Contacts of the helix formed by residues 266 - 282 (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 GLY 266 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ASN* 4.8 0.2 - - - -
264B THR 3.2 1.0 + - - -
265B THR* 1.3 77.8 - - - +
267B ALA* 1.3 58.4 + - - +
268B GLY 3.3 2.9 - - - -
269B ASP* 3.3 15.8 + - - -
270B SER 3.0 15.4 + - - -
301B SER* 4.9 0.2 - - - -
307B THR* 4.2 7.4 - - - -
311B TYR* 2.6 34.8 + - - -
402B ADP 4.7 3.6 + - - -
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Residues in contact with ALA 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B THR* 3.1 19.3 + - - +
265B THR 3.3 0.8 - - - -
266B GLY* 1.3 74.7 - - - +
268B GLY* 1.3 58.9 + - - +
270B SER* 3.3 4.7 + - - -
271B PHE* 2.9 26.5 + - - +
298B ALA* 3.6 5.6 - - - +
301B SER* 3.9 11.4 - - - -
302B VAL* 3.4 28.9 - - + -
402B ADP 3.7 25.2 + - + +
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Residues in contact with GLY 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B THR* 5.3 2.5 - - - -
266B GLY 3.3 0.4 - - - -
267B ALA* 1.3 73.6 - - - +
269B ASP* 1.3 58.9 + - - +
271B PHE* 3.1 5.1 + - - +
272B VAL* 2.8 35.0 + - - +
402B ADP 3.0 44.5 + - - -
406B MG 3.8 7.0 - - - -
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Residues in contact with ASP 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LYS* 3.6 26.9 + - - +
57B ASN* 2.7 38.6 + - + +
58B GLN* 3.1 38.3 + - + +
177B ASN* 4.4 0.3 - - - +
266B GLY* 3.3 10.2 + - - +
268B GLY* 1.3 77.7 - - - +
270B SER* 1.4 55.9 + - - +
273B GLY* 2.9 24.3 + - - -
311B TYR* 3.4 16.2 - - - +
406B MG 4.2 8.1 - - - -
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLN* 2.7 35.9 + - - +
266B GLY 3.0 6.6 + - - -
267B ALA 3.3 9.4 + - - -
269B ASP* 1.4 74.0 - - - +
271B PHE* 1.3 58.9 + - - +
274B ALA* 2.9 31.6 + - - +
297B ILE* 3.6 13.3 + - - +
298B ALA* 3.7 8.7 - - - -
301B SER* 3.7 12.2 + - - -
311B TYR* 3.6 19.2 + - - -
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Residues in contact with PHE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B CYS* 4.0 20.4 - - - -
233B ILE* 4.0 6.5 - - + -
235B THR* 3.8 21.1 - - + -
241B CYS* 4.1 11.7 - - - -
267B ALA 2.9 13.4 + - - +
268B GLY* 3.3 13.7 - - - +
270B SER* 1.3 76.9 - - - +
272B VAL* 1.3 59.4 + - - +
274B ALA* 3.4 3.2 + - - +
275B LEU* 2.9 36.0 + - + +
291B LEU* 3.6 29.6 - - + -
294B SER* 3.7 24.4 - - - -
295B ASN* 3.2 38.1 - - - -
298B ALA* 4.1 7.8 - - + +
402B ADP 4.1 13.7 - - - -
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLN* 3.3 39.9 - - + +
150B VAL* 3.9 16.4 - - + -
175B LEU* 3.7 13.8 - - + +
177B ASN* 4.3 17.7 - - + +
197B CYS* 4.1 26.9 - - + -
268B GLY* 2.8 23.7 + - - +
271B PHE* 1.3 74.9 - - + +
273B GLY* 1.3 56.1 + - - +
275B LEU* 3.4 7.5 + - - +
276B ALA* 2.9 27.0 + - - +
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Residues in contact with GLY 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLN* 3.3 29.1 - - - +
61B GLN* 4.2 2.9 - - - -
62B ALA* 3.4 19.0 - - - +
269B ASP 2.9 15.2 + - - -
270B SER 4.0 0.7 - - - -
272B VAL* 1.3 73.0 - - - +
274B ALA* 1.3 62.8 + - - +
276B ALA* 3.4 6.3 + - - +
277B PHE* 3.2 18.0 + - - +
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLN* 3.9 1.6 - - - +
65B LEU* 3.6 23.3 - - + -
270B SER 2.9 19.3 + - - +
271B PHE* 3.6 4.5 - - - +
273B GLY* 1.3 72.7 - - - +
275B LEU* 1.3 65.8 + - - +
277B PHE* 3.1 6.2 + - - +
278B TYR* 3.1 25.3 + - + -
294B SER* 3.7 23.3 - - - +
297B ILE* 4.1 15.9 - - + -
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 4.3 9.9 - - + -
