Contacts of the helix formed by residues 260 - 280 (chain D) in PDB entry 3E6G
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 THR 260 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A HIS* 4.1 15.0 - - + -
260A THR* 3.5 38.5 - - + +
264A ARG* 4.1 19.3 - - + -
343A VAL* 4.7 4.0 - - + -
379A ILE* 4.7 5.8 - - + -
215D HIS* 4.0 5.4 + - - -
256D ARG 4.4 0.5 + - - -
257D GLY* 3.2 6.1 + - - -
258D LEU 3.1 0.4 - - - -
259D LYS* 1.3 81.0 - - - +
261D LEU* 1.3 64.3 + - - +
262D PRO* 3.3 2.9 - - - -
263D LEU* 3.3 8.5 + - + +
264D ARG* 2.9 40.9 + - - +
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Residues in contact with LEU 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ALA* 5.3 0.2 - - + -
76D LEU* 4.2 20.2 - - + -
190D SER* 4.3 7.6 - - - +
191D PRO* 4.3 14.4 - - + -
192D MET* 3.8 22.7 - - + -
211D TYR 3.4 17.0 - - - +
212D LEU* 3.7 17.0 - - + +
258D LEU* 3.0 17.2 + - + +
260D THR* 1.3 76.9 - - - +
262D PRO* 1.3 67.2 - - + +
264D ARG* 3.3 29.3 - - - +
265D MET* 2.9 44.8 + - + +
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Residues in contact with PRO 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ILE* 5.9 3.6 - - + +
17D LEU 4.0 0.2 - - - +
18D ALA* 3.7 33.0 - - + +
21D ALA* 3.5 29.8 - - + -
192D MET* 3.7 29.5 - - + +
258D LEU 3.7 0.9 - - - +
259D LYS 4.1 5.2 - - - +
260D THR* 3.5 3.8 - - - -
261D LEU* 1.3 96.1 - - + +
263D LEU* 1.3 64.7 + - + +
265D MET* 4.1 1.7 - - - +
266D ARG* 3.4 20.8 + - - +
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Residues in contact with LEU 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A THR* 6.6 0.2 - - + -
263A LEU* 3.1 49.4 - - + +
264A ARG* 3.8 13.5 - - + +
267A ALA* 4.1 19.5 - - + -
379A ILE* 4.0 32.3 - - + +
260D THR* 3.3 11.2 + - + +
261D LEU 3.3 0.4 - - - -
262D PRO* 1.3 80.1 - - + +
264D ARG* 1.3 68.3 + - - +
266D ARG* 3.2 9.1 + - + +
267D ALA* 3.0 22.7 + - - +
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Residues in contact with ARG 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A THR* 4.2 9.6 - - + -
263A LEU* 4.0 12.6 - - + -
211D TYR* 2.7 25.2 + - - +
212D LEU 2.8 26.9 + - - -
213D ASN 3.8 1.2 + - - -
214D GLY* 3.4 16.6 - - - -
215D HIS* 4.0 9.8 + - - -
257D GLY 2.9 17.2 + - - -
260D THR* 2.9 37.1 + - - +
261D LEU* 3.3 21.1 - - - +
263D LEU* 1.3 71.0 - - - +
265D MET* 1.3 55.3 + - - +
267D ALA* 3.0 4.2 + - - +
268D HIS* 2.8 50.5 + - + +
341D GLY 4.6 2.4 + - - -
343D VAL* 3.8 30.7 - - + -
379D ILE* 3.9 2.9 - - + +
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Residues in contact with MET 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D PHE 4.6 3.1 - - - +
190D SER* 3.4 26.9 - - - +
192D MET* 3.5 23.1 - - + -
193D LEU* 3.9 24.7 - - + -
211D TYR* 3.6 50.3 - - + -
261D LEU* 2.9 31.0 + - + +
262D PRO 4.1 1.1 - - - +
264D ARG* 1.3 78.1 - - - +
266D ARG* 1.3 61.9 + - - +
268D HIS* 3.4 9.8 + - + +
269D CYS* 2.9 31.7 + - - -
311D GLY 5.0 4.9 - - - +
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Residues in contact with ARG 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D PRO 3.4 11.7 + - - +
