Contacts of the helix formed by residues 266 - 283 (chain B) in PDB entry 1V1A
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 PRO 266 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B GLY 4.0 4.9 - - - +
265B LEU* 1.3 83.3 - - + +
267B VAL* 1.3 53.2 - - - +
268B GLU* 2.6 32.0 + - - +
269B GLU* 2.7 51.2 + - + +
270B ARG* 3.0 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ALA* 3.8 13.2 - - + -
229B VAL* 3.7 25.8 - - + -
232B ARG* 4.0 19.7 - - - +
234B VAL* 4.0 20.0 - - + -
257B TYR* 3.6 19.5 - - - +
265B LEU 3.5 2.4 + - - -
266B PRO* 1.3 68.9 - - - +
268B GLU* 1.3 61.1 + - - +
270B ARG* 2.9 29.3 - - - +
271B LEU* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ARG* 2.5 38.0 + - - -
234B VAL* 4.3 17.4 - - + +
266B PRO* 2.6 26.1 + - - +
267B VAL* 1.3 75.5 + - - +
269B GLU* 1.3 62.7 + - + +
270B ARG 3.1 1.3 - - - -
271B LEU* 3.1 5.6 + - - +
272B ARG* 2.8 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LEU* 3.4 25.7 - - + +
266B PRO* 2.7 44.8 + - + +
268B GLU* 1.3 76.3 - - + +
270B ARG* 1.3 56.8 + - - +
272B ARG* 3.7 33.2 + - - +
273B LEU* 3.2 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ARG* 5.1 4.4 - - - +
215B GLU* 3.0 35.4 + - - -
229B VAL* 4.3 4.8 - - - +
257B TYR* 3.1 41.2 + - + +
260B GLY* 3.3 26.9 - - - -
261B ALA* 3.3 34.0 - - - +
265B LEU* 3.1 27.6 + - + +
266B PRO 3.0 5.5 + - - +
267B VAL* 2.9 41.7 - - - +
269B GLU* 1.3 77.1 - - - +
271B LEU* 1.3 58.8 + - - +
273B LEU* 4.0 1.0 - - - +
274B ALA* 3.2 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B VAL* 4.4 4.3 - - + -
225B ALA* 4.4 12.1 - - + +
227B ALA* 3.7 30.5 - - + +
234B VAL* 3.4 32.5 - - + -
235B GLU 3.7 19.3 - - - +
236B GLY* 3.8 7.4 - - - +
253B PHE* 4.3 23.1 - - + -
257B TYR* 4.3 8.5 - - + -
267B VAL 3.3 13.0 + - - +
268B GLU* 3.1 5.7 + - - +
270B ARG* 1.3 79.0 - - - +
272B ARG* 1.3 67.3 + - - +
274B ALA* 3.0 3.8 + - - +
275B ASN* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLY* 5.8 0.8 - - - -
237B SER 5.8 0.9 - - - -
239B PHE* 3.6 15.9 - - + -
268B GLU 2.8 19.5 + - - +
269B GLU* 3.7 34.8 + - - +
271B LEU* 1.3 73.0 - - - +
273B LEU* 1.3 63.6 + - - +
275B ASN* 3.4 5.6 + - - +
276B LEU* 3.1 23.2 + - - +
300B LEU 4.9 0.6 + - - -
301B LEU 3.1 21.9 + - - -
302B LYS 3.4 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 4.8 2.2 - - + -
256B GLY* 3.3 24.5 - - - +
259B ALA* 4.2 2.0 - - + -
260B GLY* 3.7 11.7 - - - +
263B TRP* 3.6 26.0 - - + -
265B LEU* 3.8 14.4 - - + -
269B GLU 3.2 14.8 + - - +
270B ARG 4.0 2.0 - - - +
271B LEU 3.2 0.8 - - - -
272B ARG* 1.3 79.5 - - - +
274B ALA* 1.3 61.8 + - - +
276B LEU* 3.1 10.9 + - + +
277B LEU* 3.1 43.8 + - + +
297B LEU* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PHE* 3.1 55.0 - - + +
