Contacts of the helix formed by residues 265 - 286 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264U PRO* 1.3 79.4 - - + +
266U THR* 1.3 55.3 + - - +
267U ASN 3.2 2.7 - - - +
268U ILE* 3.6 21.6 - - + +
269U CYS* 2.8 36.7 + - - +
340U ALA* 4.0 25.6 - - + +
342U VAL* 4.4 22.4 - - + -
439U PHE* 3.9 33.0 - - + -
502U 9CR 4.3 9.4 - - + -
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Residues in contact with THR 266 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261U PRO* 5.9 6.1 - - + -
263U ASP 5.3 2.7 - - - +
264U PRO* 2.3 26.9 + - - -
265U VAL* 1.3 67.5 - - - +
267U ASN* 1.3 61.2 + - - +
269U CYS* 3.7 6.0 - - - +
270U GLN* 2.5 59.7 + - + +
445U THR* 4.7 12.6 + - - -
446U PRO 4.8 5.1 + - - +
447U ILE* 5.7 2.8 - - - +
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Residues in contact with ASN 267 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261U PRO* 4.8 11.4 + - - +
263U ASP 3.6 21.4 + - - +
264U PRO* 3.9 11.6 - - + +
265U VAL 3.2 0.6 - - - +
266U THR* 1.3 81.7 - - - +
268U ILE* 1.3 58.0 + - + +
270U GLN* 3.1 16.9 + - - +
271U ALA* 2.8 30.7 + - - +
326U LEU* 4.0 7.7 - - + +
328U THR* 4.9 1.7 + - - -
330U LEU* 3.6 36.4 - - + +
332U VAL* 6.1 0.9 - - + -
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Residues in contact with ILE 268 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264U PRO* 6.1 1.6 - - + -
265U VAL* 3.5 20.0 + - + +
266U THR 3.3 0.4 - - - -
267U ASN* 1.3 80.4 - - + +
269U CYS* 1.3 63.8 + - - +
271U ALA* 3.1 6.4 + - - +
272U ALA* 2.9 20.1 + - - +
324U ILE* 4.3 16.6 - - + -
326U LEU* 4.0 25.4 - - + -
332U VAL* 4.5 15.0 - - + -
342U VAL* 5.9 1.6 - - + -
346U PHE* 5.0 4.3 - - + -
502U 9CR 4.0 70.8 - - + +
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Residues in contact with CYS 269 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265U VAL* 2.8 31.0 + - - +
266U THR* 3.7 6.7 - - - +
268U ILE* 1.3 73.4 - - - +
270U GLN* 1.3 63.9 + - - +
272U ALA* 3.0 11.0 + - - +
273U ASP* 2.9 22.2 + - - +
436U LEU* 3.6 30.5 - - - -
439U PHE* 5.1 2.5 - - - -
447U ILE* 4.0 19.7 - - + -
448U ASP* 5.3 0.2 - - - -
451U LEU* 3.8 19.1 - - + +
502U 9CR 4.4 10.8 - - - -
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Residues in contact with GLN 270 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266U THR* 2.5 40.1 + - + +
267U ASN* 3.5 16.3 + - - +
269U CYS* 1.3 74.0 - - - +
271U ALA* 1.3 57.7 + - - +
273U ASP* 3.4 2.8 + - - +
274U LYS* 3.0 28.3 + - - +
328U THR* 4.8 5.6 - - + +
448U ASP* 3.7 25.9 - - - +
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Residues in contact with ALA 271 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267U ASN 2.8 13.0 + - - +
268U ILE 3.2 10.8 - - - +
270U GLN* 1.3 73.7 - - - +
272U ALA* 1.3 55.8 + - - +
274U LYS* 3.0 9.8 - - - +
275U GLN* 2.8 36.6 + - - +
326U LEU* 4.0 16.6 - - + -
327U ALA 4.6 0.7 - - - +
328U THR* 4.0 14.8 - - + +
502U 9CR 3.1 28.0 - - + +
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Residues in contact with ALA 272 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268U ILE 2.9 11.9 + - - +
269U CYS* 3.2 13.7 - - - +
271U ALA* 1.3 74.0 - - - +
273U ASP* 1.3 59.5 + - - +
275U GLN* 3.0 2.8 + - - -
276U LEU* 2.8 31.5 + - - +
305U TRP* 5.1 0.9 - - - +
