Contacts of the helix formed by residues 249 - 269 (chain B) in PDB entry 1FVV
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 LEU 249 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B PRO* 6.3 1.3 - - + -
205B ASP* 3.3 24.5 - - + +
206B ILE* 4.2 0.4 - - - -
248B VAL* 1.3 76.4 - - - +
250B ARG* 1.3 57.1 + - + +
251B GLY* 3.0 5.6 - - - +
252B LYS* 2.7 29.2 + - + +
253B LEU 3.2 7.6 + - - -
26C THR 3.0 14.6 + - - +
27C GLY* 3.2 33.7 - - - +
28C GLU* 4.6 2.7 - - - +
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B ASP* 2.5 56.0 + - - +
206B ILE* 3.8 11.4 - - - +
210B MET* 3.1 37.3 - - + +
249B LEU* 1.3 71.1 - - + +
251B GLY* 1.3 68.0 + - - +
252B LYS 3.0 1.7 + - - -
253B LEU* 3.2 16.8 + - - +
254B GLN* 4.5 2.1 + - - +
286B TYR* 4.9 0.2 + - - -
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Residues in contact with GLY 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LEU* 2.9 5.5 + - - +
250B ARG* 1.3 85.9 - - - +
252B LYS* 1.3 61.4 + - - +
286B TYR* 2.7 29.3 + - - -
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Residues in contact with LYS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B VAL* 3.9 12.8 - - + -
249B LEU* 2.7 18.2 + - + +
251B GLY* 1.3 79.9 + - - +
253B LEU* 1.3 55.0 + - - +
254B GLN 3.0 3.8 - - - -
255B LEU* 2.7 31.6 + - + +
256B VAL* 3.0 10.6 + - - +
286B TYR* 3.6 14.3 - - + -
290B GLN* 4.1 19.4 - - - +
294B MET* 4.9 1.3 - - + -
22C ARG* 5.9 2.9 - - - +
24C LYS 4.3 12.3 + - - +
25C LEU 2.9 28.5 - - - +
26C THR* 3.7 14.1 - - - +
27C GLY* 4.1 8.3 - - - +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 4.1 29.6 - - + -
210B MET* 3.9 45.8 - - + +
211B ARG* 4.4 4.0 - - + +
214B LEU* 3.7 27.5 - - + +
239B ILE* 5.1 1.6 - - + -
243B LEU* 4.2 20.0 - - + -
248B VAL* 3.7 8.9 - - + +
249B LEU 3.2 7.0 + - - +
250B ARG* 3.2 16.5 + - - +
252B LYS* 1.3 75.6 - - - +
254B GLN* 1.3 56.9 + - - +
256B VAL* 3.6 4.7 - - + +
257B GLY 3.1 19.6 + - - -
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Residues in contact with GLN 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 3.9 11.1 - - + +
217B TRP* 3.9 33.5 - - + +
250B ARG 4.5 2.0 + - - +
252B LYS 2.8 1.4 + - - -
253B LEU* 1.3 76.1 - - - +
255B LEU* 1.3 56.8 - - - +
257B GLY* 3.6 0.2 - - - -
258B THR* 2.7 39.3 + - - +
282B THR* 3.6 40.6 + - - +
285B THR* 4.3 6.9 + - - +
286B TYR* 3.4 15.6 + - + +
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B LYS* 2.7 19.7 + - + +
254B GLN* 1.3 68.9 - - - +
256B VAL* 1.3 66.9 + - - +
258B THR* 3.4 3.0 + - - -
259B ALA* 3.1 16.1 + - - +
286B TYR* 3.2 52.5 - - + -
290B GLN* 4.0 13.5 - - + +
291B VAL* 4.0 31.4 - - + +
294B MET* 3.5 35.1 - - + +
24C LYS 5.6 0.2 - - - +
25C LEU* 4.2 22.4 - - + +
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ILE* 4.7 16.8 - - + -
242B PHE* 3.9 34.8 - - + -
243B LEU* 4.8 4.0 - - + -
248B VAL* 3.9 28.0 - - + -
252B LYS 3.0 12.9 + - - +
253B LEU* 3.6 8.7 - - + +
255B LEU* 1.3 78.0 - - - +
257B GLY* 1.3 64.4 + - - +
