Contacts of the helix formed by residues 286 - 302 (chain B) in PDB entry 2FV7
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 SER 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B LEU* 1.3 76.3 - - - +
287B LEU* 1.3 66.0 + - - +
288B GLU* 3.7 10.2 + - - +
289B ASP* 3.1 23.0 + - - +
290B MET* 3.0 19.7 + - - +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B VAL* 5.3 3.8 - - + -
231B VAL* 3.5 44.4 - - + -
233B ILE* 5.4 1.8 - - + -
243B VAL* 4.0 14.6 - - + -
245B SER* 5.3 4.0 - - - -
275B LEU* 4.6 12.1 - - + -
279B LEU* 4.5 13.2 - - + -
285B LEU 3.8 1.6 + - - -
286B SER* 1.3 72.4 - - - +
288B GLU* 1.3 60.0 + - + +
290B MET* 3.2 24.6 + - + +
291B LEU* 2.9 43.8 + - + +
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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
----------------------------------------------------------
243B VAL* 5.4 2.0 - - + -
252B LYS* 3.3 43.3 - - + +
254B ILE* 4.1 18.8 - - + +
286B SER* 3.2 9.1 - - - +
287B LEU* 1.3 78.0 - - + +
289B ASP* 1.3 55.6 + - - +
291B LEU* 3.6 2.5 + - - +
292B ASN* 3.0 35.6 + - - +
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Residues in contact with ASP 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 3.6 17.6 - - + +
286B SER* 3.1 22.9 + - - +
288B GLU* 1.3 75.4 - - - +
290B MET* 1.3 64.3 + - - +
292B ASN* 3.2 10.5 + - - +
293B ARG* 3.0 63.8 + - - +
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Residues in contact with MET 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU* 4.2 9.4 - - + -
278B TYR* 3.3 37.4 - - + +
279B LEU* 4.0 28.7 - - + -
282B TYR 3.0 28.5 - - - +
283B PRO* 3.9 9.4 - - + +
285B LEU* 3.6 24.9 - - + +
286B SER 3.0 14.3 + - - +
287B LEU* 3.5 20.6 - - + +
289B ASP* 1.3 75.7 - - - +
291B LEU* 1.3 53.0 + - - +
293B ARG* 3.4 8.8 + - - +
294B SER* 2.8 38.1 + - - -
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ILE* 3.5 28.5 - - + -
241B CYS* 4.3 9.0 - - - -
243B VAL* 3.6 42.8 - - + -
254B ILE* 3.7 16.6 - - + -
271B PHE* 3.6 21.8 - - + -
275B LEU* 4.0 14.1 - - + -
287B LEU* 2.9 29.2 + - + +
288B GLU 3.8 4.3 - - - +
290B MET* 1.3 73.2 - - - +
292B ASN* 1.3 60.5 + - - +
294B SER* 3.9 2.4 - - - -
295B ASN* 2.8 35.0 + - - +
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Residues in contact with ASN 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 3.8 21.5 - - - +
255B PRO* 4.0 10.2 - - - +
288B GLU* 3.0 23.2 + - - +
289B ASP* 3.5 14.4 - - - +
291B LEU* 1.3 77.2 - - - +
293B ARG* 1.3 58.4 + - + +
295B ASN* 3.5 4.6 + - - +
296B PHE* 3.1 26.5 + - - +
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Residues in contact with ARG 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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278B TYR* 3.6 30.6 - - + +
282B TYR* 4.0 7.9 - - - -
285B LEU* 3.6 25.6 - - - +
289B ASP* 3.0 54.9 + - - +
290B MET 3.7 2.9 - - - +
292B ASN* 1.3 73.9 - - + +
294B SER* 1.3 61.0 + - - +
296B PHE* 3.3 3.3 + - - +
297B ILE* 3.0 32.7 + - - +
320B THR 4.2 10.3 + - - +
321B LEU* 3.1 57.6 + - + +
322B PHE* 3.6 16.4 + - - +
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE* 3.7 38.6 - - - -
274B ALA* 3.7 12.6 - - - -
275B LEU* 3.2 27.4 + - - +
278B TYR* 3.8 2.6 - - - -
290B MET 2.8 23.6 + - - -
291B LEU* 3.9 2.9 - - - -
292B ASN 3.4 0.2 - - - -
293B ARG* 1.3 72.1 - - - +
295B ASN* 1.3 67.0 + - - +
297B ILE* 3.5 2.3 + - - +
298B ALA* 3.1 25.1 + - - +
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Residues in contact with ASN 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLY* 3.8 5.8 - - - -
241B CYS* 3.9 4.8 - - - -
254B ILE* 3.1 37.6 + - - +
