1 + - - -
310C TYR* 2.8 26.0 + - - +
314C LYS* 3.5 37.3 + - + +
317C ALA* 6.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C ASP* 2.9 29.6 + - - -
274C LEU* 3.3 11.6 + - - +
276C GLU* 1.3 77.9 - - - +
278C ALA* 1.3 62.4 + - - +
279C GLY 3.6 0.2 + - - -
321C ARG* 5.6 11.2 - - - -
152D ARG* 4.8 3.0 + - - -
340H GLU* 4.5 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C LEU* 3.9 25.6 - - + -
274C LEU* 2.9 22.2 + - + +
275C LEU* 4.1 2.9 - - - +
277C SER* 1.3 76.6 + - - +
279C GLY* 1.3 62.8 + - - +
280C TRP* 3.5 2.9 + - - +
152D ARG* 3.7 27.3 + - - +
340H GLU* 4.1 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C LEU 3.2 2.3 + - - -
276C GLU* 3.2 15.7 + - - -
277C SER 3.3 0.6 - - - -
278C ALA* 1.3 79.9 - - - +
280C TRP* 1.3 66.8 + - - +
281C GLU* 3.1 16.5 + - - +
----------------------------------------------------------
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