Contacts of the helix formed by residues 261 - 282 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ASN* 4.1 5.7 + - - -
257A ARG 5.6 0.9 - - - +
258A GLY* 3.3 8.2 + - - -
259A LEU 3.0 0.6 - - - -
260A LYS* 1.3 78.8 - - + +
262A LEU* 1.3 64.8 + - - +
263A HIS* 3.2 4.3 - - - -
264A VAL* 3.0 21.8 - - + +
265A ARG* 2.9 44.2 + - - +
261B THR* 5.7 5.5 - - - +
265B ARG* 4.4 10.3 - - + -
344B PHE* 3.5 37.2 - - + -
380B LEU* 4.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 3.9 28.9 - - + -
78A LEU* 5.2 0.4 - - + -
192A SER* 4.6 9.4 - - - +
193A PRO* 4.3 17.0 - - + -
194A TYR* 4.6 5.2 - - + -
208A TYR* 5.0 10.5 - - + +
214A MET* 5.4 2.5 - - + -
259A LEU* 2.8 36.9 + - + +
261A THR* 1.3 76.3 - - - +
263A HIS* 1.3 55.9 + - - +
265A ARG* 3.5 28.5 - - - +
266A MET* 2.9 59.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 4.3 8.3 - + + -
19A ALA* 3.7 25.1 - - + +
22A ALA* 5.2 2.2 - - + -
23A ILE* 4.3 1.6 - - - +
194A TYR* 3.5 36.2 - - + +
259A LEU 4.9 1.6 - - - -
260A LYS 3.2 27.2 + - - -
261A THR* 4.2 2.2 - - - -
262A LEU* 1.3 79.4 - - - +
264A VAL* 1.3 88.6 + - + +
266A MET 4.0 0.2 - - - -
267A GLU* 3.1 34.8 + - - +
268B LYS* 4.2 11.2 - - + -
380B LEU* 3.0 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A THR* 3.0 38.1 - - + +
263A HIS* 1.3 102.3 - - + +
265A ARG* 1.3 66.5 + - + +
267A GLU* 3.7 5.5 + - - +
268A LYS* 3.5 18.9 + - - +
264B VAL* 3.8 35.5 - - + +
265B ARG* 4.8 5.2 - - + -
268B LYS* 3.5 32.3 - - + -
380B LEU* 4.8 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A MET* 2.8 47.1 - - + +
215A ASN* 3.6 15.2 + - - +
258A GLY 2.9 28.7 + - - -
259A LEU* 4.8 0.4 - - - +
261A THR* 2.9 30.0 + - - +
262A LEU* 3.5 28.0 - - - +
264A VAL* 1.3 79.0 - - + +
266A MET* 1.3 64.6 + - - +
268A LYS 3.2 3.6 + - - -
269A HIS* 3.1 25.4 + - + -
344A PHE* 3.4 31.0 - - + -
380A LEU* 3.6 22.6 - - + +
261B THR* 4.6 8.3 - - + -
264B VAL* 4.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A THR 6.1 0.2 - - - +
190A PHE 6.2 0.4 - - - -
191A MET 3.7 9.2 - - - +
192A SER* 3.4 32.5 - - - +
194A TYR* 3.8 12.8 - - + -
195A PHE* 3.4 27.5 - - + -
208A TYR* 5.9 0.7 - - - +
214A MET* 5.3 8.1 - - - +
262A LEU* 2.9 42.1 + - + +
265A ARG* 1.3 78.5 - - - +
267A GLU* 1.3 61.9 + - - +
269A HIS* 3.2 24.8 + - - +
270A PHE 3.1 17.3 + - - -
311A THR* 4.4 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 3.0 27.3 + - - -
194A TYR* 2.9 32.5 + - + +
195A PHE* 4.7 2.7 - - - -
263A HIS 3.1 17.7 + - - +
264A VAL* 4.0 7.4 - - - +
265A ARG 3.3 0.2 - - - -
266A MET* 1.3 76.9 - - - +