259B ALA* 3.6 2.3 - - - +
260B ALA* 2.9 22.4 + - + +
294B MET* 3.6 26.5 - - + -
298B VAL* 4.8 5.4 - - + +
26C THR* 5.5 0.4 - - + -
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Residues in contact with GLY 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B LEU* 4.2 9.2 - - - +
217B TRP* 4.8 0.7 - - - -
218B LEU* 4.1 9.6 - - - +
239B ILE* 3.5 25.3 - - - +
253B LEU 3.1 12.4 + - - -
254B GLN 3.2 3.6 + - - -
256B VAL* 1.3 80.9 - - - +
258B THR* 1.3 61.6 + - - +
260B ALA* 3.3 3.6 + - - +
261B MET* 3.0 23.2 + - - +
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Residues in contact with THR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B TRP* 3.5 14.8 - - + -
254B GLN 2.7 27.2 + - - -
255B LEU* 3.8 10.8 - - - -
257B GLY* 1.3 71.6 - - - +
259B ALA* 1.3 60.3 + - - +
261B MET* 3.0 9.0 + - - +
262B LEU* 2.8 25.5 + - - +
278B PHE* 3.6 45.2 - - + +
281B ILE* 5.1 0.7 - - + -
282B THR* 3.4 21.4 - - + +
286B TYR* 4.8 0.2 - - - -
291B VAL* 4.6 13.2 - - + -
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Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B LEU 3.1 4.8 + - - +
256B VAL 3.6 2.9 - - - +
258B THR* 1.3 78.6 - - - +
260B ALA* 1.3 57.4 + - - +
262B LEU* 3.0 12.7 + - - +
263B LEU* 2.8 35.1 + - - +
291B VAL* 4.3 6.9 - - + +
294B MET* 3.6 33.4 - - + +
295B GLU* 3.8 22.6 - - + +
298B VAL* 4.3 4.3 - - + -
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Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ALA* 3.8 10.5 - - - +
238B TYR* 3.4 26.6 - - + -
239B ILE* 3.4 34.8 - - + +
256B VAL* 2.9 12.0 + - + +
257B GLY 3.4 5.4 - - - +
259B ALA* 1.3 76.4 - - - +
261B MET* 1.3 57.6 + - - +
263B LEU* 3.4 5.3 + - - -
264B ALA* 2.9 26.2 + - - +
298B VAL* 5.0 4.8 - - + +
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Residues in contact with MET 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B LEU* 3.7 33.7 - - + +
221B VAL* 4.5 6.5 - - + -
222B GLY* 4.5 12.1 - - - +
227B LEU* 3.4 30.1 - - + -
228B GLN 5.6 0.2 - - - +
231B THR* 3.8 25.6 - - + +
232B LEU* 4.4 9.2 - - + +
235B ALA* 3.7 21.5 - - - +
257B GLY 3.0 13.2 + - - +
258B THR* 3.0 10.5 + - - +
260B ALA* 1.3 75.4 - - - +
262B LEU* 1.3 65.2 + - - +
264B ALA* 3.2 2.1 + - - +
265B SER* 2.8 27.9 + - - +
278B PHE* 3.8 18.6 - - + -
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLU* 5.8 0.2 - - - +
258B THR 2.8 12.7 + - - +
259B ALA* 3.2 9.9 - - - +
261B MET* 1.3 76.7 - - - +
263B LEU* 1.3 56.7 + - - +
265B SER* 3.2 4.9 + - - -
266B LYS* 2.9 48.0 + - + +
272B PRO* 5.5 0.4 - - + -
273B PRO 4.4 7.6 - - - +
275B VAL* 4.6 10.5 - - + -
278B PHE* 3.4 41.6 - - + -
291B VAL* 3.6 28.0 - - + -
292B LEU* 4.6 9.2 - - + -
295B GLU* 3.3 32.3 - - + +
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Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 3.7 26.6 - - + +
238B TYR* 4.1 12.8 - - + -
259B ALA 2.8 19.3 + - - +
260B ALA* 3.6 4.9 - - - +
262B LEU* 1.3 71.0 - - - +
264B ALA* 1.3 66.2 + - - +
266B LYS* 3.0 7.5 + - - +
