Contacts of the helix formed by residues 290 - 302 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288D VAL* 3.8 3.3 - - - +
289D ARG* 1.3 93.0 - - + +
291D ALA* 1.3 67.4 + - - +
292D SER* 3.9 18.5 + - - +
293D ASP* 2.9 41.9 + - - +
294D VAL 4.0 1.4 + - - -
318D GLU* 5.2 1.8 - - - +
322D ARG* 3.3 29.2 - - - +
325D GLU* 3.6 10.1 - - - +
326D ILE* 3.7 14.0 - - - +
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Residues in contact with ALA 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D LYS* 1.3 69.7 - - - +
292D SER* 1.3 62.3 + - - +
294D VAL* 3.0 28.3 + - - +
295D ALA* 3.3 7.6 + - - +
325D GLU* 2.9 42.5 + - + +
326D ILE* 4.1 2.0 - - - +
329D VAL* 4.0 18.0 - - + +
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Residues in contact with SER 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D LYS* 3.3 27.4 + - - +
291D ALA* 1.3 76.3 - - - +
293D ASP* 1.3 60.5 + - - +
295D ALA* 3.5 11.5 - - - +
296D ALA* 2.9 28.9 + - - +
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Residues in contact with ASP 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D GLY* 4.6 18.2 + - - -
264D LEU* 5.3 1.2 - - - +
287D PHE 3.9 1.9 - - - +
288D VAL* 3.8 18.2 - - + -
289D ARG* 2.7 41.7 + - - +
290D LYS* 2.9 33.2 + - - +
292D SER* 1.3 82.7 + - - +
294D VAL* 1.3 55.3 + - - +
296D ALA* 3.4 8.2 + - - +
297D VAL* 3.1 28.8 + - - +
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Residues in contact with VAL 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D VAL* 4.6 9.8 - - + +
290D LYS 4.3 2.9 - - - +
291D ALA* 3.1 12.8 - - - +
293D ASP* 1.3 73.5 - - - +
295D ALA* 1.3 54.5 + - - +
297D VAL* 3.1 8.7 + - + +
298D ARG* 2.7 46.4 + - - +
310D ILE* 4.2 20.6 - - + -
312D SER* 4.4 10.8 - - - +
326D ILE* 4.7 2.5 - - + +
329D VAL* 3.1 48.7 - - + +
330D SER* 4.0 10.3 - - - +
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Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D ALA 3.3 6.4 + - - +
292D SER* 3.5 18.8 - - - +
294D VAL* 1.3 76.5 - - - +
296D ALA* 1.3 57.5 + - - +
298D ARG* 3.1 11.4 + - - +
299D ALA* 2.8 29.5 + - - +
329D VAL* 5.1 1.4 - - + +
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Residues in contact with ALA 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D LEU* 3.6 27.2 - - + +
292D SER 2.9 17.6 + - - +
293D ASP* 3.5 8.1 - - - +
294D VAL 3.2 0.2 - - - -
295D ALA* 1.3 75.6 - - - +
297D VAL* 1.3 62.4 + - - +
299D ALA* 3.1 9.2 + - - +
300D ALA* 2.9 20.1 + - - +
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Residues in contact with VAL 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D THR* 6.4 0.9 - - + -
264D LEU* 3.8 26.7 - - + +
272D LEU* 4.2 11.7 - - + -
283D VAL* 4.1 20.0 - - + -
285D ALA* 3.9 22.9 - - + -
288D VAL* 5.7 0.7 - - + -
293D ASP 3.1 15.7 + - - +
294D VAL* 3.1 11.9 + - - +
296D ALA* 1.3 74.4 - - - +
298D ARG* 1.3 57.0 + - - +
300D ALA* 3.4 2.1 + - - +
301D LEU* 2.9 30.7 + - + +
310D ILE* 3.3 25.4 - - + -
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Residues in contact with ARG 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D VAL* 2.7 27.3 + - - +
295D ALA* 3.1 13.6 + - - +
297D VAL* 1.3 73.9 - - - +
299D ALA* 1.3 62.5 + - - +
301D LEU* 3.2 18.1 + - + +
302D GLY* 3.2 11.6 + - - +
306D HIS* 5.6 11.4 - - + +
308D ILE 5.6 0.4 + - - -
310D ILE* 4.1 22.8 - - + +
329D VAL* 2.8 32.7 + - - +
330D SER 4.9 0.4 - - - -
331D ASP* 3.7 29.3 + - - +
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Residues in contact with ALA 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D ALA 2.8 15.6 + - - +
296D ALA* 3.4 11.0 - - - +
298D ARG* 1.3 70.7 - - - +
300D ALA* 1.3 59.0 + - - +
302D GLY* 2.9 21.5 + - - -
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Residues in contact with ALA 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D LEU* 3.8 10.5 - - + -
269D VAL* 4.1 19.3 - - + -
272D LEU* 3.6 30.5 - - + -
273D ARG* 2.9 32.9 + - - +
296D ALA 2.9 14.1 + - - +
297D VAL 3.7 0.2 - - - +
299D ALA* 1.3 71.4 - - - +
301D LEU* 1.3 61.8 + - - +
302D GLY 2.9 6.3 + - - -
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Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D LEU* 3.8 33.7 - - + +
273D ARG* 3.9 3.2 + - - -
275D GLY 6.3 0.2 - - - -
276D VAL* 3.1 38.1 - - + +
280D VAL* 6.2 0.2 - - + -
283D VAL* 3.8 11.9 - - + -
297D VAL* 2.9 15.1 + - + +
298D ARG* 3.2 9.8 + - + +
300D ALA* 1.3 76.5 - - - +
302D GLY* 1.3 66.4 + - - +
304D GLU 4.6 0.2 + - - -
305D GLY 3.5 24.6 + - - +
308D ILE* 3.8 28.0 - - + +
310D ILE* 4.0 24.7 - - + -
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Residues in contact with GLY 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D ARG* 4.7 8.1 - - - -
298D ARG 3.2 6.9 + - - +
299D ALA 2.9 14.8 + - - -
300D ALA 2.9 5.8 - - - -
301D LEU* 1.3 84.0 - - - +
303D PRO* 1.3 76.2 - - - +
304D GLU 3.3 0.4 - - - -
305D GLY* 3.2 12.6 + - - -
306D HIS* 4.1 3.0 + - - -
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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