Contacts of the helix formed by residues 290 - 302 (chain C) in PDB entry 2VGB
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 290 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288C VAL* 3.7 4.0 - - - +
289C ARG* 1.3 93.0 - - + +
291C ALA* 1.3 60.4 + - - +
292C SER* 3.8 18.4 + - - +
293C ASP* 2.8 49.3 + - - +
294C VAL 4.0 0.9 + - - -
318C GLU* 5.6 0.9 - - - +
322C ARG* 3.4 28.3 - - - +
325C GLU* 3.6 10.1 - - - +
326C ILE* 3.8 14.1 - - - +
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C LYS* 1.3 70.1 - - - +
292C SER* 1.3 63.4 + - - +
294C VAL* 3.0 26.9 + - - +
295C ALA* 3.2 8.7 + - - +
325C GLU* 3.0 42.9 + - + +
326C ILE* 4.2 1.7 - - - +
329C VAL* 4.0 17.5 - - + +
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Residues in contact with SER 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C LYS* 3.3 28.6 + - - +
291C ALA* 1.3 77.1 - - - +
293C ASP* 1.3 60.5 + - - +
295C ALA* 3.3 12.1 + - - +
296C ALA* 2.8 30.5 + - - +
325C GLU* 5.0 0.2 + - - -
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Residues in contact with ASP 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C GLY* 4.7 17.1 + - - -
264C LEU* 5.3 1.0 - - - +
287C PHE 3.8 1.7 - - - +
288C VAL* 3.6 19.5 - - + -
289C ARG* 2.6 41.8 + - - +
290C LYS* 2.8 34.9 + - - +
292C SER* 1.3 81.3 + - - +
294C VAL* 1.3 57.1 + - - +
296C ALA* 3.4 8.1 + - - +
297C VAL* 3.1 29.3 + - - +
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Residues in contact with VAL 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C VAL* 4.5 9.4 - - + -
290C LYS 4.3 2.7 - - - +
291C ALA* 3.1 19.7 - - - +
293C ASP* 1.3 74.1 - - - +
295C ALA* 1.3 58.6 + - - +
296C ALA 3.2 0.4 - - - -
297C VAL* 3.2 8.2 + - + +
298C ARG* 2.8 39.5 + - - +
310C ILE* 4.3 20.4 - - + +
312C SER* 4.3 11.7 - - - +
326C ILE* 4.8 2.2 - - + +
329C VAL* 3.2 41.3 - - + +
330C SER* 4.0 11.2 - - - +
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Residues in contact with ALA 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C ALA 3.2 7.2 + - - +
292C SER* 3.4 18.8 - - - +
294C VAL* 1.3 77.9 - - - +
296C ALA* 1.3 57.1 + - - +
298C ARG* 3.0 11.7 + - - +
299C ALA* 2.8 29.0 + - - +
329C VAL* 5.0 1.5 - - + +
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Residues in contact with ALA 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C LEU* 3.6 22.0 - - + +
292C SER 2.8 16.3 + - - +
293C ASP* 3.5 11.9 - - - +
294C VAL 3.2 0.2 - - - -
295C ALA* 1.3 73.1 - - - +
297C VAL* 1.3 63.5 + - - +
299C ALA* 3.1 9.0 + - - +
300C ALA* 3.0 23.2 + - - +
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Residues in contact with VAL 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C THR* 6.5 0.2 - - + -
264C LEU* 3.8 26.6 - - + +
272C LEU* 4.3 11.4 - - + +
283C VAL* 4.2 20.2 - - + -
285C ALA* 3.9 23.3 - - + -
288C VAL* 5.7 0.9 - - + -
293C ASP 3.1 19.1 + - - +
294C VAL* 3.2 11.2 + - - +
296C ALA* 1.3 73.9 - - - +
298C ARG* 1.3 54.4 + - - +
300C ALA* 3.3 2.8 + - - +
301C LEU* 2.8 37.4 + - + +
310C ILE* 3.4 26.5 - - + -
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Residues in contact with ARG 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C VAL* 2.8 27.3 + - - +
295C ALA* 3.0 13.6 + - - +
297C VAL* 1.3 75.4 - - - +
299C ALA* 1.3 64.3 + - - +
301C LEU* 3.3 10.3 + - + +
302C GLY* 3.3 15.8 + - - +
306C HIS* 5.6 12.4 - - + +
308C ILE 5.7 0.4 + - - -
310C ILE* 4.2 21.4 - - + +
329C VAL* 2.9 33.7 + - - +
330C SER 5.0 0.4 - - - -
331C ASP* 3.7 28.7 + - - +
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Residues in contact with ALA 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C ALA 2.8 15.3 + - - +
296C ALA* 3.1 10.7 + - - +
298C ARG* 1.3 71.3 - - - +
300C ALA* 1.3 59.5 + - - +
302C GLY* 2.9 21.8 + - - -
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Residues in contact with ALA 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C LEU* 3.8 9.6 - - + -
269C VAL* 4.0 19.7 - - + -
272C LEU* 3.7 25.4 - - + -
273C ARG* 2.9 31.2 + - - +
296C ALA 3.0 12.2 + - - +
297C VAL 3.5 7.4 - - - +
299C ALA* 1.3 71.4 - - - +
301C LEU* 1.3 62.8 + - - +
302C GLY 2.9 5.9 + - - -
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Residues in contact with LEU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C LEU* 3.7 35.9 - - + +
273C ARG* 3.9 3.5 + - - -
275C GLY 6.3 0.2 - - - -
276C VAL* 3.1 38.0 - - + +
280C VAL* 6.3 0.2 - - + -
283C VAL* 3.8 10.8 - - + -
297C VAL* 2.8 19.0 + - + +
298C ARG* 3.3 10.1 + - + +
300C ALA* 1.3 71.7 - - - +
302C GLY* 1.3 67.8 + - - +
304C GLU 4.5 0.3 + - - -
305C GLY 3.5 24.7 + - - +
308C ILE* 3.8 26.7 - - + +
310C ILE* 4.0 25.8 - - + -
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Residues in contact with GLY 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C ARG* 4.7 7.9 - - - -
298C ARG 3.3 5.7 + - - +
299C ALA 2.9 17.7 + - - -
300C ALA 2.9 3.3 - - - -
301C LEU* 1.3 86.9 - - - +
303C PRO* 1.3 74.4 - - - +
304C GLU 3.3 0.7 - - - -
305C GLY* 3.2 13.0 + - - -
306C HIS* 4.1 2.6 + - - -
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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