267B PHE* 2.9 23.6 + - - +
295B GLU* 3.9 27.4 - - + +
298B VAL* 3.6 38.1 - - + -
299B LEU* 3.7 28.3 - - + -
302B LEU* 5.1 1.1 - - + -
306B LEU* 3.9 10.6 - - + +
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B THR* 3.3 29.6 - - + +
234B LEU* 3.9 5.8 - - + +
235B ALA* 3.6 16.4 - - + +
238B TYR* 3.5 16.5 - - + -
260B ALA 2.9 17.4 + - - +
261B MET 3.6 4.5 - - - +
263B LEU* 1.3 75.7 - - - +
265B SER* 1.3 56.2 + - - +
267B PHE* 3.6 1.5 - - - +
268B GLU* 2.8 35.3 + - - +
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Residues in contact with SER 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LEU* 4.3 6.4 - - - +
231B THR* 3.6 17.9 - - - +
261B MET* 2.8 16.6 + - - +
262B LEU 3.3 10.3 - - - -
264B ALA* 1.3 74.3 - - - +
266B LYS* 1.3 65.1 + - - +
269B GLU* 2.8 39.5 + - - +
272B PRO* 3.6 20.0 - - - +
273B PRO* 4.0 11.2 - - - +
278B PHE* 3.8 12.4 - - - -
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Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLU* 2.6 33.6 + - - -
44A VAL 2.9 25.7 + - - +
46A SER* 3.2 34.7 + - - +
49A ILE* 3.6 20.4 - - + -
50A ARG* 3.8 6.9 + - - +
150A ARG* 4.1 1.7 + - - -
262B LEU* 2.9 34.1 + - + +
263B LEU* 3.0 7.2 + - - +
265B SER* 1.3 75.6 - - - +
267B PHE* 1.3 59.8 + - - +
269B GLU 4.5 2.8 - - - +
272B PRO* 4.0 21.7 - - + +
275B VAL* 5.5 1.3 - - - -
295B GLU* 2.7 31.8 + - - +
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Residues in contact with PHE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 4.3 12.8 - - + +
50A ARG* 3.6 22.6 - - + -
53A SER* 3.9 22.9 - - - -
54A LEU* 4.2 8.3 - - + -
150A ARG* 2.5 27.9 + - - -
151A ALA* 4.1 22.4 - - + -
234B LEU* 3.8 22.4 - - + -
238B TYR* 4.1 10.8 - - - +
263B LEU 2.9 14.6 + - - +
264B ALA 3.6 2.7 - - - +
266B LYS* 1.3 80.2 - - - +
268B GLU* 1.3 66.9 + - - +
306B LEU* 4.1 13.5 - - + -
307B ALA* 3.6 31.2 - - + -
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Residues in contact with GLU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ARG* 4.3 5.5 + - - +
151A ALA 4.9 8.3 - - - +
154A VAL* 3.6 22.7 - - - +
155A PRO 5.3 2.1 - - - +
156A VAL* 6.0 2.1 - - - +
228B GLN* 4.9 11.0 - - + +
230B GLU* 3.5 28.6 - - + +
231B THR* 3.5 17.7 - - - +
234B LEU* 3.8 12.5 - - + +
264B ALA 2.8 19.0 + - - +
267B PHE* 1.3 88.1 - - - +
269B GLU* 1.3 64.4 + - - +
270B ILE* 3.9 1.2 + - - +
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Residues in contact with GLU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ARG* 3.3 15.6 + - - -
226B LYS 4.3 2.4 - - - +
227B LEU* 3.2 28.1 - - + +
228B GLN* 2.6 49.7 + - - +
231B THR* 2.7 17.3 + - - +
265B SER* 2.8 32.9 + - - +
266B LYS 4.5 2.3 - - - +
268B GLU* 1.3 76.5 - - - +
270B ILE* 1.3 68.0 + - - +
271B TYR* 4.1 11.2 - - - +
272B PRO* 4.1 11.8 - - + +
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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
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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