Contacts of the helix formed by residues 271 - 283 (chain B) in PDB entry 3VF0
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 THR 271 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ARG* 3.8 15.7 - - - +
269B TYR* 3.9 4.2 - - - +
270B GLU* 1.3 99.0 - - + +
272B ALA* 1.3 58.1 + - - +
273B GLU* 3.5 8.9 + - - +
274B MET* 3.1 37.5 + - + +
275B ALA* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LYS* 4.7 2.0 + - - -
216B ALA 5.0 2.2 - - - +
219B HIS* 3.6 30.3 - - + +
220B SER 3.8 12.8 - - - +
221B ARG* 3.7 11.5 - - + +
271B THR* 1.3 69.5 - - - +
273B GLU* 1.4 60.8 + - - +
275B ALA* 3.4 2.3 + - - +
276B GLU* 3.0 30.5 + - - +
3007B GOL 3.4 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B THR* 3.3 7.5 + - - +
272B ALA* 1.4 76.3 - - - +
274B MET* 1.3 58.4 + - + +
276B GLU* 3.4 7.7 + - + +
277B GLU* 2.9 59.1 + - + +
3007B GOL 4.4 17.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B HIS* 3.4 52.0 - - + +
247B SER 5.7 2.7 - - - +
269B TYR* 4.0 12.2 - - + -
270B GLU* 3.7 44.6 - - - +
271B THR* 3.1 27.4 + - + +
273B GLU* 1.3 77.6 - - + +
275B ALA* 1.4 55.9 + - - +
277B GLU* 3.5 1.0 + - - +
278B ALA* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B SER 3.7 20.2 - - - +
221B ARG 3.6 26.9 - - - +
223B LEU* 3.6 15.1 - - + +
269B TYR* 3.7 17.2 - - + +
271B THR 3.1 10.4 + - - +
272B ALA 3.4 2.7 + - - +
274B MET* 1.4 73.8 - - - +
276B GLU* 1.4 52.9 + - - +
278B ALA 3.3 1.0 + - - -
279B GLN* 2.9 35.3 + - - +
296B PHE* 4.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B SER* 2.6 31.0 + - - -
168B ARG* 4.4 15.0 + - - +
173B LYS* 2.8 31.6 + - - +
272B ALA 3.0 17.3 + - - +
273B GLU* 3.6 7.6 - - - +
275B ALA* 1.4 76.1 - - - +
277B GLU* 1.3 56.8 + - + +
279B GLN* 3.4 5.0 + - - +
280B GLN* 3.1 28.9 + - + +
296B PHE* 3.7 19.9 - - + -
3007B GOL 3.0 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B VAL* 4.1 19.9 - - + +
246B HIS* 3.4 33.5 + - + +
273B GLU* 2.9 50.9 + - + +
274B MET* 5.5 0.2 - - - +
276B GLU* 1.3 72.6 - - + +
278B ALA* 1.4 65.0 + - - +
280B GLN* 3.4 8.6 + - - +
281B GLN* 3.4 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU* 4.2 2.7 - - + -
242B LEU* 4.5 5.8 - - + +
245B VAL* 4.6 12.1 - - + +
246B HIS* 4.5 5.5 - - + +
269B TYR* 3.4 41.1 - - + +
274B MET 2.9 16.6 + - - +
275B ALA 3.7 4.0 - - - +
277B GLU* 1.4 75.6 - - - +
279B GLN* 1.3 57.5 + - - +
281B GLN* 3.5 2.9 + - - +
282B ALA* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU* 3.8 21.0 - - + +
275B ALA 2.9 17.7 + - - +
276B GLU* 3.6 5.7 - - - +
278B ALA* 1.3 75.6 - - - +
280B GLN* 1.4 65.2 + - - +
283B ASP* 3.0 39.7 + - - +
294B VAL* 2.9 36.1 + - + +
295B SER 4.6 0.2 - - - -
296B PHE* 3.6 32.0 - - + -
3001B GOL 3.3 34.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 4.8 23.5 + - - +
169B THR* 5.5 3.6 - - - +
276B GLU* 3.1 17.6 + - + +
277B GLU* 3.6 9.2 - - - +
278B ALA 3.3 0.2 - - - -
279B GLN* 1.4 85.9 + - - +
281B GLN* 1.3 61.5 + - + +
283B ASP* 4.2 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ALA 3.4 24.5 + - - -
242B LEU* 5.1 1.2 - - - +
244B ALA* 3.4 19.5 - - - +
245B VAL* 3.3 30.9 - - + +
277B GLU 3.4 5.5 + - - +
278B ALA* 4.0 5.2 - - - +
280B GLN* 1.3 79.8 - - + +
282B ALA* 1.3 80.2 + - - +
283B ASP 3.6 3.8 + - - +
285B LEU* 4.3 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 3.8 33.9 - - + -
278B ALA 3.0 19.4 + - - +
279B GLN 4.4 0.2 - - - +
281B GLN* 1.3 91.8 - - - +
283B ASP* 1.4 64.1 + - - +
284B GLY 3.2 0.5 + - - -
285B LEU* 3.1 26.4 + - + +
292B LEU* 4.4 1.6 - - - +
294B VAL* 3.6 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PRO* 6.1 0.2 - - - +
201B ARG* 5.7 2.6 + - - -
279B GLN* 3.0 34.4 + - - +
280B GLN 4.2 6.1 + - - +
281B GLN 3.6 4.4 - - - +
282B ALA* 1.4 74.1 - - - +
284B GLY* 1.3 67.8 + - - +
285B LEU 3.6 0.3 + - - -
293B ARG* 3.5 12.3 - - - +
294B VAL* 3.1 35.1 + - - +
3001B GOL 4.3 8.0 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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