Contacts of the helix formed by residues 269 - 285 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A GLU* 4.5 0.2 - - - -
267A ASP* 2.9 29.7 + - - +
268A GLU* 1.3 102.2 + - + +
270A VAL* 1.3 64.2 + - - +
271A ASP 3.2 0.2 - - - -
272A LEU* 3.2 39.2 + - + +
273A TRP 3.4 0.9 + - - -
328A PRO* 3.3 41.7 - - + +
329A PRO* 3.9 15.9 - - + -
331A ARG* 3.1 16.1 + - - +
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ILE* 3.6 19.7 - - + -
215A ARG* 4.0 17.7 - - + -
257A PRO* 3.8 22.2 - - + +
259A GLU* 3.6 16.1 + - - +
260A MET* 4.2 4.9 - - + -
266A HIS* 3.5 33.0 - - + -
267A ASP* 3.2 18.5 + - - +
268A GLU 3.1 1.2 - - - -
269A LYS* 1.3 78.2 - - - +
271A ASP* 1.3 63.5 + - - +
273A TRP* 3.3 4.9 + - - +
274A CYS* 3.1 32.6 + - - -
331A ARG* 4.2 2.0 - - - +
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Residues in contact with ASP 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 4.0 22.1 - - + +
208A HIS* 2.8 30.3 + - + +
213A ILE* 3.5 6.7 - - - +
214A HIS* 2.8 31.5 + - - +
215A ARG* 2.8 29.8 + - - -
217A ILE* 4.6 5.9 - - + +
268A GLU 3.1 9.5 + - - +
270A VAL* 1.3 74.5 - - - +
272A LEU* 1.3 61.1 + - - +
274A CYS* 3.5 7.1 + - - +
275A ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A HIS* 5.2 2.9 - - + +
268A GLU* 4.7 2.9 - - + +
269A LYS* 3.2 38.1 + - + +
271A ASP* 1.3 75.5 - - - +
273A TRP* 1.3 65.2 + - - +
275A ALA* 3.2 16.0 + - - +
276A GLY 3.2 9.2 + - - -
323A LEU* 3.7 15.8 - - + +
331A ARG* 3.8 32.8 - - + +
332A LEU 3.4 23.3 - - - +
333A PRO* 4.6 3.8 - - + -
334A LEU* 3.5 40.6 - - + +
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Residues in contact with TRP 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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254A ASP 5.3 0.4 + - - -
255A TYR 3.3 20.2 + - - -
256A LEU 3.3 12.5 + - - -
257A PRO* 3.6 13.7 - - + -
258A PRO* 3.6 31.4 - - + -
269A LYS 3.4 1.8 + - - -
270A VAL 3.3 9.1 + - - +
272A LEU* 1.3 78.9 - - - +
274A CYS* 1.3 62.8 + - - +
276A GLY 3.0 11.4 + - - -
277A VAL* 3.1 22.2 + - + +
289A PHE* 3.5 31.6 - + - -
301A ILE* 3.7 24.5 - - + -
304A VAL* 4.1 10.1 - - + -
323A LEU 4.0 9.0 - - - -
324A LEU* 3.3 41.8 - - + +
325A ARG 3.6 27.4 - - - -
331A ARG* 3.8 19.4 - - - +
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Residues in contact with CYS 274 (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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215A ARG 5.1 11.7 - - - -
216A ASP* 5.5 0.7 - - - -
217A ILE* 4.0 32.9 - - + +
255A TYR* 3.3 33.4 - - + -
257A PRO* 4.7 7.0 - - - -
270A VAL* 3.1 24.1 + - - +
271A ASP* 3.9 7.4 - - - +
272A LEU 3.3 0.2 - - - -
273A TRP* 1.3 79.7 - - - +
275A ALA* 1.3 56.8 + - - +
277A VAL* 3.3 6.6 + - - +
278A LEU* 2.9 29.7 + - - +
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Residues in contact with ALA 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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197A MET* 3.4 21.4 - - + +
200A LEU* 3.8 28.3 - - + -
204A LEU* 4.8 4.3 - - + -
217A ILE* 4.8 0.8 - - - +
271A ASP 2.9 14.8 + - - +
272A LEU* 3.2 13.0 + - - +
274A CYS* 1.3 76.3 - - - +
276A GLY* 1.3 57.6 + - - +
278A LEU* 3.4 3.6 + - - +
279A CYS* 2.9 23.4 + - - +
323A LEU* 4.2 7.6 - - + -
334A LEU* 5.4 5.2 - - + -
337A VAL* 5.8 1.3 - - + -
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Residues in contact with GLY 276 (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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272A LEU 3.2 4.0 + - - -
273A TRP 3.0 8.4 + - - -
275A ALA* 1.3 77.1 - - - +
277A VAL* 1.3 64.1 + - - +
279A CYS* 3.4 4.8 + - - +
280A TYR* 3.1 23.0 + - - +
320A ILE* 4.0 9.0 - - - +
323A LEU* 3.7 25.9 - - - +
324A LEU* 3.9 13.0 - - - -
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ASP 3.7 19.3 - - - +
255A TYR* 3.5 31.4 - - + -
273A TRP* 3.1 39.3 + - + +
274A CYS* 3.3 7.4 + - - +
276A GLY* 1.3 74.5 - - - +
278A LEU* 1.3 58.0 + - - +
280A TYR* 3.2 4.7 + - - +
281A GLU* 2.9 27.2 + - - +
287A PRO* 4.4 1.8 - - + -
288A PRO* 3.7 31.1 - - + +
289A PHE* 4.6 2.5 - - + -
324A LEU* 3.7 8.7 - - + +
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Residues in contact with LEU 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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197A MET* 4.5 3.1 - - - -
