Contacts of the helix formed by residues 305 - 317 (chain B) in PDB entry 2VQO
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 SER 305 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B ASP* 2.7 31.0 + - - -
292B VAL* 4.4 2.5 - - - -
303B ASN 3.7 1.0 + - - -
304B LEU* 1.3 75.5 - - - +
306B ALA* 1.3 62.2 + - - +
307B ARG* 3.7 11.2 + - - +
308B CYS* 3.1 27.0 + - - +
309B PHE* 3.6 9.9 - - - -
356B LEU* 4.8 1.7 - - - +
357B PRO* 6.0 1.1 - - - +
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B VAL* 4.1 11.1 - - + +
305B SER* 1.3 70.0 - - - +
307B ARG* 1.3 66.4 + - - +
309B PHE* 3.1 22.9 + - - +
336B ALA 4.1 3.1 - - - +
339B ASP* 3.4 22.0 - - + +
340B ALA* 3.3 38.2 - - + +
343B ALA* 3.6 11.9 - - - +
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Residues in contact with ARG 307 (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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305B SER* 3.8 11.0 - - - +
306B ALA* 1.3 78.0 - - - +
308B CYS* 1.3 62.8 + - - +
310B GLY* 3.1 12.8 + - - -
311B TYR* 3.3 22.9 + - + -
343B ALA* 4.4 8.9 - - - +
354B ASP* 3.3 45.4 - - + +
355B PRO 2.9 23.9 + - - -
356B LEU* 4.2 9.9 - - + +
357B PRO* 3.9 19.2 - - - +
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Residues in contact with CYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ASP* 3.2 45.5 - - - +
263B TYR* 5.0 2.0 - - - -
264B LEU* 4.2 20.0 - - - -
304B LEU* 4.5 9.2 - - + -
305B SER* 3.1 15.2 + - - +
306B ALA 3.2 0.2 - - - -
307B ARG* 1.3 75.7 - - - +
309B PHE* 1.3 57.1 + - - +
311B TYR* 3.1 7.7 + - - +
312B LEU* 3.0 41.8 + - - +
356B LEU* 4.3 10.5 - - + +
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Residues in contact with PHE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B TRP* 3.5 53.6 - + + -
263B TYR* 5.7 1.6 - + - -
288B GLY 4.2 6.5 - - - -
289B PHE* 3.9 17.0 - + + -
291B ALA* 4.4 12.6 - - + -
292B VAL* 3.4 30.3 - - + -
304B LEU* 3.7 28.7 - - + -
305B SER 3.6 12.6 - - - -
306B ALA* 3.1 12.0 + - - +
308B CYS* 1.3 75.5 - - - +
310B GLY* 1.3 55.9 + - - +
312B LEU* 3.9 14.9 - - + +
313B THR* 2.8 38.3 + - - -
340B ALA* 4.7 2.0 - - + +
344B CYS* 3.8 15.9 - - - -
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Residues in contact with GLY 310 (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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306B ALA 3.7 4.0 + - - -
307B ARG 3.1 8.8 + - - -
309B PHE* 1.3 78.6 - - - +
311B TYR* 1.3 56.1 + - - +
313B THR* 4.4 0.2 - - - -
314B LYS 3.2 19.1 + - - -
343B ALA* 3.6 31.8 - - - +
344B CYS 4.3 0.2 - - - -
347B ALA* 3.3 14.1 - - - +
353B LEU* 3.4 16.6 - - - +
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Residues in contact with TYR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 4.8 10.1 - - + -
307B ARG* 3.3 20.9 - - + -
308B CYS* 3.1 8.5 + - - +
310B GLY* 1.3 77.7 - - - +
312B LEU* 1.3 59.7 + - - +
314B LYS* 3.4 10.6 + - + +
315B GLN* 3.0 35.1 + - + +
353B LEU* 3.5 30.9 + - + +
354B ASP 2.7 31.4 + - - -
