Contacts of the helix formed by residues 261 - 282 (chain D) in PDB entry 3ELP
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 261 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C THR* 5.7 5.8 - - - +
265C ARG* 4.4 10.3 - - + -
344C PHE* 3.6 36.6 - - + -
380C LEU* 4.8 2.9 - - + -
215D ASN* 4.1 5.4 + - - -
257D ARG 5.6 0.9 - - - +
258D GLY* 3.3 8.0 + - - -
259D LEU 3.0 0.8 - - - -
260D LYS* 1.3 76.9 - - - +
262D LEU* 1.3 65.8 + - - +
263D HIS* 3.2 3.4 - - - -
264D VAL* 3.0 21.5 - - + +
265D ARG* 2.9 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D PHE* 3.9 28.7 - - + -
78D LEU* 5.2 0.9 - - + -
192D SER* 4.6 9.0 - - - +
193D PRO* 4.3 17.7 - - + -
194D TYR* 4.5 5.2 - - + -
208D TYR* 5.0 10.5 - - + +
214D MET* 5.4 2.9 - - + -
259D LEU* 2.8 36.9 + - + +
261D THR* 1.3 77.3 - - - +
263D HIS* 1.3 58.3 + - - +
265D ARG* 3.5 27.2 - - - +
266D MET* 2.9 64.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C LYS* 4.2 11.3 - - + -
380C LEU* 3.0 37.8 + - + +
18D PHE* 4.3 7.5 - + + -
19D ALA* 3.7 25.8 - - + +
22D ALA* 5.2 2.9 - - + -
23D ILE* 4.3 1.2 - - - +
194D TYR* 3.5 37.0 - - + +
259D LEU 4.9 0.9 - - - -
260D LYS 3.2 27.5 + - - -
261D THR* 4.2 2.3 - - - -
262D LEU* 1.3 79.3 - - - +
264D VAL* 1.3 87.1 + - + +
266D MET 4.0 0.3 - - - -
267D GLU* 3.1 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C VAL* 3.8 35.1 - - + +
265C ARG* 4.8 5.2 - - + -
268C LYS* 3.5 32.8 - - + -
380C LEU* 4.9 4.9 - - + -
261D THR* 3.0 37.9 - - + +
263D HIS* 1.3 100.5 - - + +
265D ARG* 1.3 67.8 + - + +
267D GLU* 3.7 5.9 + - - +
268D LYS* 3.5 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C THR* 4.5 9.0 - - + -
264C VAL* 4.9 2.9 - - + -
214D MET* 2.8 46.3 - - + +
215D ASN* 3.6 15.8 + - - +
258D GLY 2.9 29.9 + - - -
259D LEU* 4.8 0.6 - - - +
261D THR* 2.9 29.8 + - - +
262D LEU* 3.5 28.5 - - - +
264D VAL* 1.3 79.1 - - + +
266D MET* 1.3 64.8 + - - +
268D LYS 3.1 3.8 + - - -
269D HIS* 3.1 24.9 + - + -
344D PHE* 3.4 30.3 - - - -
380D LEU* 3.6 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D PHE 6.2 0.2 - - - -
191D MET 3.7 9.4 - - - +
192D SER* 3.3 32.3 - - - +
194D TYR* 3.9 11.9 - - + -
195D PHE* 3.4 29.4 - - + -
208D TYR* 5.9 0.7 - - - +
214D MET* 5.3 8.1 - - - +
262D LEU* 2.9 42.5 + - + +
265D ARG* 1.3 78.1 - - + +
267D GLU* 1.3 62.0 + - - +
269D HIS* 3.2 24.0 + - - +
270D PHE 3.1 17.0 + - - -
311D THR* 4.4 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C LYS* 6.5 0.9 - - - -
14D HIS* 3.0 27.0 + - - -
194D TYR* 2.9 32.8 + - + +
195D PHE* 4.7 2.9 - - - -
263D HIS 3.1 17.2 + - - +
264D VAL* 4.1 7.0 - - - +
