Contacts of the helix formed by residues 274 - 296 (chain B) in PDB entry 1V2E
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 GLY 274 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B ALA 3.2 0.2 + - - -
271B ARG 3.1 11.2 + - - -
272B ARG 3.0 8.2 + - - -
273B GLU* 1.3 77.2 - - - +
275B PHE* 1.3 67.1 + - - +
276B TYR 3.5 2.2 - - - -
277B GLU* 3.0 30.0 - - - +
278B ALA* 3.3 7.1 + - - +
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Residues in contact with PHE 275 (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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40B PRO* 3.7 32.8 - - + -
42B PHE* 3.7 25.6 - + + -
223B ARG 3.8 12.8 - - - -
224B LEU* 3.9 12.3 - - + -
225B GLU* 4.7 4.3 - - + -
270B ALA* 3.1 22.0 + - + +
273B GLU* 3.1 6.5 - - + -
274B GLY* 1.3 76.5 - - - +
276B TYR* 1.3 73.3 + + - +
278B ALA* 3.2 8.3 + - + +
279B LEU* 2.8 63.5 + - + +
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Residues in contact with TYR 276 (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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73B GLU* 4.3 1.4 + - - -
196B GLU* 3.5 34.3 - - + +
223B ARG* 2.6 69.8 + - - +
224B LEU* 4.3 3.7 - - + +
267B LEU* 3.8 12.5 - - - +
270B ALA* 3.8 24.1 + - + +
271B ARG* 3.7 32.3 - - - -
274B GLY 3.5 0.4 - - - -
275B PHE* 1.3 90.9 - + - +
277B GLU* 1.3 69.7 + - - +
279B LEU* 3.1 9.5 + - + +
280B ARG* 3.0 33.5 + - - +
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Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B GLY* 3.0 21.8 + - - +
276B TYR* 1.3 81.7 - - - +
278B ALA* 1.3 62.0 + - + +
280B ARG* 3.1 31.9 + - - +
281B GLU* 3.4 8.3 + - - +
284B ARG* 5.5 0.7 + - - -
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B GLY 4.2 5.2 - - - +
275B PHE* 3.2 8.5 + - + +
277B GLU* 1.3 75.4 - - + +
279B LEU* 1.3 67.2 + - - +
280B ARG 3.1 2.0 - - - -
281B GLU* 3.0 24.6 + - + +
282B GLY* 3.2 6.6 + - - -
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Residues in contact with LEU 279 (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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196B GLU 6.1 0.2 - - - +
197B LEU* 5.0 4.3 - - + -
222B LYS 5.1 2.7 - - - +
223B ARG 3.6 24.7 - - - +
225B GLU* 4.3 20.6 - - + +
275B PHE* 2.8 44.0 + - + +
276B TYR* 3.1 13.2 + - + +
278B ALA* 1.3 77.3 - - - +
280B ARG* 1.3 61.9 + - + +
282B GLY* 3.9 0.7 + - - -
283B TYR* 2.8 58.8 + - + -
286B ARG* 5.5 0.7 - - - +
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Residues in contact with ARG 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLU* 2.7 72.3 + - - +
197B LEU* 4.3 11.0 - - + -
198B TYR* 3.2 64.2 + - - +
199B TYR* 4.0 4.9 - - + -
202B ARG* 4.6 1.6 - - - +
276B TYR* 3.0 19.4 + - - +
277B GLU* 3.4 35.0 + - - +
279B LEU* 1.3 78.0 - - + +
281B GLU* 1.3 67.9 - - - +
283B TYR* 3.4 2.1 + - - +
284B ARG* 3.1 30.4 + - - +
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Residues in contact with GLU 281 (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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277B GLU 3.4 4.5 + - - +
278B ALA* 3.0 21.1 + - + +
280B ARG* 1.3 75.5 - - - +
282B GLY* 1.3 56.5 + - - +
284B ARG* 2.6 64.3 + - - +
285B ARG* 3.5 28.6 + - + +
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Residues in contact with GLY 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ALA 3.2 8.3 + - - -