355B PRO* 3.1 14.2 - - - +
356B LEU* 3.8 39.9 - - + -
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B TRP* 3.9 20.6 - - + -
263B TYR* 4.7 20.9 - - + +
264B LEU* 4.2 24.2 - - + -
267B PHE* 3.8 44.7 - - + -
304B LEU* 5.0 1.1 - - + -
308B CYS* 3.0 31.3 + - - +
309B PHE* 3.4 26.2 + - + +
311B TYR* 1.3 72.9 - - - +
313B THR* 1.3 65.2 + - - +
315B GLN* 3.4 7.3 + - - +
316B LEU* 3.2 26.9 + - - +
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Residues in contact with THR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B TRP* 3.7 13.3 - - - -
309B PHE 2.8 20.9 + - - -
310B GLY 3.7 6.1 - - - -
312B LEU* 1.3 75.9 - - - +
314B LYS* 1.3 58.3 + - - +
316B LEU* 3.0 8.2 + - - +
317B MET* 2.9 34.5 + - + +
324B ILE* 4.5 1.7 - - + +
326B LEU* 3.8 12.9 - - + +
344B CYS* 3.3 28.0 - - - +
347B ALA* 4.0 17.0 - - + -
348B LEU* 4.0 23.3 - - + -
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Residues in contact with LYS 314 (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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310B GLY 3.2 14.7 + - - +
311B TYR* 3.7 13.1 - - + +
312B LEU 3.4 0.2 - - - -
313B THR* 1.3 78.5 - - - +
315B GLN* 1.3 63.8 + - + +
317B MET* 3.4 31.0 - - + +
318B GLY* 3.6 4.3 + - - -
347B ALA* 4.4 6.3 - - + +
351B ASN 5.2 5.3 + - - +
352B GLU* 5.8 1.4 - - - +
353B LEU* 3.6 30.6 - - + +
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Residues in contact with GLN 315 (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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264B LEU* 4.8 12.5 + - - +
267B PHE* 3.8 31.1 - - + +
268B ARG* 5.2 2.1 - - - +
272B MET* 3.5 41.6 - - - +
311B TYR* 3.0 19.7 + - + +
312B LEU* 3.5 14.7 - - - +
313B THR 3.2 0.2 - - - -
314B LYS* 1.3 77.6 - - - +
316B LEU* 1.3 56.8 + - - +
318B GLY* 3.1 17.0 + - - -
319B LEU* 3.6 1.6 - - - +
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU* 4.6 12.6 - - + -
193B VAL* 4.0 27.8 - - + -
195B TRP* 3.7 22.2 - - + -
267B PHE* 4.0 10.5 - - + -
271B VAL* 4.6 3.6 - - + -
272B MET* 4.0 19.1 - - - -
275B ALA* 5.4 0.2 - - + -
283B VAL* 4.5 6.9 - - + +
285B VAL* 3.7 28.9 - - + -
312B LEU 3.2 9.2 + - - +
313B THR* 3.0 6.9 + - - +
315B GLN* 1.3 74.1 - - - +
317B MET* 1.3 55.8 + - - +
318B GLY 3.0 5.2 - - - -
319B LEU* 3.0 34.3 + - + +
324B ILE* 3.4 21.0 - - + +
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Residues in contact with MET 317 (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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147B LYS* 6.0 2.0 - - + -
148B ASN* 4.2 7.9 - - - +
313B THR* 2.9 20.4 + - + +
314B LYS* 3.4 26.7 - - + +
316B LEU* 1.3 74.7 - - - +
318B GLY* 1.3 58.9 + - - +
319B LEU 3.1 3.1 + - - +
321B GLY 4.5 0.7 - - - -
322B GLY* 3.5 29.3 + - - -
324B ILE* 4.0 23.1 - - + +
347B ALA 3.1 35.0 - - - +
348B LEU* 3.9 18.6 - - - +
350B GLY* 5.0 4.9 - - - +
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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