195B VAL* 4.2 11.0 - - + -
197B CYS* 4.8 4.3 - - - -
233B ILE* 3.4 29.6 - - + -
271B PHE* 2.9 33.7 + - + +
272B VAL* 3.7 6.1 - - - +
274B ALA* 1.3 73.4 - - - +
276B ALA* 1.3 56.2 + - - +
278B TYR* 3.1 3.3 + - - +
279B LEU* 2.8 53.0 + - + +
287B LEU* 4.6 7.6 - - + -
290B MET* 4.2 19.7 - - + -
291B LEU* 4.0 17.0 - - + -
294B SER* 3.2 14.0 + - - +
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 3.9 17.5 - - + -
62B ALA* 4.7 2.0 - - + -
148B VAL* 3.6 7.4 - - + +
150B VAL* 3.8 28.3 - - + -
175B LEU* 3.8 8.4 - - + +
272B VAL 2.9 14.2 + - - +
273B GLY* 3.5 12.8 - - - +
274B ALA 3.2 0.2 - - - -
275B LEU* 1.3 74.5 - - - +
277B PHE* 1.3 57.5 + - - +
279B LEU* 3.3 3.8 + - - +
280B ALA* 2.9 31.4 + - - +
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Residues in contact with PHE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 4.6 6.2 - - - +
62B ALA* 4.5 6.9 - - + +
65B LEU* 3.6 49.1 - - + -
66B GLY* 4.4 2.5 - - - -
67B ALA* 3.9 16.6 - - + -
273B GLY 3.2 9.4 + - - +
274B ALA 3.1 7.1 + - - +
276B ALA* 1.3 78.6 - - - +
278B TYR* 1.3 88.5 + + - +
280B ALA 3.4 0.2 + - - -
281B TYR* 2.9 57.7 + + - +
282B TYR* 3.7 20.6 - + - -
314B LYS* 5.8 0.9 - - + -
322B PHE* 3.9 21.3 - + - -
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Residues in contact with TYR 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 5.1 0.9 - - + -
274B ALA* 3.1 30.8 + - + -
275B LEU 3.8 4.5 - - - +
277B PHE* 1.3 94.9 - + - +
279B LEU* 1.3 64.6 + - - +
282B TYR* 3.0 56.1 + + + +
285B LEU* 4.2 6.1 - - + -
290B MET* 3.3 30.7 - - + +
293B ARG* 3.6 35.3 - - + +
294B SER* 3.8 12.3 - - - -
297B ILE* 4.7 6.2 - - + +
321B LEU* 2.7 45.3 + - - +
322B PHE* 4.1 6.9 - - - -
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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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147B LYS* 5.3 0.7 - - - +
148B VAL* 3.8 15.2 - - + +
173B LYS* 3.6 34.5 - - + +
175B LEU* 4.0 21.3 - - + -
195B VAL* 4.2 22.9 - - + -
275B LEU* 2.8 40.8 + - + +
276B ALA* 3.6 4.3 - - - +
278B TYR* 1.3 78.2 - - - +
280B ALA* 1.3 60.7 + - - +
283B PRO* 3.9 18.0 - - - +
287B LEU* 4.5 9.0 - - + -
290B MET* 4.0 20.2 - - + -
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Residues in contact with ALA 280 (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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17B ALA* 4.1 4.1 - - + +
18B VAL* 3.9 13.7 - - + -
147B LYS* 3.7 28.6 - - + +
148B VAL* 3.3 22.4 - - + +
276B ALA 2.9 12.7 + - - +
279B LEU* 1.3 78.4 - - - +
281B TYR* 1.3 75.8 + - + +
282B TYR 3.7 0.2 - - - -
283B PRO* 4.3 6.5 - - - +
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Residues in contact with TYR 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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17B ALA* 3.3 30.1 - - + +
18B VAL* 4.5 0.2 - - + -
66B GLY 4.4 5.1 + - - -
67B ALA* 3.6 27.1 - - + -
68B MET* 2.9 39.5 + - + +
277B PHE* 2.9 39.7 + + + +
280B ALA* 1.3 79.5 - - + +
282B TYR* 1.3 80.3 + - + +
283B PRO* 3.3 10.1 - - - +
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Residues in contact with TYR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B PHE* 3.7 26.6 - + - -
278B TYR* 3.0 30.0 + + + +
281B TYR* 1.3 94.6 - - + +
283B PRO* 1.3 63.0 - - - +
284B ASN 3.2 2.2 - - - -
285B LEU* 3.1 44.6 + - + +
290B MET* 3.0 17.5 - - - +
293B ARG* 4.0 6.1 - - - -
314B LYS* 5.1 1.7 + - - -
322B PHE* 3.0 50.9 + - - +
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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