263D LEU* 3.2 13.2 + - + +
265D MET* 1.3 74.9 - - - +
267D ALA* 1.3 56.2 + - - +
269D CYS* 3.1 7.6 + - - +
270D GLU* 2.8 64.0 + - + +
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Residues in contact with ALA 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU* 3.6 30.3 - - + -
266A ARG* 5.3 4.5 - - - +
263D LEU 3.0 8.8 + - - +
264D ARG 3.4 7.9 - - - +
266D ARG* 1.3 80.2 - - - +
268D HIS* 1.3 62.1 + - - +
270D GLU* 3.4 8.0 + - - +
271D ASN* 3.1 32.3 + - - +
379D ILE* 3.7 16.4 - - + +
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Residues in contact with HIS 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D TYR* 3.6 33.0 - + + -
264D ARG* 2.8 36.9 + - + +
265D MET* 3.6 12.3 - - + +
267D ALA* 1.3 73.1 - - - +
269D CYS* 1.3 56.5 + - - +
271D ASN* 3.8 1.2 - - - +
272D ALA* 2.9 33.3 + - - +
311D GLY* 4.0 17.1 - - - +
341D GLY* 4.2 2.6 + - - -
342D GLY 3.1 29.5 + - - -
343D VAL* 4.5 1.6 - - - -
376D SER* 5.9 0.4 - - - -
377D VAL* 2.6 26.8 + - - +
378D GLY* 3.4 12.9 + - - -
379D ILE* 3.5 19.4 - - + +
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Residues in contact with CYS 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D LEU* 3.4 32.1 - - - -
265D MET* 2.9 23.2 + - - +
266D ARG* 3.5 8.3 - - - +
268D HIS* 1.3 69.5 - - - +
270D GLU* 1.3 70.1 + - + +
271D ASN 3.2 0.2 + - - -
272D ALA 3.3 0.2 + - - -
273D LEU* 3.0 27.5 + - - +
290D TYR* 3.9 1.5 + - - +
308D GLY* 4.0 4.7 - - - -
309D PHE 3.9 9.4 - - - +
310D GLY* 3.6 28.7 - - - -
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Residues in contact with GLU 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A ARG* 5.0 10.3 + - - -
266D ARG* 2.8 51.7 + - + +
267D ALA* 3.9 6.8 - - - +
269D CYS* 1.3 76.2 - - + +
271D ASN* 1.3 61.5 + - - +
273D LEU* 4.2 4.3 - - - +
274D ALA* 3.2 27.0 + - - +
382D LEU* 4.9 1.2 - - - +
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Residues in contact with ASN 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D ALA* 3.1 19.8 + - - +
268D HIS 3.8 0.7 - - - +
270D GLU* 1.3 80.2 - - - +
272D ALA* 1.3 58.7 + - - +
274D ALA* 4.1 0.9 - - - +
275D LEU* 3.1 36.1 + - + +
377D VAL* 3.6 20.1 - - + +
378D GLY 3.6 11.8 - - - +
379D ILE* 4.1 4.3 - - - +
380D GLU 3.2 21.3 + - - +
382D LEU* 3.0 41.5 - - - +
385D LEU* 4.8 2.9 - - - +
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Residues in contact with ALA 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D HIS 2.9 19.1 + - - +
271D ASN* 1.3 74.0 - - - +
273D LEU* 1.3 59.1 + - - +
275D LEU* 3.2 2.3 + - - +
276D ALA* 2.8 30.8 + - - +
290D TYR* 3.7 12.3 - - + +
310D GLY 3.4 19.7 - - - +
311D GLY 3.8 13.0 - - - +
313D VAL* 3.8 16.5 - - + +
377D VAL* 4.1 10.0 - - + +
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Residues in contact with LEU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D CYS 3.0 17.1 + - - +
270D GLU* 4.2 4.5 - - - +
272D ALA* 1.3 75.4 - - - +
274D ALA* 1.3 64.7 + - - +
276D ALA* 3.6 0.5 - - - +
277D GLN* 2.9 60.7 + - + +
290D TYR* 3.7 21.2 + - + +
