Contacts of the helix formed by residues 266 - 282 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ASN* 4.8 0.4 - - - -
264A THR 3.2 1.0 + - - -
265A THR* 1.3 78.4 - - - +
267A ALA* 1.3 64.2 + - - +
268A GLY 3.2 2.7 - - - -
269A ASP* 3.3 14.7 + - - -
270A SER 3.2 9.0 + - - -
301A SER* 5.1 0.2 - - - -
307A THR* 4.3 7.6 - - - -
311A TYR* 2.6 33.2 + - - -
401A ADP 4.5 4.3 + - - -
510A UNX 4.6 6.1 - - - -
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Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A THR* 3.1 19.1 + - - +
265A THR 3.3 1.0 + - - -
266A GLY* 1.3 74.5 - - - +
268A GLY* 1.3 60.4 + - - +
270A SER* 3.2 3.8 + - - -
271A PHE* 3.0 28.4 + - - +
298A ALA* 3.7 4.8 - - - +
301A SER* 3.9 14.6 - - - +
302A VAL* 3.7 22.9 - - + -
401A ADP 3.7 28.9 + - + +
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Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A THR* 5.3 2.6 - - - +
266A GLY 3.2 0.2 - - - -
267A ALA* 1.3 73.8 - - - +
269A ASP* 1.3 57.5 + - - +
271A PHE* 3.3 5.4 + - - +
272A VAL* 3.0 32.3 + - - +
401A ADP 2.6 48.8 + - - -
404A MG 3.8 5.6 - - - -
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Residues in contact with ASP 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LYS* 3.6 12.5 - - - +
57A ASN* 2.8 43.7 + - + -
58A GLN* 3.0 40.4 + - + +
61A GLN* 4.3 0.7 - - - +
177A ASN* 4.2 2.6 - - - +
266A GLY* 3.3 4.7 + - - +
267A ALA 3.3 0.6 - - - -
268A GLY* 1.3 73.7 - - - +
270A SER* 1.3 61.2 + - - +
273A GLY* 2.9 24.4 + - - -
311A TYR* 3.5 7.2 - - - +
404A MG 4.2 4.0 - - - -
510A UNX 2.6 29.0 - - - -
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Residues in contact with SER 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN* 2.5 40.1 + - - +
266A GLY 3.2 5.6 + - - -
267A ALA 3.4 8.3 - - - -
269A ASP* 1.3 76.7 - - - +
271A PHE* 1.3 57.0 + - - +
274A ALA* 2.9 29.3 + - - +
297A ILE* 3.8 5.2 + - - +
298A ALA* 3.6 15.6 - - - -
301A SER* 3.8 11.8 - - - -
311A TYR* 3.7 19.4 + - - -
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Residues in contact with PHE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A CYS* 3.8 20.9 - - - -
233A ILE* 4.0 5.2 - - + -
235A THR* 3.8 22.7 - - + -
241A CYS* 4.0 13.7 - - - -
267A ALA 3.0 13.2 + - - +
268A GLY* 3.3 10.1 - - - +
270A SER* 1.3 76.7 - - - +
272A VAL* 1.3 60.8 + - + +
274A ALA* 3.5 2.8 + - - +
275A LEU* 2.9 35.5 + - + +
291A LEU* 3.8 24.5 - - + -
294A SER* 3.8 33.4 - - - -
295A ASN* 3.4 25.6 - - - -
298A ALA* 3.9 8.8 - - + +
401A ADP 4.1 18.4 - - - -
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN* 3.5 38.1 - - + +
150A VAL* 3.9 15.7 - - + -
175A LEU* 3.8 13.8 - - + +
177A ASN* 4.4 16.4 - - + +
197A CYS* 4.0 27.8 - - + -
268A GLY 3.0 21.2 + - - +
270A SER 3.2 0.2 - - - -
271A PHE* 1.3 75.5 - - + +
273A GLY* 1.3 61.5 + - - +
275A LEU* 3.3 6.6 + - + +
276A ALA* 2.9 26.9 + - - +
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Residues in contact with GLY 273 (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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58A GLN* 3.3 30.9 - - - +
61A GLN* 4.3 1.1 - - - -
62A ALA* 3.3 21.4 - - - +
269A ASP 2.9 14.0 + - - -
270A SER 3.9 0.7 - - - -
272A VAL* 1.3 76.0 - - - +
274A ALA* 1.3 56.4 + - - +
276A ALA* 3.4 4.6 + - - +
277A PHE* 3.0 23.6 + - - +
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN* 4.0 1.6 - - + +
65A LEU* 3.6 23.8 - - + -
270A SER 2.9 18.8 + - - +
271A PHE* 3.6 5.2 - - - +
273A GLY* 1.3 76.8 - - - +
275A LEU* 1.3 56.7 + - - +
277A PHE* 3.2 3.6 + - - +
278A TYR* 3.0 34.5 + - + -
294A SER* 3.7 24.0 - - - +
297A ILE* 4.0 14.4 - - + -
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Residues in contact with LEU 275 (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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175A LEU* 4.2 14.6 - - + -
