Contacts of the helix formed by residues 262 - 286 (chain A) in PDB entry 1LC7
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 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A PRO* 4.1 13.8 - - + +
40A VAL* 5.1 2.1 + - - +
41A SER* 4.4 14.8 + - - +
218A TYR* 5.5 1.0 + - - -
258A VAL 3.7 1.4 + - - -
259A ALA 3.2 17.5 + - - +
260A LEU 4.8 2.6 - - - +
261A GLN* 1.3 76.3 - - - +
263A SER* 1.3 57.3 + - - +
264A ALA* 3.0 24.3 + - - +
265A TRP* 3.0 44.2 + - + +
266A GLN* 4.7 1.9 + - - +
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Residues in contact with SER 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A GLN 2.9 10.5 + - - -
262A ASP* 1.3 70.9 + - - +
264A ALA* 1.3 57.9 + - - +
266A GLN* 5.1 3.6 + - - +
267A GLN* 5.4 3.6 + - - +
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Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ASP* 3.0 7.7 + - - +
263A SER* 1.3 79.7 - - - +
265A TRP* 1.3 66.2 + - - +
266A GLN 3.4 1.6 - - - -
267A GLN* 3.6 8.2 + - - +
268A ALA* 3.1 25.4 + - + +
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Residues in contact with TRP 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 3.7 19.5 + - - -
36A LEU* 4.0 16.4 - - + -
37A GLY 2.9 31.4 - - - -
38A MET 4.1 1.1 - - - -
39A PRO* 3.7 33.7 - - + -
40A VAL 5.1 0.9 - - - -
217A PHE* 2.9 36.5 + + - -
218A TYR* 3.4 31.4 - + + +
262A ASP* 3.0 37.9 + - + +
264A ALA* 1.3 78.8 - - - +
266A GLN* 1.3 64.8 + - - +
268A ALA* 3.3 7.4 + - + +
269A THR* 3.0 31.3 + - - -
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Residues in contact with GLN 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A PHE* 3.9 21.7 - - + -
262A ASP 4.7 2.9 + - - +
263A SER 5.1 3.8 - - - +
264A ALA 3.4 0.6 - - - +
265A TRP* 1.3 79.3 - - - +
267A GLN* 1.3 63.2 + - - +
269A THR* 3.4 1.2 + - - -
270A TRP* 3.0 50.2 + - + -
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Residues in contact with GLN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A SER 5.4 3.1 + - - +
264A ALA* 3.6 11.5 + - - +
265A TRP 3.3 0.4 - - - -
266A GLN* 1.3 79.2 - - - +
268A ALA* 1.3 58.4 + - - +
270A TRP* 3.3 25.1 + - + +
271A HIS* 2.9 40.5 + - - +
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ALA* 3.1 19.8 + - + +
265A TRP* 3.7 9.6 - - + +
267A GLN* 1.3 76.9 - - - +
269A THR* 1.3 62.0 + - - +
271A HIS* 3.6 6.3 + - - +
272A TRP* 3.2 22.9 + - - +
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Residues in contact with THR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ASN* 3.1 26.9 + - - +
36A LEU* 5.4 2.1 - - - +
191A PHE* 3.8 19.5 - - + +
217A PHE* 3.5 27.1 - - + -
265A TRP* 3.0 28.7 + - - -
266A GLN 3.8 3.8 - - - -
268A ALA* 1.3 74.5 - - - +
270A TRP* 1.3 68.0 + - + +
272A TRP* 3.3 17.4 + - + -
273A LEU* 3.0 20.1 + - + +
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Residues in contact with TRP 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ASP* 2.7 27.0 + - - -
191A PHE* 3.4 23.7 + - - -
192A ILE 4.3 2.2 - - - -
193A PRO* 3.1 46.7 - - + +
195A GLU 5.6 2.0 - - - -
217A PHE* 4.7 1.9 - + - -
266A GLN* 3.0 37.9 + - + +
267A GLN* 3.8 26.7 - - + +
269A THR* 1.3 79.7 - - + +
271A HIS* 1.3 58.6 + - - +
273A LEU* 3.3 5.4 + - - +
274A ARG* 2.8 30.9 + - - +
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Residues in contact with HIS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A GLN* 2.9 29.6 + - - +
268A ALA* 3.8 6.7 + - - +
270A TRP* 1.3 77.2 - - - +
272A TRP* 1.3 61.4 + - - +
274A ARG* 3.1 8.2 + - + +
275A GLU* 2.9 40.8 + - + +
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Residues in contact with TRP 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 4.9 2.7 - - - -
35A PRO* 3.3 39.8 - - + +
191A PHE* 4.2 20.2 - + - -
268A ALA 3.2 12.6 + - - +
269A THR* 3.4 25.8 - - + +
271A HIS* 1.3 82.9 + - - +
273A LEU* 1.3 82.8 + - + +
275A GLU* 4.8 1.6 - - - -
276A GLU* 2.9 43.7 + - + +
277A GLY 3.2 4.2 + - - -
298A ASN* 3.9 14.6 - - + -
340A ILE* 3.2 35.0 - - + -
341A ARG 3.2 21.1 + - - -
342A SER* 4.5 3.9 - - - +
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A PHE* 3.2 37.9 - - + +
269A THR* 3.0 17.8 + - + +
270A TRP* 3.7 5.8 - - - +
272A TRP* 1.3 99.5 - - + +
274A ARG* 1.3 62.0 + - - +
277A GLY* 3.2 23.8 - - - +
278A ALA* 3.3 4.2 + - - +
296A ARG 4.1 7.6 - - - +
297A ALA 3.7 35.4 - - - +
