Contacts of the helix formed by residues 265 - 286 (chain A) in PDB entry 1FM6
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 VAL 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ASP 3.4 1.2 + - - -
264A PRO* 1.3 75.5 - - - +
266A THR* 1.3 67.3 + - - +
267A ASN 3.3 0.8 + - - -
268A ILE* 3.5 10.0 + - - +
269A CYS* 3.2 31.6 + - - -
340A ALA* 4.0 21.7 - - + +
342A VAL* 3.7 31.2 - - + -
439A PHE* 4.0 32.1 - - + -
501A 9CR 4.3 9.6 - - + -
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Residues in contact with THR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PRO* 6.3 3.8 - - + -
263A ASP* 2.6 29.4 + - - -
265A VAL* 1.3 83.1 + - - +
267A ASN* 1.3 58.8 + - - +
269A CYS* 3.3 7.9 + - + +
270A GLN* 2.9 43.4 + - + +
445A THR* 5.5 10.3 + - - +
446A PRO 5.5 3.1 - - - +
447A ILE* 5.8 4.9 - - + -
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Residues in contact with ASN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PRO* 5.5 7.6 + - - +
263A ASP 3.3 17.9 + - - +
264A PRO* 4.3 15.5 - - + +
265A VAL 3.3 0.6 - - - -
266A THR* 1.3 79.9 - - - +
268A ILE* 1.3 55.3 + - + +
270A GLN* 3.4 13.8 + - - +
271A ALA* 3.0 27.5 + - - +
326A LEU* 3.7 9.1 - - + +
328A THR* 4.7 2.6 + - - -
330A LEU* 2.6 40.7 - - + +
332A VAL* 5.4 2.2 - - + -
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Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PRO 4.3 15.0 - - - +
265A VAL* 3.5 8.7 + - - +
267A ASN* 1.3 73.4 - - - +
269A CYS* 1.3 61.7 + - - +
271A ALA* 3.8 3.5 - - - +
272A ALA* 2.9 27.1 + - + +
324A ILE* 6.2 1.1 - - + -
326A LEU* 4.0 28.3 - - + -
332A VAL* 4.4 15.9 - - + -
342A VAL* 6.0 2.0 - - + -
346A PHE* 5.0 9.4 - - + -
501A 9CR 3.9 77.4 - - + +
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Residues in contact with CYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A VAL* 3.2 25.9 + - - +
266A THR* 3.7 10.1 - - + +
268A ILE* 1.3 78.5 - - - +
270A GLN* 1.3 67.1 + - - +
272A ALA* 3.4 7.0 + - - +
273A ASP* 3.0 23.6 + - - +
436A LEU* 3.9 27.8 - - - -
439A PHE* 5.5 1.1 - - - -
447A ILE* 4.2 26.7 - - + -
448A ASP* 4.8 2.3 - - - +
451A LEU* 4.0 13.9 - - + +
501A 9CR 4.4 7.0 - - - -
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Residues in contact with GLN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A SER* 5.3 5.7 - - - +
266A THR* 2.9 32.0 + - + +
267A ASN* 3.5 12.9 + - - +
268A ILE 3.2 0.2 - - - -
269A CYS* 1.3 77.6 - - - +
271A ALA* 1.3 63.8 + - - +
273A ASP* 3.2 4.7 + - - +
274A LYS* 3.0 22.2 + - - +
328A THR* 4.8 10.1 + - + +
448A ASP* 3.7 20.5 - - - +
227U ASN* 5.4 7.3 - - - +
234U ARG* 4.6 24.7 + - - +
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ASN 3.0 17.0 + - - +
268A ILE 3.8 5.4 - - - +
269A CYS 3.3 0.2 - - - -
270A GLN* 1.3 76.5 - - - +
272A ALA* 1.3 56.1 + - - +
274A LYS* 3.3 2.3 + - - +
275A GLN* 2.9 34.1 + - - +
326A LEU* 3.8 17.9 - - + -
327A ALA* 4.3 1.3 - - - +
328A THR* 4.0 20.1 - - + +
501A 9CR 3.4 26.7 - - + +
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ILE 2.9 19.1 + - - +
269A CYS* 3.5 8.3 - - - +
271A ALA* 1.3 76.1 - - - +
273A ASP* 1.3 62.8 + - - +
275A GLN* 3.1 4.0 + - - +
276A LEU* 2.9 24.4 + - - +
305A TRP* 5.0 0.7 - - + -
309A LEU* 3.8 11.6 - - + +
451A LEU* 4.7 15.0 - - + -