292D GLY* 3.8 28.7 - - - +
293D LEU* 4.7 2.9 - - + -
309D PHE* 5.2 13.0 - - + -
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Residues in contact with ALA 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D GLU 3.2 14.3 + - - +
271D ASN 4.1 0.9 - - - +
273D LEU* 1.3 80.6 - - - +
275D LEU* 1.3 58.8 + - - +
277D GLN* 3.3 11.2 + - - +
278D TRP* 2.9 29.5 + - - +
382D LEU* 3.6 30.5 - - + -
386D ARG* 4.8 9.2 + - - +
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Residues in contact with LEU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D ASN* 3.1 23.4 + - + +
272D ALA* 3.8 3.1 - - - +
274D ALA* 1.3 78.9 - - + +
276D ALA* 1.3 51.2 + - - +
278D TRP* 3.3 14.6 + - + +
279D LEU* 2.8 47.4 + - + +
313D VAL* 5.7 1.8 - - + -
334D PHE* 4.6 0.9 - - + -
375D LEU* 6.4 0.2 - - + -
377D VAL* 3.9 32.3 - - + -
382D LEU* 4.7 9.2 - - + +
385D LEU* 4.3 16.6 - - + -
386D ARG* 4.0 31.6 - - + +
389D LEU* 3.8 27.4 - - + -
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Residues in contact with ALA 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D ALA 2.8 21.0 + - - +
273D LEU 3.6 3.8 - - - +
275D LEU* 1.3 68.2 - - - +
277D GLN* 1.3 67.6 + - - +
279D LEU* 2.9 14.6 + - - +
280D GLU* 3.1 15.2 + - - +
288D VAL* 3.9 13.2 - - + +
290D TYR* 3.9 24.9 - - + -
293D LEU* 3.8 23.1 - - + -
313D VAL* 4.2 7.7 - - + +
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Residues in contact with GLN 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D LEU* 2.9 54.1 + - + +
274D ALA* 3.6 9.2 - - - +
276D ALA* 1.3 75.7 - - - +
278D TRP* 1.3 64.2 + - - +
280D GLU* 3.5 16.7 + - - +
281D THR* 4.0 8.5 - - - +
293D LEU* 4.0 17.8 - - + +
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Residues in contact with TRP 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ALA 2.9 17.2 + - - +
275D LEU* 3.4 17.5 - - + +
276D ALA 3.0 0.2 - - - -
277D GLN* 1.3 78.4 - - - +
279D LEU* 1.3 93.8 + - + +
281D THR* 2.9 43.0 + - + -
282D HIS* 4.0 19.4 + + + -
386D ARG* 3.8 53.7 - - + +
389D LEU* 3.9 18.2 - - + -
390D GLU* 3.7 31.0 - - - -
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Residues in contact with LEU 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D LEU* 2.8 28.3 + - + +
276D ALA* 2.9 4.7 + - - +
278D TRP* 1.3 94.3 - - + +
280D GLU* 1.3 60.0 + - - +
281D THR 3.0 7.0 + - - -
282D HIS* 3.1 14.3 + - + +
285D ILE* 3.0 45.9 - - + +
288D VAL* 3.8 13.9 - - + -
313D VAL* 4.7 6.3 - - + -
315D ILE* 4.2 24.2 - - + -
327D PHE* 6.2 0.9 - - + -
375D LEU* 4.2 12.1 - - + -
389D LEU* 4.0 26.7 - - + -
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Residues in contact with GLU 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D ALA 3.1 5.6 + - - +
277D GLN* 3.6 11.9 - - - +
278D TRP 3.2 0.6 - - - -
279D LEU* 1.3 75.3 - - - +
281D THR* 1.3 59.9 + - + +
282D HIS 3.4 1.4 + - - +
285D ILE* 4.8 3.6 - - - +
288D VAL* 3.7 18.4 + - + +
293D LEU* 3.4 39.1 - - + +
294D ALA* 5.5 0.3 + - - +
295D SER* 2.7 30.7 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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