Contacts of the helix formed by residues 275 - 295 (chain A) in PDB entry 3W6V
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 ALA 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ASP 5.9 0.2 - - - +
268A PHE* 3.7 1.6 - - - -
269A ARG* 3.6 13.0 - - - +
274A SER* 1.3 79.1 + - - +
276A PRO* 1.4 78.1 - - + +
277A LEU 3.5 0.9 - - - -
278A GLN* 2.9 10.4 + - + +
279A TRP* 2.8 19.8 + - - +
5B C 3.3 25.8 - - - +
6B C 3.4 24.2 - - - +
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Residues in contact with PRO 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A VAL* 3.7 25.6 - - + -
253A LEU* 4.7 4.3 - - + -
264A PHE* 3.7 27.4 - - + -
265A ASP* 4.0 19.7 - - + +
268A PHE* 3.4 28.9 - - + -
275A ALA* 1.4 89.0 - - + +
277A LEU* 1.3 52.3 + - - +
279A TRP* 3.2 5.2 + - - +
280A LEU* 2.7 38.8 + - - +
5B C 3.5 10.3 - - - +
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE 5.6 3.8 - - - +
250A VAL* 3.8 16.8 - - + +
276A PRO* 1.3 73.1 - - - +
278A GLN* 1.3 64.7 + - - +
280A LEU* 3.7 24.2 - - + -
281A ILE* 3.2 29.9 + - + +
284A ARG* 5.6 3.6 - - - +
4B C 4.1 25.1 - - - +
5B C 2.9 17.3 + - - +
10C C 3.9 36.3 - - - +
11C A 4.8 9.9 - - - +
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Residues in contact with GLN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ARG* 6.2 0.7 - - - +
274A SER* 3.2 17.5 - - - +
275A ALA* 2.9 12.4 + - + +
277A LEU* 1.3 77.8 + - - +
279A TRP* 1.3 54.9 + - - +
281A ILE* 3.4 19.1 - - - +
282A THR* 2.8 40.5 + - - +
320A ARG* 4.1 12.6 + - - -
5B C 3.1 12.6 + - - +
9C T 4.1 6.5 + - - -
10C C 3.3 26.8 + - - -
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Residues in contact with TRP 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A VAL* 3.7 42.1 - - + +
240A ALA* 3.7 22.7 - - + -
241A LEU* 4.1 12.6 - - + -
244A LEU* 5.3 0.7 - - + -
253A LEU* 6.0 1.8 - - + -
268A PHE* 3.6 29.2 - + + -
272A THR* 3.4 25.7 + - + +
274A SER* 3.3 10.9 + - - +
275A ALA 2.8 10.9 + - - +
276A PRO 3.4 8.3 - - - +
278A GLN* 1.3 75.1 - - - +
280A LEU* 1.3 70.3 + - + +
282A THR* 4.0 6.3 - - + -
283A GLN* 2.8 79.2 + - + +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ALA* 4.7 2.5 - - + -
244A LEU* 4.1 17.7 - - + -
248A PHE* 3.5 47.3 - - + +
250A VAL* 4.8 2.7 - - + -
253A LEU* 4.0 16.4 - - + -
276A PRO 2.7 19.6 + - - +
277A LEU* 3.8 30.5 - - + +
278A GLN 3.2 0.2 - - - -
279A TRP* 1.3 91.6 - - + +
281A ILE* 1.3 66.1 + - + +
283A GLN* 2.9 1.7 + - - +
284A ARG* 2.7 45.3 + - - +
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Residues in contact with ILE 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 LEU* 3.2 31.3 + - + +
278A GLN* 3.4 21.5 - - - +
280A LEU* 1.3 78.0 - - - +
282A THR* 1.3 69.2 + - - +
284A ARG* 3.1 9.2 + - - +
285A VAL* 2.8 27.5 + - + +
308A PHE* 5.2 2.7 - - + -
317A HIS* 3.9 48.2 - - + +
320A ARG* 5.3 3.8 - - - +
321A GLN* 4.6 3.6 - - - +
10C C 3.6 27.8 - - - +
11C A 5.4 2.7 - - - +
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Residues in contact with THR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A SER* 5.3 1.7 + - - -
278A GLN* 2.8 25.8 + - - -
279A TRP* 3.4 11.8 - - + -
280A LEU 3.1 0.4 + - - -
281A ILE* 1.3 75.1 - - - +
283A GLN* 1.3 80.3 + - - +
285A VAL* 3.4 4.2 + - - +
286A LEU* 3.2 29.5 + - + +
321A GLN* 3.4 23.6 + - - +
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Residues in contact with GLN 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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241A LEU* 3.7 27.5 - - + +
244A LEU* 3.6 23.0 - - + +
279A TRP* 2.8 73.2 + - + +
280A LEU* 2.9 4.0 + - - +
282A THR* 1.3 85.3 - - - +
284A ARG* 1.3 65.5 + - - +
286A LEU* 2.9 35.7 + - - +
287A GLN 3.0 9.9 + - - -
290A ARG* 5.4 0.3 + - - -
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Residues in contact with ARG 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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244A LEU* 2.4 55.9 + - + +
246A GLU 2.9 18.7 + - - -
247A GLN* 4.4 2.6 - - - +
248A PHE* 3.9 21.8 + - - +
277A LEU* 5.6 3.2 - - - +
280A LEU* 2.7 57.5 + - - +
281A ILE* 3.6 6.1 - - - +
283A GLN* 1.3 70.9 - - - +
285A VAL* 1.3 57.4 + - - +
287A GLN* 3.2 6.0 + - - +
288A ALA* 2.9 23.7 + - - +
306A CYS* 3.0 30.7 - - - +
307A GLY* 4.1 17.0 + - - -
308A PHE* 3.7 19.4 - - + +
