Contacts of the helix formed by residues 269 - 285 (chain B) in PDB entry 2VGO
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 269 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B GLU* 5.1 0.2 - - - +
267B ASP* 2.9 28.8 + - - +
268B GLU* 1.3 102.8 + - + +
270B VAL* 1.3 64.4 + - - +
271B ASP 3.1 1.6 - - - -
272B LEU* 3.1 34.8 + - + +
273B TRP 3.3 4.3 + - - -
328B PRO* 3.4 40.6 - - + +
329B PRO* 3.8 18.2 - - + -
331B ARG* 3.0 17.9 + - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ILE* 3.6 21.1 - - + -
215B ARG* 4.1 15.5 - - + -
257B PRO* 3.8 20.9 - - + -
259B GLU* 3.5 15.7 + - + +
260B MET* 4.5 7.6 - - + -
266B HIS* 3.5 29.6 - - + -
267B ASP 3.2 19.9 + - - +
268B GLU 3.1 1.0 - - - -
269B LYS* 1.3 77.3 - - - +
271B ASP* 1.3 64.9 + - - +
273B TRP* 3.4 4.2 + - - +
274B CYS* 3.1 32.6 + - - -
331B ARG* 4.0 2.7 - - - +
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Residues in contact with ASP 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 3.9 22.7 - - + +
208B HIS* 2.8 30.5 + - + +
213B ILE* 3.5 7.8 - - - +
214B HIS* 2.9 29.5 + - - +
215B ARG* 2.9 29.8 + - - -
216B ASP 4.7 0.5 + - - -
217B ILE* 4.7 5.0 + - + +
268B GLU 3.1 8.9 + - - +
270B VAL* 1.3 75.6 - - - +
272B LEU* 1.3 61.7 + - - +
274B CYS* 3.5 6.5 + - - +
275B ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B HIS* 5.3 2.0 - - + -
268B GLU* 5.0 2.5 - - + +
269B LYS* 3.1 33.0 + - + +
271B ASP* 1.3 75.5 - - - +
273B TRP* 1.3 65.5 + - - +
275B ALA* 3.3 7.0 + - + +
276B GLY 3.1 16.6 + - - -
323B LEU* 3.6 20.9 - - + +
331B ARG* 3.9 28.7 - - + +
332B LEU 3.3 28.0 - - - +
333B PRO* 4.1 5.2 - - + -
334B LEU* 3.4 42.6 - - + +
337B VAL* 5.1 0.2 - - + -
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Residues in contact with TRP 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ASP 5.4 0.4 + - - -
255B TYR 3.3 19.8 + - - -
256B LEU 3.3 11.5 + - - -
257B PRO* 3.5 13.7 - - + -
258B PRO* 3.6 37.5 - - + -
269B LYS 3.3 2.8 + - - -
270B VAL 3.6 7.6 - - - +
272B LEU* 1.3 78.4 - - - +
274B CYS* 1.3 62.6 + - - +
276B GLY 2.9 12.0 + - - -
277B VAL* 3.0 22.5 + - + +
289B PHE* 3.5 31.4 - + - -
301B ILE* 3.9 18.2 - - + -
304B VAL* 4.1 11.0 - - + -
323B LEU 4.1 7.4 - - - -
324B LEU* 3.3 40.8 - - + +
325B ARG 3.6 26.9 - - - -
331B ARG* 3.8 18.7 - - - +
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Residues in contact with CYS 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ARG 5.1 10.8 - - - -
216B ASP* 5.5 0.9 - - - -
217B ILE* 3.9 35.1 - - + +
255B TYR* 3.4 32.8 - - + -
257B PRO* 4.1 10.5 - - - -
270B VAL* 3.1 21.3 + - - +
271B ASP* 3.9 7.2 - - - +
273B TRP* 1.3 81.5 - - - +
275B ALA* 1.3 56.6 + - - +
277B VAL* 3.2 2.9 + - - +
278B LEU* 2.8 30.6 + - - +
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Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B MET* 3.4 20.5 - - + +
200B LEU* 3.7 29.6 - - + -
201B ALA* 6.5 0.4 - - + -
204B LEU* 4.5 5.2 - - + -
217B ILE* 4.7 0.8 - - - +
271B ASP 2.9 18.9 + - - +
272B LEU* 3.5 9.2 - - - +
273B TRP 3.2 0.2 - - - -
274B CYS* 1.3 75.3 - - - +
276B GLY* 1.3 58.3 + - - +
278B LEU* 3.4 2.6 + - - +
279B CYS 2.9 23.7 + - - -
323B LEU* 4.5 6.3 - - + -
334B LEU* 5.3 5.6 - - + -
337B VAL* 6.0 1.3 - - + -
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Residues in contact with GLY 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU 3.1 6.9 + - - -
273B TRP 2.9 8.6 + - - -
275B ALA* 1.3 74.5 - - - +
277B VAL* 1.3 63.3 + - - +
279B CYS* 3.4 5.6 + - - +
280B TYR* 3.1 22.9 + - - +
320B ILE* 4.0 8.3 - - - +
323B LEU* 3.7 27.7 - - - +
324B LEU* 3.8 11.7 - - - -
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ASP 3.8 10.1 - - - +
255B TYR* 3.5 43.1 - - + +
273B TRP* 3.0 41.9 + - + +
274B CYS 3.2 1.5 + - - +
276B GLY* 1.3 74.8 - - - +
278B LEU* 1.3 58.3 + - - +
280B TYR* 3.2 8.1 + - - +
281B GLU* 2.9 27.5 + - - +
287B PRO* 4.6 0.7 - - + -
288B PRO* 3.5 30.2 - - + +