501A 9CR 3.9 35.4 - - + +
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Residues in contact with ASP 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A CYS 3.0 13.6 + - - +
270A GLN 3.5 7.9 - - - +
272A ALA* 1.3 76.0 - - - +
274A LYS* 1.3 65.3 + - - +
276A LEU* 3.0 21.0 + - - +
277A PHE* 3.2 22.5 - - - -
448A ASP* 3.3 19.4 - - + +
449A THR 2.2 27.8 - - - +
450A PHE* 3.6 2.3 - - - +
451A LEU* 3.2 14.5 + - + +
233U GLU* 5.3 0.3 - - - +
237U GLU* 2.3 33.3 - - - +
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Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A THR* 5.9 4.4 + - - +
270A GLN 3.0 12.9 + - - +
271A ALA* 3.5 7.9 - - - +
273A ASP* 1.3 77.5 + - - +
275A GLN* 1.3 76.9 + - - +
276A LEU 3.1 1.2 + - - -
277A PHE* 3.1 28.6 + - - +
278A THR* 3.7 7.5 + - + +
327A ALA* 3.0 26.6 + - + +
328A THR* 3.5 28.4 - - + +
227U ASN* 4.0 12.8 - - + +
228U GLU* 6.0 1.6 - - - +
233U GLU* 3.7 35.3 - - + +
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Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A VAL 4.7 1.0 - - - +
243A GLU 3.9 16.3 + - - +
244A PRO* 5.2 0.8 - - - +
271A ALA 2.9 16.4 + - - +
272A ALA 3.8 3.8 - - - +
274A LYS* 1.3 86.6 - - - +
276A LEU* 1.3 59.6 + - - +
278A THR* 2.8 30.3 + - - +
279A LEU* 2.8 30.9 + - - +
309A LEU* 4.1 20.1 - - + +
312A SER* 5.8 2.0 - - - -
316A ARG* 4.1 5.2 + - - -
327A ALA* 3.3 26.8 - - + +
501A 9CR 3.2 26.0 - - + +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ALA 2.9 10.0 + - - +
273A ASP* 3.0 13.8 + - - +
275A GLN* 1.3 78.4 - - - +
277A PHE* 1.3 61.0 + - - +
279A LEU* 3.3 16.8 + - + +
280A VAL* 3.4 17.3 - - - +
305A TRP* 3.7 26.2 - - + -
309A LEU* 3.5 28.3 - - + -
450A PHE* 3.6 20.3 - - + +
451A LEU* 3.7 34.8 - - + +
454A MET* 3.5 32.5 - - + -
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Residues in contact with PHE 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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273A ASP* 3.2 32.5 - - - -
274A LYS* 3.1 22.8 + - - +
276A LEU* 1.3 75.4 - - - +
278A THR* 1.3 65.1 + - + +
280A VAL* 3.4 13.9 + - - +
281A GLU* 3.5 8.7 + - - +
450A PHE* 3.6 26.2 - + + -
632B ILE* 4.4 9.9 - - + -
636B LEU* 3.9 20.1 - - + +
233U GLU* 3.5 35.4 - - + -
236U LEU* 3.9 25.4 - - + -
237U GLU* 3.9 17.0 - - + -
240U LEU* 5.6 0.4 - - + -
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Residues in contact with THR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A VAL* 4.7 19.9 + - - +
243A GLU 5.4 1.3 - - - +
274A LYS* 3.8 11.2 - - + +
275A GLN* 2.8 49.6 + - - +
277A PHE* 1.3 75.1 - - + +
279A LEU* 1.3 60.3 + - - +
281A GLU* 2.8 31.6 + - - +
282A TRP* 2.9 14.4 + - - +
309A LEU* 5.7 0.3 - - - +
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Residues in contact with LEU 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 GLN 2.8 19.9 + - - +
276A LEU* 3.5 12.1 - - + +
278A THR* 1.3 74.3 + - - +
280A VAL* 1.3 58.3 + - + +
282A TRP* 3.3 16.5 + - + +
283A ALA* 2.9 27.2 + - - +
301A LEU* 4.0 20.0 - - + +
305A TRP* 3.7 37.5 - - + -
308A LEU* 3.8 19.1 - - + -
309A LEU* 4.0 17.0 - - + -
371A ARG* 3.8 26.7 - - - +
454A MET* 5.6 1.6 - - + -
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Residues in contact with VAL 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 LEU 3.4 15.9 - - - +
