Contacts of the helix formed by residues 279 - 299 (chain B) in PDB entry 3RU0
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 ASP 279 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B GLY* 1.3 71.6 - - - -
280B GLU* 1.3 66.2 + - - +
281B GLN* 3.0 25.1 + - - +
282B VAL* 2.7 43.7 + - + +
283B TRP* 3.0 13.6 + - - -
319B ARG 5.5 1.8 + - - +
320B LEU* 4.6 2.6 - - - +
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B GLY 3.7 1.6 + - - -
279B ASP* 1.3 75.2 + - - +
281B GLN* 1.3 58.8 + - - +
283B TRP* 3.4 45.9 - - + +
284B LYS* 2.9 40.3 + - + +
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Residues in contact with GLN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ASP* 3.0 17.9 + - - +
280B GLU* 1.3 77.6 - - - +
282B VAL* 1.3 61.5 + - + +
284B LYS* 4.6 4.1 - - - +
285B GLU* 3.8 17.5 - - - +
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Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ASP* 2.7 37.0 + - + +
281B GLN* 1.3 72.6 - - + +
283B TRP* 1.3 64.3 + - - +
284B LYS 3.4 0.2 - - - -
285B GLU* 3.3 21.4 + - - +
286B VAL* 3.9 5.5 + - - +
316B ASN* 3.9 23.5 + - - +
319B ARG* 4.6 19.3 - - + +
320B LEU* 3.9 31.4 - - + -
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Residues in contact with TRP 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 3.2 49.8 + - + -
277B THR 3.9 4.9 - - - -
278B GLY 3.8 2.7 + - - -
279B ASP 3.0 25.1 + - - -
280B GLU* 3.4 45.5 - - + +
282B VAL* 1.3 72.4 - - - +
284B LYS* 1.3 72.7 - - + +
285B GLU 3.1 2.2 - - - -
286B VAL* 3.1 5.5 + - - +
287B GLN* 2.9 36.8 + - - +
320B LEU* 3.9 16.6 - - + -
324B ASN* 3.2 37.2 - - - +
326B TYR* 3.5 26.8 - + + -
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Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B GLU* 2.9 30.7 + - + +
281B GLN* 4.6 5.8 - - - +
282B VAL 3.4 0.2 - - - -
283B TRP* 1.3 84.4 - - + +
285B GLU* 1.3 60.6 + - + +
287B GLN* 3.5 9.1 + - - +
288B GLU* 3.0 27.5 + - - +
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLN 3.8 18.9 - - - +
282B VAL 3.3 8.0 + - - +
283B TRP 3.1 0.8 - - - -
284B LYS* 1.3 77.6 - - + +
286B VAL* 1.3 61.7 + - + +
288B GLU* 3.5 11.3 + - - +
289B SER* 3.0 32.1 + - - -
316B ASN* 6.1 0.9 - - - +
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B VAL 4.0 7.2 - - - +
283B TRP* 3.1 6.2 + - - +
285B GLU* 1.3 76.7 - - + +
287B GLN* 1.3 63.0 + - - +
289B SER* 3.3 6.2 + - - -
290B LEU* 3.1 23.7 + - - +
312B ILE* 4.1 15.7 - - + -
316B ASN* 3.4 29.6 - - - +
320B LEU* 3.8 17.7 - - + -
326B TYR* 3.7 23.1 - - + -
327B GLN* 3.8 4.3 - - - +
330B VAL* 3.6 28.0 - - + +
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Residues in contact with GLN 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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248B GLU* 3.4 24.4 + - - +
283B TRP* 2.9 28.2 + - - +
284B LYS* 3.6 12.7 - - - +
286B VAL* 1.3 74.4 - - - +
288B GLU* 1.3 63.0 + - - +
290B LEU* 3.4 16.9 + - + +
291B LYS* 3.9 11.8 + - - +
326B TYR* 3.6 37.7 + - + +
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Residues in contact with GLU 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 LYS 3.0 17.1 + - - +
285B GLU* 3.8 13.9 - - - +
286B VAL 3.3 0.4 - - - -
287B GLN* 1.3 76.2 - - - +
289B SER* 1.3 63.5 + - - +
291B LYS* 3.3 48.3 + - - +
292B LYS* 4.4 0.9 + - - +
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Residues in contact with SER 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLU 3.0 18.0 + - - -
286B VAL 3.3 3.6 + - - -
288B GLU* 1.3 75.7 - - - +
290B LEU* 1.3 64.5 + - - +
291B LYS 3.2 0.7 + - - -
292B LYS* 3.2 6.0 + - - +
293B ILE* 3.1 23.1 + - - +
308B MET* 3.8 13.7 - - - +
312B ILE* 3.5 31.0 - - - +
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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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286B VAL 3.1 16.8 + - - +
287B GLN* 3.6 9.6 - - + +
288B GLU 3.2 0.4 - - - -