279B LEU* 4.4 0.9 - - - -
281B GLU* 1.3 80.0 - - - +
283B TYR* 1.3 60.2 + - - +
285B ARG* 3.7 24.3 + - - +
286B ARG* 3.3 37.0 + - - +
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Residues in contact with TYR 283 (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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35B PRO* 3.9 2.9 - - - +
197B LEU* 3.8 13.9 - - + -
199B TYR* 3.3 22.1 - - + +
225B GLU* 2.5 30.5 + - - -
279B LEU* 2.8 54.3 + - + +
280B ARG 3.8 0.9 - - - +
281B GLU 2.9 1.6 + - - -
282B GLY* 1.3 73.7 - - - +
284B ARG* 1.3 65.2 + - - +
286B ARG* 3.2 30.1 + - - +
287B ARG* 3.1 22.6 + - - +
308B TYR* 3.3 48.2 - + + -
350B PHE* 3.2 12.1 - + - -
351B CYS* 3.6 17.7 - - + +
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Residues in contact with ARG 284 (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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198B TYR 5.6 1.6 + - - -
199B TYR* 3.7 32.1 + - + +
277B GLU 5.5 0.8 + - - -
280B ARG* 3.1 17.9 + - - +
281B GLU* 2.6 51.6 + - - +
283B TYR* 1.3 68.5 - - - +
285B ARG* 1.3 69.5 + - + +
287B ARG* 2.6 35.8 + - - +
288B ASP* 2.8 20.4 + - - +
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Residues in contact with ARG 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLU* 4.0 27.4 - - + +
282B GLY* 3.8 23.6 - - - +
284B ARG* 1.3 77.7 - - + +
286B ARG* 1.3 56.9 + - + +
287B ARG 2.6 12.8 + - - -
288B ASP* 2.7 18.3 + - - +
289B LEU* 2.8 18.1 + - + -
354B GLU* 5.0 15.3 + - - +
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Residues in contact with ARG 286 (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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37B ASN* 4.2 17.8 - - - +
225B GLU* 5.1 1.6 + - - -
279B LEU* 5.5 1.2 - - - +
282B GLY* 3.3 19.5 + - - +
283B TYR* 3.2 51.5 + - - +
284B ARG 3.4 0.2 - - - -
285B ARG* 1.3 79.6 - - + +
287B ARG* 1.3 60.3 + - - +
289B LEU* 4.1 6.3 - - + +
290B LEU* 3.5 12.0 + - - +
350B PHE* 3.4 36.9 + - + +
351B CYS* 4.1 4.9 - - - +
352B LYS 3.1 37.8 + - - +
353B THR* 4.9 3.3 - - - +
354B GLU* 4.7 15.0 - - + +
357B LEU* 3.6 19.8 - - + +
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Residues in contact with ARG 287 (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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199B TYR* 3.7 31.8 - - + +
283B TYR 3.1 15.2 + - - +
284B ARG* 2.6 25.8 + - - +
285B ARG 2.6 5.1 + - - -
286B ARG* 1.3 72.4 - - - +
288B ASP* 1.3 93.2 + - - +
290B LEU* 4.0 2.3 - - - +
291B ALA* 3.3 20.3 + - + +
303B VAL* 3.2 22.9 - - + +
304B PRO* 3.0 41.4 + - + -
305B GLU* 5.0 0.2 - - - +
310B LEU* 4.3 3.1 - - + +
350B PHE* 3.4 28.7 - - + -
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Residues in contact with ASP 288 (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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284B ARG* 2.8 19.5 + - - +
285B ARG* 2.7 13.9 + - - +
287B ARG* 1.3 107.0 + - - +
289B LEU* 1.3 63.5 + - - +
291B ALA* 3.1 6.3 + - - +
292B GLY* 2.8 24.6 + - - -
303B VAL* 4.9 3.2 - - - +
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Residues in contact with LEU 289 (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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285B ARG* 2.8 20.5 + - + +
286B ARG* 4.3 6.1 - - + +
288B ASP* 1.3 71.7 - - - +
290B LEU* 1.3 69.4 + - - +
292B GLY* 5.5 0.2 - - - -
293B GLY* 3.1 22.9 + - - -