268A LYS* 1.3 57.6 + - - +
270A PHE* 3.2 21.4 + - - +
271A LYS* 2.9 34.0 + - + +
268B LYS* 6.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A VAL 3.5 3.2 + - - +
265A ARG 3.2 4.1 + - - +
267A GLU* 1.3 74.6 - - - +
269A HIS* 1.3 66.3 + - - +
270A PHE 3.0 1.8 - - - -
271A LYS* 4.1 25.1 - - + +
272A ASN* 3.0 57.1 + - - +
380A LEU* 3.6 31.6 - - + -
381A GLU 3.6 10.7 + - - -
382A ASP* 5.0 4.2 + - - +
383A GLU* 4.4 7.7 - - - +
19B ALA* 5.8 0.2 - - - +
263B HIS* 4.4 9.4 + - - +
264B VAL* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A MET* 3.3 27.5 - - + +
265A ARG 3.1 24.2 + - - -
266A MET* 3.2 32.9 + - - +
268A LYS* 1.3 76.0 - - - +
270A PHE* 1.3 52.6 + - - +
272A ASN* 4.0 1.2 - - - +
273A GLY* 2.7 30.5 + - - -
311A THR* 4.6 4.0 - - + -
312A GLY* 3.5 23.7 + - - +
342A GLY* 4.1 5.4 - - - -
343A GLY 3.3 23.8 - - - -
377A SER* 6.1 0.2 - - - -
378A VAL 2.9 25.5 + - - +
379A GLY* 3.8 6.7 - - - -
380A LEU* 3.8 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 4.1 23.8 - + - -
14A HIS* 6.0 1.6 - + - -
195A PHE* 3.8 7.0 - + + -
266A MET 3.1 10.8 + - - +
267A GLU* 3.3 23.6 - - - +
268A LYS 3.0 0.2 - - - -
269A HIS* 1.3 75.9 - - - +
271A LYS* 1.3 62.6 + - + +
274A MET* 2.8 48.4 + - + +
291A TYR* 3.2 18.8 - - - -
293A GLY* 4.9 0.2 - - - -
308A THR 4.7 3.1 - - - -
309A GLY* 3.8 17.7 - - - -
310A CYS* 3.1 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLU* 2.9 24.0 + - + +
268A LYS* 3.4 29.1 + - + +
270A PHE* 1.3 77.6 - - + +
272A ASN* 1.3 60.0 + - - +
274A MET* 3.8 4.9 - - - +
275A ALA* 3.1 28.9 + - - +
383A GLU* 3.7 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LYS* 3.0 42.8 + - - +
269A HIS 4.0 0.7 - - - +
271A LYS* 1.3 77.3 + - - +
273A GLY* 1.3 64.7 + - - +
275A ALA* 3.5 5.3 + - - +
276A VAL* 2.9 29.8 + - - +
378A VAL* 3.3 18.8 - - + -
379A GLY 3.0 20.2 + - - +
380A LEU 3.7 0.8 - - - -
381A GLU 2.8 26.2 + - - -
383A GLU* 3.6 16.8 - - - +
386A LEU* 3.6 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A HIS 2.7 23.7 + - - -
270A PHE 3.3 1.5 + - - -
272A ASN* 1.3 73.0 - - - +
274A MET* 1.3 51.7 + - - +
276A VAL* 3.2 1.0 + - - +
277A ALA* 2.8 37.1 + - - +
291A TYR* 3.7 13.7 - - - -
312A GLY* 4.3 3.1 - - - -
314A VAL* 3.6 16.0 - - - +
378A VAL* 4.0 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 5.8 0.9 - - - -
270A PHE* 2.8 36.6 + - + +
271A LYS* 3.8 6.1 - - - +
273A GLY* 1.3 70.7 - - - +
275A ALA* 1.3 63.1 + - - +
277A ALA* 3.1 3.5 + - - +
278A GLN* 2.9 46.8 + - - +
291A TYR* 3.5 19.0 + - + -
293A GLY* 3.0 33.9 - - - +
294A LEU* 3.3 33.2 - - + -