298A ASN 4.4 0.4 - - - +
340A ILE* 3.9 18.8 - - + -
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A TRP 2.8 18.1 + - - +
271A HIS* 3.5 10.3 - - + +
273A LEU* 1.3 78.9 - - - +
275A GLU* 1.3 55.9 + - - +
278A ALA* 3.4 19.9 - - - +
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A HIS* 2.9 32.0 + - + +
272A TRP* 3.2 2.2 + - - +
274A ARG* 1.3 77.5 - - - +
276A GLU* 1.3 67.2 + - + +
277A GLY 3.3 0.7 - - - -
278A ALA* 3.3 2.8 + - - +
279A ARG* 3.0 23.7 + - - +
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A TRP* 2.9 24.8 + - + +
275A GLU* 1.3 75.7 - - + +
277A GLY* 1.3 60.1 + - - +
279A ARG* 2.9 38.8 + - - +
280A PHE* 2.8 30.7 + - - +
340A ILE* 5.2 0.2 - - + -
341A ARG 3.9 6.7 - - - +
343A ALA* 3.4 37.1 - - + +
346A ASN* 2.8 31.3 + - - +
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Residues in contact with GLY 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A TRP* 3.2 10.7 + - - +
273A LEU* 3.2 20.6 + - - -
275A GLU 3.3 0.2 - - - -
276A GLU* 1.3 78.2 - - - +
278A ALA* 1.3 60.0 + - - +
280A PHE* 3.4 2.3 + - - +
281A TYR* 3.1 21.7 + - - +
340A ILE* 3.9 29.5 - - - +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A LEU 3.3 5.8 + - - +
274A ARG* 3.4 21.5 - - - +
275A GLU 3.3 3.4 + - - +
276A GLU 3.3 0.2 - - - -
277A GLY* 1.3 72.2 - - - +
279A ARG* 1.3 65.4 + - - +
281A TYR* 3.3 6.3 + - - +
282A GLN* 3.0 33.1 + - + +
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Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A GLU 3.0 17.5 + - - +
276A GLU* 2.9 39.6 + - - +
278A ALA* 1.3 77.0 - - - +
280A PHE* 1.3 57.4 + - - +
282A GLN* 3.4 8.0 + - + +
283A ALA* 3.0 32.3 + - + +
343A ALA* 3.8 17.0 + - - +
346A ASN* 4.4 4.2 - - - +
347A GLU* 2.3 43.5 + - - +
350A LEU* 4.3 10.0 - - - +
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Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLU* 2.8 21.3 + - - +
277A GLY* 3.6 5.6 - - - +
279A ARG* 1.3 75.8 - - - +
281A TYR* 1.3 64.8 + - - +
283A ALA* 3.2 4.1 + - - +
284A LEU* 3.0 50.8 + - + +
300A LEU* 4.1 5.2 - - + -
338A VAL* 4.4 2.9 - - + -
339A ALA 3.4 21.8 - - - -
340A ILE* 3.6 29.2 - - + -
346A ASN* 3.5 48.0 - - + +
349A LEU* 3.5 27.1 - - + -
350A LEU* 4.1 18.4 - - + -
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Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A GLY 3.1 14.5 + - - +
278A ALA* 3.3 10.1 + - - +
280A PHE* 1.3 75.3 - - - +
282A GLN* 1.3 81.4 + - - +
284A LEU* 3.3 3.1 + - - +
285A CYS* 3.0 40.4 + - - -
292A VAL* 2.8 39.2 + - + -
293A TYR 3.4 20.4 - - - -
294A PRO* 3.5 26.2 - - + +
300A LEU* 4.0 23.5 - - + +
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Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ALA* 3.0 24.5 + - + +
279A ARG* 3.5 8.5 - - - +
280A PHE 3.2 0.2 - - - -
281A TYR* 1.3 96.1 - - - +
283A ALA* 1.3 62.0 + - - +
285A CYS* 3.2 16.8 + - - +
286A GLN* 3.2 23.5 + - + +
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ARG* 3.0 25.7 + - - +
280A PHE* 3.2 2.7 + - - +
282A GLN* 1.3 76.3 - - - +
284A LEU* 1.3 62.8 + - - +
286A GLN* 3.1 21.5 + - - +
287A LEU* 3.6 10.7 + - - +
350A LEU* 3.4 33.1 - - + +
354A ARG* 5.0 7.0 + - - +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A PHE* 3.0 41.1 + - + +
281A TYR 3.6 3.8 - - - +
283A ALA* 1.3 76.4 - - - +
285A CYS* 1.3 62.9 + - - +
287A LEU* 3.3 24.4 + - + +
290A LEU* 3.9 8.4 - - + +
292A VAL* 3.7 19.6 - - + +
300A LEU* 3.5 31.6 - - + -
302A LEU* 4.4 16.6 - - + -
338A VAL* 4.5 4.0 - - + -
349A LEU* 5.0 1.1 - - + -
350A LEU* 3.7 15.9 - - + -
353A LEU* 3.6 31.9 - - + -
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Residues in contact with CYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A TYR* 3.0 57.4 + - - +
282A GLN* 3.2 12.3 + - - +
284A LEU* 1.3 76.3 - - - +
286A GLN* 1.3 62.9 + - + +
287A LEU 3.2 7.0 + - - +
290A LEU 5.0 3.8 - - - +
292A VAL* 4.0 16.6 - - - -
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Residues in contact with GLN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLN* 3.2 21.0 + - + +
283A ALA* 3.1 12.6 + - - +
285A CYS* 1.3 78.5 - - - +
287A LEU* 1.3 62.5 + - + +
288A PRO* 3.6 4.9 - - - +
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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
------------------------------------------------------------
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