289B SER* 1.3 74.5 - - - +
291B LYS* 1.3 59.4 + - - +
292B LYS 3.3 0.2 - - - -
293B ILE* 3.8 19.3 - - + -
294B GLU* 2.9 51.2 + - + +
326B TYR* 3.6 41.5 - - + +
329B LYS* 3.9 32.1 - - + +
330B VAL* 3.7 25.4 - - + +
333B CYS* 4.7 1.3 - - - -
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Residues in contact with LYS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLN* 4.1 10.8 - - - +
288B GLU* 3.4 40.0 + - - +
289B SER 3.1 1.0 - - - -
290B LEU* 1.3 78.9 - - - +
292B LYS* 1.3 61.5 + - - +
294B GLU* 4.1 6.2 - - - +
295B GLU* 3.3 20.1 + - - +
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Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLU 4.4 0.6 + - - -
289B SER* 3.2 9.1 + - - +
291B LYS* 1.3 76.5 - - - +
293B ILE* 1.3 60.4 - - - +
295B GLU* 3.3 13.7 + - + +
296B LEU* 2.9 55.4 + - + +
304B GLN* 5.3 2.4 + - - -
308B MET* 3.9 22.8 - - + -
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Residues in contact with ILE 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 SER 3.1 19.7 + - - +
290B LEU* 3.9 9.4 - - + +
292B LYS* 1.3 76.7 - - - +
294B GLU* 1.3 57.8 + - - +
296B LEU* 3.3 7.6 + - - +
297B LYS* 2.9 27.9 + - - +
305B VAL* 4.1 9.6 - - + +
308B MET* 3.8 25.1 - - + -
309B CYS* 3.8 32.1 - - - -
312B ILE* 3.7 30.3 - - + -
330B VAL* 4.1 13.2 - - + -
333B CYS* 3.8 22.4 - - + -
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Residues in contact with GLU 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 44.7 + - + +
291B LYS* 4.1 5.7 - - - +
293B ILE* 1.3 72.9 - - - +
295B GLU* 1.3 60.3 + - - +
297B LYS* 3.5 10.2 + - + +
298B ALA* 2.9 28.8 + - - +
329B LYS* 4.3 21.7 + - - +
333B CYS* 5.0 8.5 - - - -
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Residues in contact with GLU 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 LYS 3.3 14.3 + - - +
292B LYS* 3.3 21.5 + - + +
294B GLU* 1.3 73.4 - - - +
296B LEU* 1.3 65.8 + - - +
298B ALA* 3.2 7.2 + - + +
299B HIS* 3.1 45.9 + - + +
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Residues in contact with LEU 296 (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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292B LYS* 2.9 35.5 + - - +
293B ILE* 3.6 7.6 - - - +
295B GLU* 1.3 74.3 - - + +
297B LYS* 1.3 60.4 + - - +
299B HIS* 3.2 8.0 + - - -
301B LYS* 2.9 42.7 + - + +
304B GLN* 3.2 57.2 - - + +
305B VAL* 3.7 13.5 - - + +
308B MET* 3.9 25.6 - - + -
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Residues in contact with LYS 297 (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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190B MET 4.7 4.6 + - - -
191B GLN* 2.9 50.9 + - - +
192B GLU* 5.3 1.6 - - - +
293B ILE 2.9 16.9 + - - +
294B GLU* 3.7 9.4 - - + +
296B LEU* 1.3 74.5 - - - +
298B ALA* 1.3 59.7 + - - +
300B TRP* 2.8 18.7 + - - +
301B LYS 4.7 0.2 - - - +
302B TRP* 3.9 21.0 - - + -
305B VAL* 3.5 14.9 - - + +
332B ASP* 5.2 4.4 + - - -
333B CYS* 3.9 28.5 - - + +
336B ASP* 4.3 20.5 + - - -
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Residues in contact with ALA 298 (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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41B CYS* 5.5 1.0 - - - -
43B GLY* 3.2 23.4 - - - +
44B SER* 3.9 2.6 + - - -
191B GLN* 4.2 5.4 + - - +
192B GLU 5.1 3.0 - - - +
294B GLU 2.9 18.3 + - - +
295B GLU* 3.2 10.3 + - - +
297B LYS* 1.3 77.7 - - - +
299B HIS* 1.3 64.5 - - + +
300B TRP* 3.6 8.5 + - - -
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Residues in contact with HIS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LYS* 4.5 9.7 - - + +
43B GLY* 3.4 34.1 + - - +
47B VAL* 4.5 5.4 - - - +
295B GLU* 3.1 35.6 + - + +
296B LEU* 3.2 6.9 + - - +
297B LYS 3.1 0.6 - - - -
298B ALA* 1.3 81.6 - - + +
300B TRP* 1.3 70.7 + - - +
301B LYS* 3.2 31.1 + - + +
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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