195A VAL* 3.9 13.5 - - + -
197A CYS* 4.8 3.1 - - - -
233A ILE* 3.4 30.3 - - + -
271A PHE* 2.9 26.6 + - + +
272A VAL* 3.6 7.0 - - - +
274A ALA* 1.3 74.4 - - - +
276A ALA* 1.3 57.7 + - - +
278A TYR* 3.4 1.9 + - - +
279A LEU* 2.8 48.3 + - + +
287A LEU* 4.8 4.0 - - + -
290A MET* 4.3 20.6 - - + -
291A LEU* 3.8 21.3 - - + -
294A SER* 3.3 9.5 + - - +
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.0 17.5 - - + -
62A ALA* 4.9 0.7 - - + -
148A VAL* 3.6 5.7 - - + +
150A VAL* 3.8 28.7 - - + -
175A LEU* 3.7 10.0 - - + +
272A VAL 2.9 17.3 + - - +
273A GLY* 3.6 8.1 - - - +
275A LEU* 1.3 71.0 - - - +
277A PHE* 1.3 67.4 + - - +
279A LEU* 3.3 5.0 + - - +
280A ALA* 3.0 26.9 + - - +
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Residues in contact with PHE 277 (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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18A VAL* 4.4 9.1 - - - +
62A ALA* 4.5 5.8 - - + +
65A LEU* 3.2 52.3 - - + -
66A GLY* 4.2 2.2 - - - -
67A ALA* 3.8 23.1 - - + -
273A GLY 3.0 14.2 + - - +
274A ALA 3.3 7.0 - - - +
276A ALA* 1.3 74.9 - - - +
278A TYR* 1.3 84.2 + + - +
281A TYR* 2.9 45.8 + + + +
282A TYR* 3.6 32.5 - + - -
314A LYS* 5.6 1.1 - - + -
322A PHE* 4.1 17.3 - + - -
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Residues in contact with TYR 278 (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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65A LEU* 4.9 1.6 - - + -
274A ALA* 3.0 35.0 + - + +
275A LEU* 3.4 4.0 + - - +
277A PHE* 1.3 91.5 - + - +
279A LEU* 1.3 61.4 + - - +
282A TYR* 3.0 59.3 + + + +
285A LEU* 4.3 3.6 - - + -
290A MET* 3.5 27.9 - - + +
293A ARG* 3.5 41.1 - - + +
294A SER* 3.9 15.3 - - - -
297A ILE* 4.7 5.4 - - + +
321A LEU* 2.7 41.4 + - - +
322A PHE* 4.1 7.2 - + - -
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Residues in contact with LEU 279 (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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147A LYS* 5.4 2.0 - - - +
148A VAL* 4.5 13.9 - - + -
173A LYS* 4.2 28.3 - - + +
175A LEU* 4.0 27.8 - - + -
195A VAL* 3.9 27.6 - - + -
275A LEU* 2.8 36.6 + - + +
276A ALA* 3.3 4.5 + - - +
278A TYR* 1.3 74.1 - - - +
280A ALA* 1.3 59.7 + - - +
283A PRO* 3.7 20.3 - - - +
287A LEU* 4.8 6.1 - - + -
290A MET* 3.7 24.7 - - + -
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Residues in contact with ALA 280 (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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17A ALA* 4.1 3.6 - - + +
18A VAL* 3.7 13.7 - - + -
147A LYS* 3.5 40.9 + - + +
148A VAL* 3.6 18.4 - - + -
276A ALA 3.0 16.3 + - - +
279A LEU* 1.3 78.6 - - - +
281A TYR* 1.3 72.2 + - + +
282A TYR 3.7 0.2 - - - -
283A PRO* 3.8 9.7 - - - +
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Residues in contact with TYR 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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17A ALA* 3.4 28.7 - - + +
18A VAL* 4.5 0.4 - - + -
66A GLY 4.7 2.9 - - - -
67A ALA* 3.6 25.4 - - + -
68A MET* 2.9 34.2 + - + +
147A LYS* 6.1 3.8 - - + -
277A PHE* 2.9 39.9 + + + +
280A ALA* 1.3 80.1 - - + +
282A TYR* 1.3 80.1 + - + +
283A PRO* 3.5 8.2 - - - +
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Residues in contact with TYR 282 (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 PHE* 3.6 28.6 - + - -
278A TYR* 3.0 29.4 + + + +
281A TYR* 1.3 93.2 - - + +
283A PRO* 1.4 61.5 - - - +
284A ASN 3.3 2.7 - - - -
285A LEU* 3.3 36.2 + - + +
290A MET* 3.0 19.1 - - - +
293A ARG* 4.2 7.0 - - - -
322A PHE* 3.4 46.7 + - - +
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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
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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