Contacts of the helix formed by residues 260 - 284 (chain D) in PDB entry 2GP7
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 SER 260 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D PRO* 2.8 19.2 + - - +
259D ASP* 1.3 74.3 - - - +
261D ASP* 1.3 68.9 + - - +
262D ILE* 3.2 15.4 + - - -
263D LYS* 4.0 11.5 + - - +
264D ALA* 3.5 20.3 + - - +
339D LEU* 4.5 13.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D SER* 1.3 77.5 - - - +
262D ILE* 1.3 80.4 + - + +
264D ALA* 3.9 3.1 - - - +
265D LEU* 3.3 33.6 + - + +
339D LEU* 3.1 38.9 - - + +
340D ALA* 4.2 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D SER* 3.2 7.1 - - - -
261D ASP* 1.3 104.3 - - - +
263D LYS* 1.3 56.3 + - - +
264D ALA 3.3 0.2 - - - -
265D LEU* 4.0 7.2 - - + +
266D THR* 2.5 43.6 + - - +
443D LYS* 3.7 38.1 - - + +
444D VAL* 4.3 11.9 - - + -
445D PRO* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D VAL 5.2 4.9 - - - +
258D PRO 3.8 22.2 - - - +
259D ASP* 4.8 4.3 - - - +
260D SER* 3.8 14.0 + - - +
262D ILE* 1.3 77.6 - - - +
264D ALA* 1.3 52.4 + - - +
266D THR* 3.3 5.6 + - - -
267D THR* 2.3 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D SER 3.5 14.9 + - - +
261D ASP* 3.9 5.4 - - - +
262D ILE 3.3 0.4 - - - -
263D LYS* 1.3 78.7 - - - +
265D LEU* 1.3 56.9 + - - +
267D THR* 3.2 5.3 + - - -
268D LEU* 2.8 37.0 + - + +
330D TYR* 3.2 25.9 + - - +
332D MET* 5.7 1.6 - - + -
336D GLN 5.7 0.4 - - - +
339D LEU* 6.2 1.6 - - + -
340D ALA* 4.0 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D ASP* 3.3 20.4 + - + +
262D ILE* 3.5 7.6 + - + +
263D LYS 3.4 0.2 - - - -
264D ALA* 1.3 75.7 - - - +
266D THR* 1.3 60.6 + - - +
268D LEU* 3.4 6.9 + - + +
269D CYS* 2.9 37.2 + - - -
340D ALA* 3.6 25.8 - - + +
342D LEU* 4.0 23.8 - - + -
435D PHE* 4.6 5.6 - - + -
438D ILE* 3.6 38.6 - - + -
444D VAL* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D ILE* 2.5 26.5 + - - +
263D LYS* 3.5 6.6 - - - -
265D LEU* 1.3 76.4 - - - +
267D THR* 1.3 58.4 + - - +
269D CYS* 3.4 2.5 + - - +
270D ASP* 2.9 32.7 + - + +
444D VAL* 3.6 17.7 - - - +
445D PRO* 3.8 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D ALA* 4.0 28.0 - - + +
253D PRO* 3.9 35.9 - - + +
254D ASP 5.5 0.2 + - - -
263D LYS* 2.3 30.6 + - - +
264D ALA* 3.3 8.0 - - - -
266D THR* 1.3 78.0 - - - +
268D LEU* 1.3 56.6 + - - +
270D ASP* 3.4 6.2 + - - +
271D LEU* 3.0 28.2 + - - +
330D TYR* 4.2 14.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D ALA* 2.8 24.7 + - + +
265D LEU* 3.8 9.9 - - + +
267D THR* 1.3 74.8 - - - +
269D CYS* 1.3 58.3 + - - +
271D LEU* 3.4 10.2 + - + +
272D ALA* 2.9 28.2 + - - +
326D TYR* 3.6 44.4 - - + -
330D TYR* 4.0 20.4 - - + -