309U LEU* 3.6 11.5 - - + +
451U LEU* 4.6 16.4 - - + -
502U 9CR 3.9 36.3 - - + +
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Residues in contact with ASP 273 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269U CYS 2.9 10.6 + - - +
270U GLN 3.7 2.5 - - - +
272U ALA* 1.3 75.5 - - - +
274U LYS* 1.3 65.9 + - - +
276U LEU* 3.1 25.5 + - - +
277U PHE* 3.3 28.9 - - - -
448U ASP* 3.2 38.1 - - + +
450U PHE* 2.9 18.1 + - - +
451U LEU* 2.8 34.0 + - + +
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Residues in contact with LYS 274 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243U GLU* 3.6 24.4 + - - +
270U GLN 3.0 15.2 + - - +
271U ALA* 3.0 16.8 - - - +
273U ASP* 1.3 81.0 + - - +
275U GLN* 1.3 68.0 + - - +
276U LEU 3.4 0.2 + - - -
277U PHE* 3.4 24.4 + - + +
278U THR* 3.9 5.1 + - - +
327U ALA* 4.2 19.3 + - + -
328U THR* 3.8 19.5 - - + +
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Residues in contact with GLN 275 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242U VAL 4.8 1.4 - - - +
243U GLU* 4.0 18.1 + - - +
271U ALA 2.8 17.7 + - - +
272U ALA 3.7 3.1 - - - +
274U LYS* 1.3 80.9 + - - +
276U LEU* 1.3 55.5 + - - +
277U PHE 3.0 2.2 - - - -
278U THR* 3.0 23.9 + - - +
279U LEU* 2.7 35.0 + - - +
309U LEU* 3.9 26.2 - - + -
312U SER* 5.9 3.8 - - - -
316U ARG* 4.5 5.9 + - - +
327U ALA* 3.0 33.8 - - - +
502U 9CR 4.2 13.9 - - + +
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Residues in contact with LEU 276 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272U ALA 2.8 6.9 + - - +
273U ASP* 3.1 18.3 + - - +
275U GLN* 1.3 75.7 - - - +
277U PHE* 1.3 64.5 + - - +
279U LEU* 3.3 21.3 + - + +
280U VAL* 3.5 13.2 + - - +
305U TRP* 2.9 44.9 - - + +
309U LEU* 3.4 11.2 - - + -
450U PHE* 3.5 29.9 - - + +
451U LEU* 3.6 43.3 - - + +
454U MET* 4.4 10.1 - - + -
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Residues in contact with PHE 277 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273U ASP* 3.3 41.5 - - - -
274U LYS* 3.6 13.9 - - + +
275U GLN 3.0 0.4 - - - -
276U LEU* 1.3 77.7 - - - +
278U THR* 1.3 63.4 + - - +
280U VAL* 3.2 19.7 + - - +
281U GLU* 3.8 10.0 + - - +
449U THR* 6.2 0.2 - - - -
450U PHE* 3.5 29.6 - + + -
632V ILE* 4.3 11.9 - - + -
636V LEU* 3.9 16.9 - - + +
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Residues in contact with THR 278 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242U VAL* 3.3 39.7 - - + -
243U GLU* 3.2 23.9 + - - +
274U LYS* 4.1 9.2 + - - +
275U GLN* 3.0 23.2 + - - +
277U PHE* 1.3 75.0 - - - +
279U LEU* 1.3 67.3 + - - +
281U GLU* 2.9 12.6 + - + +
282U TRP* 2.9 19.2 + - - +
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Residues in contact with LEU 279 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275U GLN* 2.7 17.1 + - - +
276U LEU* 3.4 16.8 - - + +
277U PHE 3.2 0.2 - - - -
278U THR* 1.3 72.8 - - - +
280U VAL* 1.3 57.5 - - + +
282U TRP* 3.4 27.8 + - + -
283U ALA* 3.0 26.7 + - - +
301U LEU* 4.0 17.5 - - + +
305U TRP* 3.8 35.2 - - + +
308U LEU* 4.0 11.0 - - + -
309U LEU* 4.0 18.4 - - + -
371U ARG* 3.8 20.9 - - - +
454U MET* 6.1 0.9 - - + -
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Residues in contact with VAL 280 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276U LEU 3.5 15.3 - - - +