255B PRO 3.4 12.8 + - - +
256B THR* 3.2 18.9 + - - +
271B PHE* 3.2 15.8 - - - -
291B LEU 2.8 19.3 + - - +
292B ASN* 3.5 7.0 - - - +
294B SER* 1.3 73.8 - - - +
296B PHE* 1.3 56.5 + - - +
299B ALA* 2.9 29.5 + - - +
402B ADP 2.5 34.6 + - - +
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Residues in contact with PHE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B THR* 5.0 0.4 - - - -
257B GLU* 5.1 17.5 - - + +
292B ASN 3.1 13.7 + - - +
293B ARG* 3.5 11.2 - - - +
294B SER 3.2 0.4 - - - -
295B ASN* 1.3 74.9 - - - +
297B ILE* 1.3 66.8 + - - +
299B ALA* 3.0 16.6 + - + +
300B VAL* 3.0 33.5 + - + +
317B LEU* 4.0 2.7 - - + -
318B PRO* 3.8 35.7 - - + -
321B LEU* 3.4 26.5 - - + -
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Residues in contact with ILE 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLN* 3.5 33.7 - - - +
65B LEU* 3.3 14.4 - - + -
270B SER* 3.6 7.2 + - - +
274B ALA* 4.1 18.8 - - + -
278B TYR* 4.7 7.0 - - + +
293B ARG 3.0 18.6 + - - +
294B SER 3.9 4.7 - - - +
296B PHE* 1.3 80.4 - - - +
298B ALA* 1.3 55.6 - - - +
300B VAL* 3.1 9.4 + - - +
301B SER* 3.0 23.2 + - - -
312B PRO* 4.1 6.0 - - + +
317B LEU* 2.9 38.8 - - + -
321B LEU* 4.0 11.7 - - + -
322B PHE* 5.0 0.2 - - + -
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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
----------------------------------------------------------
267B ALA 3.6 15.3 - - - +
270B SER* 3.7 9.6 + - - -
271B PHE* 4.1 9.2 - - + +
294B SER 3.1 19.0 + - - +
295B ASN 3.8 1.8 - - - +
297B ILE* 1.3 76.8 - - - +
299B ALA* 1.3 57.8 + - - +
301B SER* 3.1 18.3 + - - -
302B VAL* 3.1 19.8 + - - +
402B ADP 3.4 31.6 - - - +
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Residues in contact with ALA 299 (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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256B THR* 3.7 13.9 - - - +
257B GLU* 4.4 15.7 - - + +
259B VAL* 3.8 3.6 - - + +
295B ASN 2.9 18.4 + - - +
296B PHE* 3.0 11.8 + - + +
298B ALA* 1.3 74.8 - - - +
300B VAL* 1.3 59.0 + - + +
302B VAL* 3.2 17.8 - - - +
303B GLN* 3.0 19.4 + - - +
402B ADP 3.7 20.1 - - + +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PHE* 3.0 43.1 + - + +
297B ILE* 3.1 8.7 + - - +
299B ALA* 1.3 77.6 - - + +
301B SER* 1.3 63.7 + - - +
302B VAL 3.2 0.2 - - - -
303B GLN* 3.1 29.2 + - + +
304B ALA* 3.9 5.2 + - - +
310B SER 4.5 2.3 - - - +
312B PRO* 3.7 29.6 - - + -
316B ASP 5.9 1.1 - - - +
317B LEU* 4.2 7.4 - - + -
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B THR 5.5 0.7 + - - -
267B ALA* 3.9 12.8 + - - -
270B SER* 3.7 21.1 - - - -
297B ILE 3.0 7.2 + - - -
298B ALA 3.1 12.3 + - - -
300B VAL* 1.3 78.3 - - - +
302B VAL* 1.3 53.2 + - - +
303B GLN 3.1 0.4 - - - -
304B ALA 3.1 8.1 + - - +
310B SER* 3.4 33.4 + - - -
311B TYR* 3.9 15.8 - - - -
312B PRO* 4.3 2.2 - - - -
405B NA 2.4 27.0 - - - -
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Residues in contact with VAL 302 (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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259B VAL* 3.8 19.5 - - + -
261B ALA* 3.5 3.9 - - + -
262B VAL 2.7 30.5 + - - -
263B ASP 3.1 19.2 + - - +
264B THR* 4.1 14.4 - - + -
267B ALA* 3.4 28.3 - - + -
298B ALA 3.1 14.2 + - - +
299B ALA* 3.2 23.3 - - - +
301B SER* 1.3 76.3 + - - +
303B GLN* 1.3 49.9 + - - +
304B ALA 3.3 1.1 - - - -
402B ADP 3.7 28.3 - - + +
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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
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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