Contacts of the helix formed by residues 279 - 300 (chain B) in PDB entry 3V4R
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 LYS 279 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B GLN* 5.9 1.8 - - - +
273B VAL* 6.1 2.6 - - - +
274B MET* 2.9 36.3 + - + +
277B ASN* 4.1 27.6 + - + +
278B GLY* 1.4 72.3 - - - +
280B LEU* 1.4 56.9 + - - +
282B GLU* 3.6 30.1 + - + +
283B ALA* 3.1 28.5 + - - +
363B ASP* 3.8 29.7 + - - +
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B HIS* 3.7 39.5 - - + +
278B GLY* 3.0 25.7 + - - +
279B LYS* 1.4 68.4 - - - +
281B LEU* 1.3 60.1 + - - +
282B GLU* 3.3 0.4 + - - -
283B ALA* 3.7 6.9 - - - +
284B GLN* 3.1 27.4 + - - +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 3.7 28.0 - - + -
106B ASP* 6.0 0.4 - - - +
279B LYS 3.6 0.4 - - - -
280B LEU* 1.3 76.0 - - - +
282B GLU* 1.3 67.6 + - + +
284B GLN* 3.2 28.1 + - - +
285B ARG* 3.0 65.9 + - - +
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B MET* 3.9 8.2 - - + +
279B LYS* 3.6 42.8 - - + +
281B LEU* 1.3 89.6 + - - +
283B ALA* 1.4 55.8 + - - +
285B ARG* 3.5 7.0 + - - +
286B LEU* 3.0 29.8 + - - +
363B ASP 4.0 8.0 - - - +
364B HIS* 3.5 48.5 + - + +
365B GLY* 3.6 8.2 - - - +
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Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 3.8 19.4 - - + +
274B MET* 3.6 25.1 - - + -
275B HIS* 5.1 9.2 - - + +
279B LYS 3.1 19.1 + - - +
280B LEU* 3.7 9.2 - - - +
281B LEU 3.2 0.4 - - - -
282B GLU* 1.4 75.0 - - - +
284B GLN* 1.3 63.2 + - - +
287B GLU* 3.2 23.4 + - - +
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Residues in contact with GLN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 4.5 15.0 - - - +
280B LEU 3.1 12.9 + - - +
281B LEU* 3.2 31.4 + - - +
283B ALA* 1.3 75.9 - - - +
285B ARG* 1.4 63.2 + - - +
287B GLU* 3.4 4.7 + - - +
288B GLN* 3.1 47.1 + - - +
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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
----------------------------------------------------------
186A ILE* 3.0 30.9 + - + +
187A ASP* 3.1 20.8 + - - +
101B TYR* 5.1 3.0 - - - -
106B ASP* 4.5 10.5 + - - -
281B LEU* 3.0 49.6 + - + +
282B GLU* 3.7 7.0 - - - +
283B ALA 3.4 0.2 - - - -
284B GLN* 1.4 78.3 - - - +
286B LEU* 1.3 55.6 + - - +
288B GLN* 3.8 7.9 - - - +
289B ARG* 3.0 44.9 + - - +
364B HIS* 2.8 42.8 + - - +
365B GLY 3.4 11.7 - - - +
366B PHE* 3.2 35.4 - - - -
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 3.8 15.3 - - + -
270B GLN* 3.7 30.3 - - + -
271B LEU* 3.7 19.3 - - + -
274B MET* 3.8 8.3 - - + -
282B GLU 3.0 18.3 + - - +
283B ALA* 3.9 4.7 - - - +
284B GLN 3.3 0.4 - - - -
285B ARG* 1.3 73.2 - - - +
287B GLU* 1.3 59.4 + - - +
289B ARG* 4.1 1.1 - - - +
290B THR* 2.6 45.8 + - - +
365B GLY* 3.3 20.8 + - - +
366B PHE 4.5 1.6 - - - +
367B ARG* 3.8 31.9 - - - +
368B LEU* 4.0 8.1 - - + +
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 4.3 11.6 - - + +
271B LEU* 4.3 16.8 - - + +
283B ALA 3.2 15.1 + - - +
284B GLN* 3.9 3.8 - - - +
286B LEU* 1.3 75.8 - - - +
288B GLN* 1.4 56.8 + - - +
291B ARG* 2.8 48.1 + - + +
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Residues in contact with GLN 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 6.2 1.8 - - - +
284B GLN* 3.1 39.8 + - - +
285B ARG* 3.8 7.0 - - - +
287B GLU* 1.4 75.7 - - - +
289B ARG* 1.3 64.1 + - + +
291B ARG* 4.4 2.4 - - - +
292B TYR* 3.3 23.0 + - - +
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Residues in contact with ARG 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASP* 4.1 11.2 + - - +
99B GLU* 3.5 16.8 + - - -
108B PHE* 3.4 29.7 - - - -
285B ARG* 3.0 38.5 + - + +
286B LEU* 4.1 2.0 - - - +
288B GLN* 1.3 77.4 - - + +
290B THR* 1.3 67.2 + - - +
292B TYR* 3.5 4.1 + - - +
293B ASP* 3.2 30.1 + - - +