277U PHE 3.4 9.0 - - - +
278U THR 3.1 1.0 - - - -
279U LEU* 1.3 77.9 - - + +
281U GLU* 1.3 70.8 + - - +
283U ALA* 3.5 3.1 + - - +
284U LYS* 3.2 27.7 + - - +
301U LEU* 4.4 9.9 - - + -
450U PHE* 4.4 10.8 - - + -
633V LEU* 4.4 13.0 - - + -
636V LEU* 3.9 39.3 - - + -
637V LEU* 4.1 24.9 - - + +
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Residues in contact with GLU 281 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242U VAL* 4.0 7.2 - - + -
277U PHE 4.0 11.4 - - - +
278U THR* 2.9 13.2 + - + +
280U VAL* 1.3 88.6 - - - +
282U TRP* 1.3 65.1 + - - +
284U LYS* 3.4 18.5 + - - +
285U ARG* 3.2 48.8 + - - +
636V LEU* 5.2 2.1 - - - +
639V GLU* 3.6 19.9 - - - +
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Residues in contact with TRP 282 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235U ILE 4.8 0.4 + - - -
238U ALA* 3.6 17.5 - - + +
239U GLU* 2.8 20.4 + - - -
242U VAL* 3.4 40.5 - - + +
278U THR 2.9 8.9 + - - +
279U LEU* 3.6 24.7 - - + +
281U GLU* 1.3 77.0 - - - +
283U ALA* 1.3 77.1 + - + +
285U ARG* 3.1 14.9 + - - +
286U ILE* 3.3 41.2 + - + +
301U LEU* 5.6 0.2 - - + -
308U LEU* 4.0 17.5 - - + -
368U GLY 4.0 4.3 - - - -
371U ARG* 3.5 59.2 - - + +
372U ALA* 3.8 7.2 - - - -
375U LEU* 3.8 20.4 - - + -
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Residues in contact with ALA 283 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279U LEU 3.0 17.6 + - - +
280U VAL 3.7 5.2 - - - +
281U GLU 3.3 0.2 - - - -
282U TRP* 1.3 88.5 - - + +
284U LYS* 1.3 61.7 + - - +
286U ILE* 2.9 16.0 + - - +
289U PHE* 3.2 48.0 - - + +
301U LEU* 4.0 18.2 - - + -
375U LEU* 4.5 2.5 - - + -
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Residues in contact with LYS 284 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234U ARG* 5.5 1.7 + - - -
280U VAL* 3.2 20.7 + - + +
281U GLU* 3.6 25.4 - - - +
282U TRP 3.3 0.2 - - - -
283U ALA* 1.3 78.0 - - - +
285U ARG* 1.3 64.5 + - - +
286U ILE 3.4 6.4 + - - +
289U PHE* 4.0 1.3 - - + -
290U SER* 3.3 32.6 + - - +
297U GLN* 4.9 2.0 - - - +
636V LEU 3.5 14.4 - - - -
637V LEU* 2.6 37.6 + - + +
639V GLU* 3.1 24.7 + - - -
640V GLY* 5.1 3.2 - - - -
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Residues in contact with ARG 285 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234U ARG* 4.2 22.2 + - - +
237U GLU 5.9 0.2 - - - -
238U ALA* 3.7 21.1 - - + +
241U ALA* 3.7 29.8 - - + +
242U VAL* 4.7 4.9 - - - +
281U GLU* 3.2 41.8 + - - +
282U TRP* 3.1 11.1 + - - +
283U ALA 3.1 1.2 - - - -
284U LYS* 1.3 80.9 - - - +
286U ILE* 1.3 61.6 + - - +
287U PRO* 3.5 6.8 - - - +
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Residues in contact with ILE 286 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230U MET* 4.8 2.9 - - + -
234U ARG* 4.6 1.2 + - - -
235U ILE* 4.2 22.7 - - + -
238U ALA* 3.9 12.1 - - + -
282U TRP* 3.4 59.2 - - + +
283U ALA* 2.9 11.2 + - - +
284U LYS 3.8 4.6 - - - +
285U ARG* 1.3 78.5 - - - +
287U PRO* 1.3 76.6 - - + +
288U HIS 3.3 0.9 + - - -
289U PHE* 3.1 17.4 + - + +
290U SER 4.6 0.2 + - - -
372U ALA* 4.3 12.6 - - + -
375U LEU* 4.3 6.5 - - + -
376U PHE* 3.8 30.3 - - + -
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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