265D ARG 3.3 0.4 - - - -
266D MET* 1.3 75.9 - - - +
268D LYS* 1.3 58.3 + - - +
270D PHE* 3.2 19.9 + - - +
271D LYS* 3.0 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ALA* 5.8 0.6 - - - +
263C HIS* 4.4 9.3 + - - -
264C VAL* 3.8 25.4 - - + -
264D VAL 3.5 3.3 + - - +
265D ARG 3.1 3.9 + - - +
267D GLU* 1.3 75.3 - - - +
269D HIS* 1.3 66.1 + - - +
270D PHE 3.0 1.6 - - - -
271D LYS* 4.1 26.4 - - + +
272D ASN* 3.0 56.5 + - - +
380D LEU* 3.6 33.4 - - + -
381D GLU 3.6 10.3 + - - -
382D ASP* 5.0 4.0 + - - +
383D GLU* 4.5 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D MET* 3.3 27.7 - - + +
265D ARG 3.1 24.4 + - - -
266D MET* 3.5 31.6 - - - +
268D LYS* 1.3 76.8 - - - +
270D PHE* 1.3 52.3 + - - +
272D ASN* 3.8 1.4 - - - +
273D GLY* 2.7 31.0 + - - -
311D THR* 4.6 4.9 - - + -
312D GLY* 3.5 24.1 + - - +
342D GLY* 4.1 5.2 - - - -
343D GLY 3.3 23.1 - - - -
377D SER* 6.2 0.2 - - - -
378D VAL 2.9 25.6 + - - +
379D GLY* 3.8 6.5 - - - -
380D LEU* 3.8 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PHE* 4.1 22.7 - + - -
14D HIS* 6.0 1.6 - + - -
195D PHE* 3.8 7.0 - + + -
266D MET 3.1 10.9 + - - +
267D GLU* 3.3 25.4 - - - +
268D LYS 3.0 0.2 - - - -
269D HIS* 1.3 76.6 - - - +
271D LYS* 1.3 61.1 + - + +
272D ASN 3.2 0.2 - - - -
274D MET* 2.8 50.1 + - + +
291D TYR* 3.2 19.7 - - - -
308D THR 4.7 3.4 - - - -
309D GLY* 3.8 17.5 - - - -
310D CYS* 3.1 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D GLU* 3.0 24.2 + - + +
268D LYS* 3.4 28.9 + - + +
270D PHE* 1.3 76.8 - - + +
272D ASN* 1.3 59.1 + - - +
274D MET* 3.8 5.0 - - - +
275D ALA* 3.1 28.1 + - - +
383D GLU* 3.7 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D LYS* 3.0 42.5 + - - +
269D HIS 4.0 0.4 - - - +
271D LYS* 1.3 76.5 - - - +
273D GLY* 1.3 66.5 + - - +
275D ALA* 3.5 4.7 + - - +
276D VAL* 3.0 29.3 + - - +
378D VAL* 3.3 18.6 - - + -
379D GLY 3.0 20.8 + - - +
380D LEU* 3.7 0.4 - - - +
381D GLU 2.8 26.4 + - - +
383D GLU* 3.6 16.6 - - - +
386D LEU* 3.6 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D HIS 2.7 23.3 + - - -
270D PHE 3.3 1.1 + - - -
272D ASN* 1.3 74.8 - - - +
274D MET* 1.3 52.0 + - - +
276D VAL* 3.2 1.6 + - - +
277D ALA* 2.8 36.7 + - - +
291D TYR* 3.8 13.7 - - - -
312D GLY* 4.3 3.1 - - - -
314D VAL* 3.6 15.1 - - - +
378D VAL* 4.0 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PHE* 5.8 0.9 - - - -
270D PHE* 2.8 38.1 + - + +
271D LYS* 3.8 5.8 - - - +
273D GLY* 1.3 70.0 - - - +
275D ALA* 1.3 63.8 + - - +
277D ALA* 3.1 3.8 + - - +
278D GLN* 2.9 46.5 + - - +
291D TYR* 3.5 18.1 + - + -
293D GLY* 3.0 33.4 - - - +