354B GLU* 4.7 17.0 - - + -
357B LEU* 3.6 41.7 - - + -
358B HIS* 3.8 29.2 - - + +
361B LEU* 4.7 7.0 - - + +
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Residues in contact with LEU 290 (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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30B LEU* 4.8 7.0 - - + -
286B ARG 3.5 16.2 + - - +
287B ARG 3.4 2.8 + - - +
288B ASP 3.3 0.8 - - - -
289B LEU* 1.3 86.4 - - + +
291B ALA* 1.3 57.5 + - - +
293B GLY* 4.0 1.3 + - - -
294B LEU* 2.9 36.4 + - + +
310B LEU* 3.7 35.2 - - + -
348B PHE* 4.1 26.5 - - + -
350B PHE* 4.1 17.7 - - + -
357B LEU* 4.4 17.3 - - + +
360B ALA* 5.8 0.4 - - + -
361B LEU* 4.1 24.4 - - + +
364B LEU* 5.7 0.4 - - + -
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Residues in contact with ALA 291 (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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287B ARG* 3.3 14.8 + - + +
288B ASP* 3.1 6.1 + - - +
290B LEU* 1.3 76.5 - - - +
292B GLY* 1.3 66.5 + - - +
293B GLY 3.2 1.3 - - - -
294B LEU* 3.0 14.4 + - - +
295B ARG* 3.1 20.8 + - - +
301B VAL* 3.5 26.9 - - + -
303B VAL* 4.3 17.3 - - + -
310B LEU* 3.7 12.1 - - + -
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Residues in contact with GLY 292 (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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288B ASP 2.8 17.1 + - - -
289B LEU* 4.2 0.7 - - - -
291B ALA* 1.3 72.6 - - - +
293B GLY* 1.3 57.5 + - - +
295B ARG* 2.8 35.2 + - - +
296B ALA* 3.0 12.9 + - - +
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Residues in contact with GLY 293 (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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289B LEU 3.1 18.3 + - - -
290B LEU 4.3 0.7 - - - -
291B ALA 3.2 0.2 - - - -
292B GLY* 1.3 74.5 - - - +
294B LEU* 1.3 61.8 + - - +
296B ALA* 4.0 10.1 - - - +
297B MET* 3.3 24.6 + - - +
361B LEU* 3.9 23.1 - - - +
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Residues in contact with LEU 294 (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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290B LEU* 2.9 34.3 - - + +
291B ALA* 3.0 8.2 + - - +
292B GLY 2.9 1.2 - - - -
293B GLY* 1.3 77.2 - - - +
295B ARG* 1.3 61.4 + - - +
297B MET* 3.4 14.3 + - - +
298B GLY 3.0 17.7 + - - -
299B LEU* 3.1 24.3 + - + +
301B VAL* 3.5 21.8 - - + -
310B LEU* 4.5 3.6 - - + -
312B ALA* 4.4 6.7 - - + -
348B PHE* 3.8 28.5 - - + -
361B LEU* 3.3 29.4 - - + -
364B LEU* 4.0 15.9 - - + -
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Residues in contact with ARG 295 (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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291B ALA* 3.1 26.9 + - - +
292B GLY* 2.8 15.3 + - - +
294B LEU* 1.3 73.8 - - - +
296B ALA* 1.3 60.1 + - - +
297B MET 2.9 1.6 - - - -
298B GLY* 2.5 26.6 + - - +
299B LEU 4.3 9.8 + - - +
301B VAL* 3.2 43.8 + - - +
303B VAL* 3.8 24.2 - - - +
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Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLY 3.0 13.5 + - - +
293B GLY* 4.0 11.7 - - - +
295B ARG* 1.3 76.9 - - - +
297B MET* 1.3 61.3 + - + +
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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
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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