200A LEU* 3.7 29.4 - - + -
217A ILE* 3.8 9.2 - - + -
218A LYS* 3.8 9.4 - - - +
219A PRO* 3.5 40.4 - - + -
222A LEU* 4.1 9.9 - - + -
230A LEU* 5.1 0.2 - - + -
255A TYR* 3.6 10.0 - - + +
274A CYS 2.9 17.0 + - - +
275A ALA* 3.6 5.2 - - - +
277A VAL* 1.3 76.9 - - - +
279A CYS* 1.3 56.7 + - - +
281A GLU* 3.2 2.1 + - - +
282A PHE* 2.8 68.1 + - + -
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Residues in contact with CYS 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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193A SER* 5.4 1.3 - - - -
197A MET* 3.6 33.2 - - + -
275A ALA 2.9 16.7 + - - +
276A GLY* 3.7 6.5 - - - +
277A VAL 3.4 0.2 - - - -
278A LEU* 1.3 76.2 - - - +
280A TYR* 1.3 63.1 + - - +
282A PHE* 3.4 6.9 + - - +
283A LEU* 3.2 41.2 + - - +
316A SER 5.2 0.9 - - - -
319A LEU* 4.2 9.2 - - + -
320A ILE* 3.9 19.1 - - + -
323A LEU* 5.3 0.9 - - + -
342A TRP* 4.0 16.2 - - - -
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Residues in contact with TYR 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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276A GLY 3.1 13.2 + - - +
277A VAL 3.4 8.5 - - - +
279A CYS* 1.3 76.5 - - - +
281A GLU* 1.3 57.3 + - - +
283A LEU* 3.2 2.4 + - - -
284A VAL* 2.8 50.6 + - + +
286A MET* 3.2 23.1 - - + -
287A PRO 3.9 1.1 - - - -
288A PRO* 3.4 40.8 + - + +
306A LEU* 3.8 23.8 - - + -
307A LYS 3.3 19.6 + - - -
308A PHE* 3.9 26.0 - + - -
309A PRO* 3.5 13.8 - - + +
320A ILE* 3.8 16.2 - - + +
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Residues in contact with GLU 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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182A LEU* 3.7 18.9 - - + +
219A PRO* 3.5 20.3 - - + +
220A GLU* 5.2 3.1 - - - +
255A TYR* 2.7 44.8 + - - +
277A VAL 2.9 14.4 + - - +
278A LEU 3.2 2.4 + - - +
280A TYR* 1.3 73.5 - - - +
282A PHE* 1.3 58.8 + - - +
285A GLY* 2.7 33.5 + - - +
286A MET* 3.6 25.8 - - - +
287A PRO* 3.8 20.4 - - + +
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Residues in contact with PHE 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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178A LEU* 3.5 33.9 - - + -
182A LEU* 3.9 8.5 - - + +
187A ARG* 3.6 3.1 - - - -
188A PHE* 2.8 50.9 + + + -
193A SER* 3.6 26.5 - - - +
196A PHE* 3.4 36.8 - + + -
197A MET* 4.4 5.8 - - - -
219A PRO* 4.6 3.6 - - + -
222A LEU* 4.3 2.2 - - + -
230A LEU* 4.9 0.4 - - + -
278A LEU* 2.8 57.1 + - + -
279A CYS* 3.4 14.6 - - - +
280A TYR 3.3 0.2 - - - -
281A GLU* 1.3 79.8 - - - +
283A LEU* 1.3 56.2 + - - +
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Residues in contact with LEU 283 (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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187A ARG* 3.4 21.5 + - - +
188A PHE 3.9 12.2 - - - +
189A ASP 4.2 0.2 - - - -
190A GLU* 4.1 26.2 - - + -
193A SER* 3.4 25.1 - - - +
279A CYS* 3.2 34.7 + - - +
280A TYR* 3.9 2.7 - - - +
282A PHE* 1.3 81.0 - - - +
284A VAL* 1.3 59.7 + - + +
311A PHE* 3.5 10.6 - - - -
312A LEU* 3.7 17.0 - - + -
316A SER* 3.6 29.4 - - - +
320A ILE* 4.1 8.3 - - + -
342A TRP* 4.1 4.7 - - + -
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Residues in contact with VAL 284 (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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186A GLY 5.2 0.3 - - - -
187A ARG* 3.9 15.0 + - - +
280A TYR* 2.8 47.1 + - + +
283A LEU* 1.3 84.1 - - + +
285A GLY* 1.3 57.8 + - - +
286A MET* 4.0 13.7 - - + +
309A PRO* 3.9 31.2 - - + -
311A PHE* 4.2 9.0 - - + -
312A LEU* 4.1 19.7 - - + -
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Residues in contact with GLY 285 (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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182A LEU* 4.7 4.8 - - - +
186A GLY 3.2 24.9 - - - +
187A ARG* 4.1 1.0 - - - +
281A GLU* 2.7 31.7 + - - +
283A LEU 3.8 0.4 - - - -
284A VAL* 1.3 72.7 - - - +
286A MET* 1.3 71.6 + - - +
287A PRO* 4.9 0.3 - - - +
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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
------------------------------------------------------------
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