295A PRO* 5.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LYS 3.1 12.4 + - - +
272A ASN 3.7 3.1 - - - +
274A MET* 1.3 79.2 - - - +
276A VAL* 1.3 63.7 + - - +
278A GLN* 3.3 10.6 + - - +
279A PHE* 3.0 25.3 + - - +
383A GLU* 3.0 44.9 - - + +
387A LEU* 4.2 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ASN 2.9 21.1 + - - +
273A GLY 3.6 3.1 - - - +
275A ALA* 1.3 75.7 - - - +
277A ALA* 1.3 64.7 + - - +
279A PHE* 3.4 1.8 + - - +
280A LEU* 3.1 29.6 + - + +
314A VAL* 4.4 4.5 - - + -
335A PHE* 4.7 2.5 - - + -
376A LEU* 3.7 22.0 - - + -
378A VAL* 3.7 25.6 - - + -
386A LEU* 4.5 11.4 - - + -
387A LEU* 4.0 21.1 - - + -
390A LEU* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLY 2.8 21.2 + - - +
274A MET 3.5 3.4 - - - +
276A VAL* 1.3 74.4 - - - +
278A GLN* 1.3 60.7 + - - +
280A LEU* 3.8 2.2 - - - +
281A GLU* 3.2 24.1 + - - +
289A VAL* 3.8 3.6 - - + +
291A TYR* 3.3 41.3 - - + -
294A LEU* 3.7 12.9 - - + +
314A VAL* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A MET* 2.9 46.6 + - - +
275A ALA* 3.6 7.5 - - - +
277A ALA* 1.3 74.5 - - - +
279A PHE* 1.3 68.8 + - - +
280A LEU 3.1 0.3 + - - -
281A GLU* 3.1 5.1 + - - +
282A SER* 3.0 28.9 + - - +
294A LEU* 3.7 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ALA 3.0 15.1 + - - +
276A VAL 3.7 2.7 - - - +
278A GLN* 1.3 79.0 - - - +
280A LEU* 1.3 72.8 + - + +
282A SER* 3.2 7.2 + - - -
283A ASN* 3.1 38.6 + - - +
387A LEU* 3.8 33.7 - - + -
390A LEU* 3.9 16.6 - - + -
391A ASP* 3.2 52.9 - - + -
394A LEU* 4.3 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A VAL* 3.1 36.2 + - + +
277A ALA 3.8 1.1 - - - +
279A PHE* 1.3 86.7 - - + +
281A GLU* 1.3 56.0 + - - +
282A SER 3.0 0.2 - - - -
283A ASN* 2.8 28.8 + - - +
286A VAL* 3.3 29.3 - - + +
289A VAL* 3.6 13.0 - - + -
314A VAL* 4.0 13.9 - - + -
316A PHE* 3.4 41.3 - - + -
328A PHE* 5.8 0.2 - - + -
376A LEU* 4.1 2.9 - - + -
390A LEU* 4.1 17.7 - - + -
394A LEU* 4.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ALA 3.2 15.0 + - - +
278A GLN* 3.1 5.6 + - - +
280A LEU* 1.3 77.8 - - - +
282A SER* 1.3 60.1 + - - +
283A ASN 3.3 3.5 + - - +
286A VAL* 5.0 4.8 - - - +
288A LYS* 5.8 0.8 - - - +
289A VAL* 3.3 28.5 + - + +
294A LEU* 3.5 18.6 - - + +
295A PRO* 5.6 2.1 - - - +
296A SER* 2.7 38.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLN* 3.0 19.1 + - - +
279A PHE* 3.5 7.2 - - - -
281A GLU* 1.3 79.0 - - - +
283A ASN* 1.3 60.1 + - - +
284A PRO* 3.7 6.9 - - - +
----------------------------------------------------------
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