332D MET* 4.3 10.3 - - + -
342D LEU* 3.4 32.5 - - + -
435D PHE* 4.5 18.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D LEU* 2.9 27.5 + - - +
266D THR 3.9 3.6 - - - +
268D LEU* 1.3 74.7 - - - +
270D ASP* 1.3 60.3 + - - +
272D ALA* 3.7 3.3 - - - +
273D ASP* 3.0 28.1 + - - +
435D PHE* 3.6 23.8 - - - -
438D ILE* 5.4 0.2 - - - -
444D VAL* 4.6 2.5 - - - -
445D PRO 4.5 6.3 - - - +
446D MET* 3.9 27.1 - - + -
447D HIS* 5.2 2.8 + - - -
450D PHE* 3.5 37.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D ALA 4.7 3.2 - - - +
252D MET 5.6 0.9 - - - +
266D THR* 2.9 21.3 + - + +
267D THR* 3.7 6.5 - - - +
269D CYS* 1.3 76.1 - - - +
271D LEU* 1.3 62.0 + - - +
273D ASP* 3.4 3.3 + - - +
274D ARG* 3.2 48.6 + - - +
445D PRO 5.7 0.2 + - - -
447D HIS* 3.1 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ILE* 3.3 33.9 - - + -
250D TYR 4.5 0.2 - - - +
251D ALA* 4.3 26.9 - - + +
267D THR 3.0 17.4 + - - +
268D LEU* 3.6 12.3 - - + +
269D CYS 3.3 0.2 - - - -
270D ASP* 1.3 74.1 - - - +
272D ALA* 1.3 54.3 + - - +
274D ARG* 3.2 14.5 + - - +
275D GLU* 2.8 47.3 + - + +
309D LEU* 6.0 0.9 - - + -
326D TYR* 3.7 46.4 - - + +
327D ALA* 4.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D LEU 2.9 17.2 + - - +
269D CYS 3.7 3.1 - - - +
270D ASP 3.4 0.2 - - - -
271D LEU* 1.3 74.8 - - - +
273D ASP* 1.3 66.9 + - - +
275D GLU* 3.2 9.7 + - - +
276D LEU* 2.9 27.0 + - - +
305D TRP* 5.2 0.4 - - + -
309D LEU* 4.1 20.0 - - + +
435D PHE* 6.4 0.7 - - + -
450D PHE* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D CYS 3.0 15.0 + - - +
270D ASP 3.5 10.3 - - - +
272D ALA* 1.3 77.1 - - - +
274D ARG* 1.3 69.8 + - - +
276D LEU* 3.4 17.4 + - - +
277D VAL* 3.5 13.1 + - - +
447D HIS* 3.5 36.6 - - + +
449D LEU* 3.3 30.2 + - - +
450D PHE* 3.5 18.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ILE* 3.6 28.2 - - + +
250D TYR 3.0 29.9 + - - +
251D ALA 3.3 17.8 + - - -
252D MET* 5.0 8.3 - - - +
270D ASP* 3.2 35.3 + - - +
271D LEU* 3.2 18.6 + - - +
273D ASP* 1.3 85.4 - - - +
275D GLU* 1.3 66.2 + - - +
276D LEU 3.4 0.2 + - - -
277D VAL* 3.5 10.1 + - + +
278D VAL* 3.4 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ILE* 4.0 17.0 - - + +
271D LEU* 2.8 35.3 + - + +
272D ALA 3.3 8.5 - - - +
274D ARG* 1.3 73.6 - - - +
276D LEU* 1.3 57.0 + - + +
278D VAL* 3.1 9.8 + - - +
279D ILE* 2.9 42.1 + - + +
309D LEU* 3.0 40.0 - - + +
312D GLY* 5.4 0.9 - - - -
316D ARG* 3.4 31.0 + - - -
326D TYR 4.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D ALA 2.9 15.9 + - - +
273D ASP* 3.4 8.7 - - - +
274D ARG 3.2 0.2 - - - -
275D GLU* 1.3 73.8 - - - +
277D VAL* 1.3 65.8 + - - +
279D ILE* 3.1 11.9 + - + +
280D ILE* 2.9 33.2 + - + +