309B TYR* 4.9 1.1 - - - -
366B PHE* 2.6 52.6 + - - +
367B ARG* 3.9 19.2 - - - +
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ILE* 3.9 8.7 - - + -
267B LEU* 3.6 24.3 - - + +
286B LEU* 2.6 39.5 + - - +
289B ARG* 1.3 72.0 - - - +
291B ARG* 1.3 62.3 + - - +
293B ASP* 3.1 6.1 + - - +
294B LEU* 3.0 39.6 + - + +
309B TYR* 4.0 15.5 + - + +
366B PHE 5.8 0.2 + - - -
368B LEU* 3.8 26.1 - - + +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B GLU* 4.3 23.6 + - - +
267B LEU* 3.7 28.6 - - + +
268B GLU* 5.4 6.3 - - - +
271B LEU* 5.3 6.1 - - - +
287B GLU* 2.8 33.4 + - + +
288B GLN* 4.5 2.0 - - - +
290B THR* 1.3 71.3 - - - +
292B TYR* 1.3 60.0 + - - +
294B LEU* 3.5 17.5 + - - +
295B GLU* 3.3 21.1 + - - +
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Residues in contact with TYR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLN 3.3 20.0 + - - +
289B ARG* 3.6 4.5 - - - +
290B THR 3.2 0.6 - - - -
291B ARG* 1.3 75.7 - - - +
293B ASP* 1.4 77.2 + - - +
295B GLU* 3.1 12.8 + - - +
296B MET* 3.1 30.8 + - + +
303B CYS* 6.3 0.7 - - + -
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Residues in contact with ASP 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ARG* 3.2 13.8 + - - +
290B THR 3.1 6.1 + - - +
292B TYR* 1.4 94.4 - - - +
294B LEU* 1.3 56.8 + - - +
296B MET* 3.3 7.8 + - - +
297B MET* 3.0 33.8 + - - +
303B CYS* 3.8 13.7 - - - +
304B SER 3.9 11.1 + - - +
309B TYR* 2.9 44.3 + - + +
367B ARG* 3.4 14.0 + - - -
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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
----------------------------------------------------------
260B ILE* 3.7 30.7 - - + +
263B ILE* 3.8 28.5 - - + -
264B GLU* 4.9 5.8 - - + +
267B LEU* 4.5 3.6 - - + -
290B THR* 3.0 39.0 + - + +
291B ARG* 3.8 27.4 - - - +
293B ASP* 1.3 73.0 - - + +
295B GLU* 1.3 60.0 + - - +
297B MET* 3.5 19.8 + - + +
298B ARG* 3.1 44.5 + - - +
309B TYR* 5.8 0.2 - - + -
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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
----------------------------------------------------------
291B ARG 3.3 11.6 + - - +
292B TYR* 3.1 14.2 + - - +
294B LEU* 1.3 73.5 - - - +
296B MET* 1.4 64.5 + - - +
298B ARG* 3.3 11.0 + - + +
299B GLU* 3.1 56.4 + - + +
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Residues in contact with MET 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TYR* 3.1 24.3 + - + +
293B ASP* 3.4 11.0 - - - +
295B GLU* 1.4 76.2 + - - +
297B MET* 1.3 57.3 + - - +
299B GLU* 4.8 4.0 - - - -
300B MET* 3.1 32.5 + - + +
302B PHE 3.0 15.7 - - - +
303B CYS* 3.9 18.2 - - + -
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Residues in contact with MET 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ILE* 4.3 24.2 - - + +
263B ILE* 4.5 11.0 - - + -
293B ASP* 3.0 33.7 + - + +
294B LEU* 3.7 27.4 - - + +
295B GLU 3.2 0.2 - - - -
296B MET* 1.3 75.7 - - - +
298B ARG* 1.3 61.0 + - - +
301B GLY* 3.1 31.0 + - - +
302B PHE 4.0 3.4 - - - -
303B CYS* 3.9 13.2 - - + -
306B ILE* 3.6 34.1 - - + -
309B TYR* 4.3 19.1 - - + -
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ILE* 3.7 41.3 + - + +
261B GLN* 5.5 1.8 - - - +
294B LEU* 3.1 31.4 + - - +
295B GLU* 3.3 12.0 + - + +
297B MET* 1.3 77.6 - - - +
299B GLU* 1.3 63.8 + - + +
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 3.1 43.4 + - + +
296B MET* 4.2 4.2 - - - +
298B ARG* 1.3 80.9 - - + +
300B MET* 1.4 77.8 + - + +
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Residues in contact with MET 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B MET* 3.1 18.5 + - + +
299B GLU* 1.4 88.4 - - + +
301B GLY* 1.3 57.8 + - - +
302B PHE* 3.4 17.7 - - + +
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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