277A PHE 3.5 7.4 - - - +
278A THR 3.1 0.6 - - - -
279A LEU* 1.3 74.1 - - + +
281A GLU* 1.3 65.9 + - - +
283A ALA* 3.3 7.0 + - - +
284A LYS* 3.2 32.7 + - - +
301A LEU* 4.3 6.3 - - + -
450A PHE* 4.2 9.0 - - + -
633B LEU* 3.8 25.1 - - + -
636B LEU* 3.9 32.1 - - + +
637B LEU* 3.8 27.8 - - + -
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Residues in contact with GLU 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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241A ALA 4.9 0.2 - - - +
242A VAL* 4.0 20.2 - - + +
277A PHE 3.5 3.6 + - - +
278A THR* 2.8 24.6 + - - +
280A VAL* 1.3 79.3 - - - +
282A TRP* 1.3 60.3 + - - +
284A LYS* 3.4 20.2 + - + +
285A ARG* 3.5 30.1 + - - +
406U HIS* 3.1 27.7 + - - -
407U LYS* 2.7 34.3 + - - +
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Residues in contact with TRP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ALA* 3.6 28.5 - - + +
239A GLU* 2.7 20.9 + - - +
242A VAL* 4.0 19.2 - - + +
278A THR 2.9 10.4 + - - +
279A LEU* 3.5 22.9 - - + +
281A GLU* 1.3 74.9 - - - +
283A ALA* 1.3 84.7 + - + +
285A ARG* 2.9 18.4 + - - +
286A ILE* 3.2 38.7 + - + +
301A LEU* 5.4 0.2 - - + -
308A LEU* 3.9 16.8 - - + -
368A GLY 4.1 2.5 - - - -
371A ARG* 3.2 66.6 - - + +
372A ALA 4.1 2.7 - - - -
375A LEU* 3.9 27.8 - - + -
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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
----------------------------------------------------------
279A LEU 2.9 14.4 + - - +
280A VAL 3.5 8.7 - - - +
282A TRP* 1.3 88.9 - - + +
284A LYS* 1.3 62.4 + - - +
285A ARG 3.3 0.7 + - - -
286A ILE* 3.3 9.2 + - - +
289A PHE* 3.1 54.2 - - + +
301A LEU* 4.0 18.2 - - + -
375A LEU* 4.6 2.2 - - + -
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Residues in contact with LYS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ARG* 5.5 1.2 + - - -
280A VAL* 3.2 22.4 + - + +
281A GLU* 3.6 11.9 - - + +
282A TRP 3.2 0.4 - - - -
283A ALA* 1.3 76.9 - - + +
285A ARG* 1.3 61.5 + - + +
286A ILE 3.7 4.5 + - - +
289A PHE* 4.2 4.5 - - + -
290A SER* 3.5 31.4 + - - +
297A GLN* 5.4 0.4 - - - +
636B LEU 2.6 29.8 + - - -
637B LEU* 3.3 30.8 + - + +
639B GLU* 3.8 23.0 + - - +
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Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ARG* 3.9 25.0 + - - +
237A GLU 5.2 0.2 - - - -
238A ALA* 3.5 30.2 - - + +
241A ALA* 3.7 32.5 + - - +
242A VAL* 4.5 9.4 - - - +
281A GLU* 3.6 26.5 + - - +
282A TRP* 2.9 4.7 + - - +
284A LYS* 1.3 78.2 - - + +
286A ILE* 1.3 64.2 + - - +
287A PRO* 3.2 8.5 - - - +
406U HIS* 5.5 6.5 + - - -
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Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A MET* 4.6 6.7 - - + -
235A ILE* 4.2 19.1 - - + +
238A ALA* 3.2 31.2 - - + -
282A TRP* 3.2 45.6 + - + +
283A ALA 3.3 9.9 + - - +
284A LYS 4.0 3.8 - - - +
285A ARG* 1.3 76.0 - - - +
287A PRO* 1.3 84.1 - - + +
288A HIS 3.3 0.3 + - - -
289A PHE* 3.3 14.3 + - + +
372A ALA* 4.4 9.6 - - + -
375A LEU* 4.4 6.1 - - + -
376A PHE* 3.7 26.7 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
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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