305D TRP* 3.4 47.3 - - + -
309D LEU* 5.9 0.4 - - + -
449D LEU* 4.0 9.9 - - + +
450D PHE* 3.7 43.1 - - + +
453D MET* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D ASP* 3.5 11.4 + - - +
274D ARG* 3.5 11.6 + - - +
275D GLU 3.4 0.2 - - - -
276D LEU* 1.3 75.8 - - - +
278D VAL* 1.3 66.1 + - + +
280D ILE* 3.4 8.0 + - - +
281D GLY* 3.1 19.1 + - - -
449D LEU* 3.5 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D PRO* 3.3 38.4 - - + -
247D GLU 5.3 1.8 - - - +
249D ILE* 3.3 33.2 - - + -
274D ARG 3.5 4.9 - - - +
275D GLU* 3.1 13.6 + - - +
277D VAL* 1.3 78.7 - - + +
279D ILE* 1.3 62.8 + - + +
281D GLY* 3.4 1.6 + - - -
282D TRP* 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D GLU* 2.9 32.9 + - + +
276D LEU* 3.1 13.9 + - + +
278D VAL* 1.3 75.8 - - + +
280D ILE* 1.3 61.7 + - + +
282D TRP* 3.1 12.4 + - + +
283D ALA* 2.9 29.6 + - - +
301D LEU* 4.0 18.6 - - + -
305D TRP* 3.7 26.7 - - + +
308D ILE* 3.7 43.1 - - + -
309D LEU* 3.9 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D LEU* 2.9 27.1 + - + +
277D VAL* 3.7 5.6 - - - +
279D ILE* 1.3 77.4 - - + +
281D GLY* 1.3 63.5 + - - +
283D ALA* 3.6 11.4 + - - +
284D LYS* 3.9 18.8 + - - +
289D PHE* 5.6 0.3 - - - -
301D LEU* 4.3 31.6 - - + +
449D LEU* 4.4 26.5 - - + -
453D MET* 4.7 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D VAL 3.1 13.8 + - - -
278D VAL* 3.8 2.9 - - - -
280D ILE* 1.3 78.8 - - - +
282D TRP* 1.3 60.4 + - - +
284D LYS* 3.4 25.5 + - - +
285D HIS* 4.3 11.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D LEU* 4.9 8.5 + - + +
244D ALA* 3.5 34.1 + - + +
245D GLU* 4.6 3.0 + - - +
246D PRO* 3.9 23.1 - - + +
278D VAL 2.8 18.8 + - - +
279D ILE* 3.1 18.1 + - + +
281D GLY* 1.3 72.3 - - - +
283D ALA* 1.3 77.0 + - + +
284D LYS 3.1 2.2 - - - -
285D HIS* 3.0 28.1 + - - +
286D ILE* 3.5 34.5 + - + +
308D ILE* 3.9 28.3 - - + -
367D VAL* 4.6 5.5 - - + +
370D LYS* 3.8 53.8 - - + +
371D ALA* 4.2 4.7 - - + -
374D LEU* 4.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D ILE 2.9 16.7 + - - +
280D ILE 3.8 7.0 - - - +
281D GLY 3.4 0.4 - - - -
282D TRP* 1.3 84.6 - - + +
284D LYS* 1.3 62.8 + - - +
286D ILE* 3.2 18.2 + - - +
289D PHE* 3.2 33.2 - - + +
301D LEU* 3.9 13.0 - - + -
374D LEU* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D ILE* 3.9 17.9 + - - +
281D GLY* 3.4 17.1 + - - +
282D TRP 3.1 1.0 + - - -
283D ALA* 1.3 77.4 - - - +
285D HIS* 1.3 67.6 + - + +
286D ILE 3.3 3.7 + - - +
289D PHE* 4.2 12.3 - - + -
290D SER* 3.7 29.1 + - - -
294D LEU* 6.1 4.7 - - - -
297D GLN* 5.1 8.3 - - - +
----------------------------------------------------------
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