289B PHE* 4.7 0.7 - - + -
324B LEU* 3.7 9.2 - - + -
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B MET* 4.7 2.2 - - - -
200B LEU* 3.8 26.5 - - + -
217B ILE* 4.0 5.8 - - + -
218B LYS* 3.8 10.5 - - - +
219B PRO* 3.7 36.3 - - + -
222B LEU* 3.8 14.4 - - + -
230B LEU* 4.9 1.6 - - + -
255B TYR* 3.5 9.5 - - + +
274B CYS 2.8 17.0 + - - +
275B ALA* 3.5 5.8 - - - +
277B VAL* 1.3 73.8 - - - +
279B CYS* 1.3 65.1 + - - +
281B GLU* 3.2 2.1 + - - +
282B PHE* 2.9 68.4 + - + -
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Residues in contact with CYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B SER* 5.6 1.3 - - - -
197B MET* 3.6 34.2 - - + -
275B ALA 2.9 16.9 + - - +
276B GLY* 3.6 7.4 - - - +
277B VAL 3.4 0.2 - - - -
278B LEU* 1.3 75.3 - - - +
280B TYR* 1.3 63.4 + - - +
282B PHE* 3.4 7.4 + - - +
283B LEU* 3.2 37.7 + - - +
316B SER 5.2 0.9 - - - -
319B LEU* 4.0 17.7 - - + -
320B ILE* 3.9 19.3 - - + -
323B LEU* 5.4 0.7 - - + -
342B TRP* 4.1 5.6 - - - -
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Residues in contact with TYR 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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276B GLY 3.1 14.2 + - - +
277B VAL* 3.4 9.4 - - - +
279B CYS* 1.3 75.5 - - - +
281B GLU* 1.3 57.1 + - - +
283B LEU* 3.1 2.3 + - - -
284B VAL* 2.8 59.0 + - + +
286B MET* 3.2 24.2 - - + -
287B PRO 3.9 1.1 - - - -
288B PRO* 3.4 45.6 + - + +
306B LEU* 4.1 10.1 - - + -
307B LYS 3.3 21.2 + - - -
308B PHE* 3.9 36.8 - + - -
309B PRO* 3.5 7.7 - - + +
320B ILE* 3.8 16.0 - - + +
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Residues in contact with GLU 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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182B LEU* 3.9 21.1 - - + +
219B PRO* 4.0 12.8 - - + +
255B TYR* 2.6 47.1 + - - +
277B VAL 2.9 10.7 + - - +
278B LEU 3.2 1.5 + - - +
280B TYR* 1.3 75.3 - - - +
282B PHE* 1.3 59.2 + - - +
285B GLY* 2.7 29.7 + - - +
286B MET* 3.6 25.2 - - - +
287B PRO* 3.9 24.5 - - + +
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Residues in contact with PHE 282 (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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178B LEU* 3.4 37.2 - - + -
182B LEU* 4.0 7.7 - - + +
187B ARG* 3.6 3.6 - - - -
188B PHE* 2.8 49.9 + + + -
193B SER* 3.6 24.5 - - - +
196B PHE* 3.5 38.8 - + + -
197B MET* 4.6 4.9 - - - -
219B PRO* 4.8 3.4 - - + -
222B LEU* 4.2 2.0 - - + -
230B LEU* 4.9 0.2 - - + -
278B LEU* 2.9 63.6 + - + +
279B CYS* 3.5 9.9 - - - +
281B GLU* 1.3 76.9 - - - +
283B LEU* 1.3 56.0 + - - +
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Residues in contact with LEU 283 (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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187B ARG* 3.3 21.9 - - - +
188B PHE 4.0 11.9 - - - +
189B ASP 4.3 0.2 - - - -
190B GLU* 4.1 23.3 - - + -
193B SER* 3.4 26.0 - - - +
279B CYS* 3.2 24.6 + - - +
280B TYR* 3.1 4.0 + - - +
282B PHE* 1.3 78.6 - - - +
284B VAL* 1.3 59.7 + - + +
311B PHE* 3.5 9.0 - - - -
312B LEU* 3.6 17.6 - - + +
316B SER* 3.5 31.4 - - - +
320B ILE* 4.3 6.3 - - + -
342B TRP* 3.9 16.4 - - + -
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ARG* 2.9 31.1 + - - +
280B TYR* 2.8 52.2 + - + +
283B LEU* 1.3 82.3 - - + +
285B GLY* 1.3 56.9 + - - +
286B MET* 4.0 11.7 - - + +
309B PRO* 3.7 23.6 - - + -
311B PHE* 4.1 4.2 - - + -
312B LEU* 3.8 32.8 - - + -
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Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 4.8 4.4 - - - +
186B GLY 3.2 26.3 - - - +
187B ARG* 4.0 2.8 - - - +
281B GLU* 2.7 32.0 + - - +
283B LEU 3.8 0.6 - - - -
284B VAL* 1.3 72.9 - - - +
286B MET* 1.3 67.3 + - - +
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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
------------------------------------------------------------
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