294D LEU* 3.3 32.5 - - + +
295D PRO* 5.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D LYS 3.1 12.0 + - - +
272D ASN 3.7 4.0 - - - +
274D MET* 1.3 78.8 - - - +
276D VAL* 1.3 63.3 + - - +
278D GLN* 3.2 10.7 + - - +
279D PHE* 3.0 24.9 + - - +
383D GLU* 3.0 45.5 - - + +
387D LEU* 4.2 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D ASN 3.0 22.6 + - - +
273D GLY 3.6 3.1 - - - +
275D ALA* 1.3 76.5 - - - +
277D ALA* 1.3 64.9 + - - +
278D GLN 3.3 0.2 + - - -
279D PHE* 3.5 1.3 + - - +
280D LEU* 3.1 30.0 + - + +
314D VAL* 4.4 5.2 - - + -
335D PHE* 4.7 2.2 - - + -
376D LEU* 3.7 21.8 - - + -
378D VAL* 3.7 25.1 - - + -
386D LEU* 4.5 11.7 - - + -
387D LEU* 4.0 20.9 - - + -
390D LEU* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D GLY 2.8 21.6 + - - +
274D MET 3.5 3.4 - - - +
276D VAL* 1.3 75.3 - - - +
278D GLN* 1.3 60.8 + - - +
280D LEU* 3.7 2.0 + - - +
281D GLU* 3.2 24.8 + - - +
289D VAL* 3.8 2.8 - - + +
291D TYR* 3.3 40.6 - - + -
294D LEU* 3.7 12.8 - - + +
314D VAL* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D MET* 2.9 47.4 + - - +
275D ALA* 3.6 7.8 - - - +
277D ALA* 1.3 74.3 - - - +
279D PHE* 1.3 68.8 + - - +
280D LEU 3.1 0.3 + - - -
281D GLU* 3.1 5.1 + - - +
282D SER* 3.0 28.8 + - - +
294D LEU* 3.7 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D ALA 3.0 14.9 + - - +
276D VAL 3.7 2.7 - - - +
278D GLN* 1.3 78.0 - - - +
280D LEU* 1.3 74.4 + - + +
282D SER* 3.3 6.4 + - - -
283D ASN* 3.1 39.1 + - - +
387D LEU* 3.8 33.2 - - + -
390D LEU* 3.9 16.6 - - + -
391D ASP* 3.2 53.2 - - + -
394D LEU* 4.3 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D VAL* 3.1 37.1 + - + +
277D ALA 3.8 1.1 - - - +
279D PHE* 1.3 85.3 - - + +
281D GLU* 1.3 58.8 + - - +
283D ASN* 2.8 25.7 + - - +
286D VAL* 3.3 28.8 - - + +
289D VAL* 3.6 13.5 - - + -
314D VAL* 4.0 15.0 - - + -
316D PHE* 3.4 40.4 - - + -
376D LEU* 4.0 2.2 - - + -
390D LEU* 4.1 19.1 - - + -
394D LEU* 4.2 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D ALA 3.2 13.5 + - - +
278D GLN* 3.1 6.1 + - - +
280D LEU* 1.3 77.8 - - - +
282D SER* 1.3 59.5 + - - +
283D ASN 3.3 3.2 - - - +
286D VAL* 5.0 5.6 - - - +
288D LYS* 5.8 0.6 - - - +
289D VAL* 3.3 28.0 + - + +
294D LEU* 3.6 20.0 - - + +
295D PRO* 5.6 1.7 - - - +
296D SER* 2.8 37.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D GLN* 3.0 18.9 + - - +
279D PHE* 3.5 6.7 - - - -
280D LEU 3.0 0.2 - - - -
281D GLU* 1.3 78.7 - - - +
283D ASN* 1.3 60.2 + - - +
284D PRO* 3.7 7.3 - - - +
----------------------------------------------------------
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