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Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ILE* 2.8 19.3 + - + +
282A THR 3.5 7.9 - - - +
284A ARG* 1.3 73.0 - - - +
286A LEU* 1.3 56.8 + - - +
288A ALA* 2.9 8.6 + - - +
289A GLN* 2.8 26.3 + - - +
308A PHE* 3.7 20.0 - - + -
317A HIS* 3.9 27.8 - - + -
318A PHE* 4.1 20.8 - - + +
321A GLN* 3.4 37.7 - - + +
322A LEU* 4.4 10.1 - - + -
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A THR* 3.2 18.8 + - + +
283A GLN* 2.9 32.3 + - - +
285A VAL* 1.3 77.3 - - - +
287A GLN* 1.3 56.8 + - - +
289A GLN* 3.5 25.5 + - - +
290A ARG* 3.1 39.3 + - - +
321A GLN* 4.1 16.2 - - - +
322A LEU* 5.1 4.0 - - + -
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Residues in contact with GLN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU 4.6 4.2 - - - +
244A LEU* 3.9 30.6 - - + +
245A HIS* 4.7 4.4 - - - +
283A GLN 3.0 10.5 + - - +
284A ARG* 3.4 9.6 - - - +
286A LEU* 1.3 73.8 - - - +
288A ALA* 1.3 66.7 + - - +
290A ARG* 3.2 35.2 + - - +
291A LEU* 3.0 34.3 + - + +
305A ARG 2.9 28.7 + - - -
306A CYS* 3.5 13.8 - - - +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ARG 2.9 10.5 + - - +
285A VAL* 3.1 11.7 - - - +
287A GLN* 1.3 75.7 - - - +
289A GLN* 1.3 53.6 + - - +
291A LEU* 3.0 3.3 + - - +
292A LEU* 2.8 40.4 + - + +
302A VAL* 4.0 13.5 - - + -
306A CYS* 3.1 20.9 - - + -
308A PHE* 4.6 0.4 - - + -
314A LEU* 4.1 12.6 - - + -
318A PHE* 4.0 19.1 - - + -
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Residues in contact with GLN 289 (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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285A VAL 2.8 11.6 + - - +
286A LEU* 3.5 30.4 - - - +
287A GLN 3.3 0.2 - - - -
288A ALA* 1.3 76.2 - - - +
290A ARG* 1.3 62.4 + - + +
292A LEU* 3.5 4.4 + - - +
293A GLU* 3.2 42.1 + - - +
318A PHE* 4.0 9.5 - - - -
322A LEU* 3.5 28.6 - - + +
329A TYR* 2.8 33.8 + - + +
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Residues in contact with ARG 290 (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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244A LEU* 5.7 1.4 - - - +
283A GLN 5.4 0.4 + - - -
286A LEU* 3.1 27.0 + - - +
287A GLN* 3.3 47.4 + - - +
288A ALA 3.2 0.2 - - - -
289A GLN* 1.3 76.4 - - + +
291A LEU* 1.3 61.5 + - + +
293A GLU* 2.9 12.6 + - - +
294A THR* 2.8 38.2 + - - +
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Residues in contact with LEU 291 (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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287A GLN* 3.0 27.9 + - + +
288A ALA 3.8 2.9 - - - +
290A ARG* 1.3 80.8 - - + +
292A LEU* 1.3 58.9 + - - +
294A THR* 4.8 4.5 - - - -
295A SER* 2.6 51.4 + - - +
297A TYR* 5.2 7.9 - - + -
302A VAL* 4.1 18.2 - - + -
305A ARG* 3.9 29.2 - - + -
306A CYS* 3.9 23.1 - - - -
330A ARG* 3.5 1.0 + - - -
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Residues in contact with LEU 292 (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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288A ALA* 2.8 17.7 + - + +
289A GLN* 3.7 5.4 - - - +
290A ARG 3.2 0.2 - - - -
291A LEU* 1.3 77.8 - - - +
293A GLU* 1.3 59.6 + - - +
299A VAL* 4.8 8.3 - - + -
302A VAL* 4.6 17.3 - - + -
314A LEU* 6.0 0.2 - - + -
318A PHE* 3.6 35.0 - - + -
326A PRO* 3.7 41.5 - - + +
329A TYR* 4.5 7.6 - - + -
330A ARG* 3.2 59.8 + - + +
333A TYR* 5.5 0.7 - - - -
334A ARG* 3.8 7.1 + - - -
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Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLN* 3.2 25.0 + - - +
290A ARG* 2.9 13.5 + - - +
292A LEU* 1.3 79.2 - - - +
294A THR* 1.3 65.2 + - - +
295A SER 3.5 0.2 - - - -
329A TYR* 2.7 30.0 + - + -
333A TYR* 3.7 47.7 + - + +
334A ARG* 2.9 25.1 + - - +
340A GLY* 5.9 1.4 - - - +
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Residues in contact with THR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ARG* 2.8 24.9 + - - +
291A LEU* 5.0 4.2 - - - +
293A GLU* 1.3 76.2 - - - +
295A SER* 1.3 60.8 + - - +
296A ASP* 5.5 0.7 - - - +
334A ARG* 4.7 1.4 + - - -
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 2.6 30.5 + - - +
294A THR* 1.3 79.3 - - - +
296A ASP* 1.3 59.6 + - - +
297A TYR* 3.1 41.6 + - - +
302A VAL* 4.7 0.2 - - - +
330A ARG* 2.4 22.9 + - - -
334A ARG* 2.8 17.4 + - - -
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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