256B GLY* 3.9 6.3 - - - -
257B TYR* 3.8 10.3 - - + +
270B ARG 3.2 13.8 + - - +
271B LEU* 3.0 10.6 + - - +
273B LEU* 1.3 78.5 - - - +
275B ASN* 1.3 62.8 + - - +
276B LEU 3.1 0.3 + - - -
277B LEU* 3.2 2.4 + - - -
278B GLY 3.0 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B GLY* 3.8 10.2 - - - -
225B ALA* 4.5 2.8 - - - +
236B GLY* 3.6 24.5 + - - -
237B SER 3.2 29.5 + - - +
238B ALA* 4.2 3.8 - - - -
239B PHE* 3.4 10.7 + - + +
253B PHE* 3.1 13.5 - - - -
271B LEU* 2.9 23.7 + - - +
272B ARG* 3.8 5.8 - - - +
274B ALA* 1.3 75.5 - - - +
276B LEU* 1.3 57.7 + - - +
278B GLY 3.5 0.9 + - - -
279B ALA* 3.0 28.9 + - - +
1303B ADP 2.5 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PHE* 3.4 35.0 - - + -
272B ARG* 3.1 9.8 + - - +
273B LEU* 3.3 13.9 - - + +
274B ALA 3.1 0.2 - - - -
275B ASN* 1.3 74.9 - - - +
277B LEU* 1.3 71.6 + - + +
279B ALA* 3.1 12.8 + - + +
280B SER* 3.1 18.7 + - - +
292B PRO* 5.2 0.9 - - + -
297B LEU* 4.1 16.4 - - + +
300B LEU* 3.5 55.4 - - + +
301B LEU 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 4.7 9.2 - - + -
46B LEU* 3.5 24.5 - - + -
252B ALA* 3.1 30.0 - - + +
255B ALA* 4.0 7.0 - - + -
256B GLY* 3.3 29.4 - - - +
273B LEU* 3.1 32.1 + - + +
274B ALA 3.9 2.5 - - - +
276B LEU* 1.3 85.0 - - + +
278B GLY* 1.3 60.4 + - - +
280B SER* 3.4 6.7 + - - -
281B VAL* 3.2 20.1 + - - +
291B ALA* 5.7 0.2 - - - -
292B PRO* 3.6 30.4 - - + +
297B LEU* 4.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA* 3.5 30.6 - - - +
252B ALA* 4.0 1.1 - - - +
253B PHE* 4.3 0.9 - - - -
274B ALA 3.0 15.7 + - - -
275B ASN 3.9 2.2 - - - -
277B LEU* 1.3 78.8 - - - +
279B ALA* 1.3 56.8 + - - +
280B SER 3.3 0.2 - - - -
282B ALA* 3.1 27.9 + - - +
1303B ADP 3.9 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PHE* 3.4 27.6 - - + -
241B VAL* 3.6 15.6 - - + +
275B ASN 3.0 18.1 + - - +
276B LEU* 3.1 6.0 + - + +
278B GLY* 1.3 75.1 - - - +
280B SER* 1.3 60.7 + - - +
282B ALA* 4.3 0.4 - - - -
283B ALA* 2.9 31.9 + - - +
1303B ADP 4.0 14.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 3.1 23.4 + - - +
277B LEU 3.6 8.3 - - - -
278B GLY 3.3 0.2 - - - -
279B ALA* 1.3 75.0 - - - +
281B VAL* 1.3 65.3 + - - +
283B ALA* 3.2 13.1 + - - +
284B SER* 3.3 19.9 + - - -
290B GLY* 3.0 25.4 - - - -
292B PRO* 3.8 16.7 - - - +
300B LEU* 5.4 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 6.4 0.2 - - + -
245B ASP 3.3 9.5 - - - +
247B VAL 3.4 11.6 - - - +
248B GLY 3.1 31.4 - - - +
249B ALA* 3.2 10.5 - - - +
252B ALA* 3.2 26.2 - - + -
277B LEU 3.2 7.0 + - - +
280B SER* 1.3 76.4 - - - +
282B ALA* 1.3 61.0 + - - +
284B SER* 3.4 14.4 + - - +
285B ARG 5.2 0.3 - - - +
286B GLY 4.8 2.0 - - - +
287B ASP 3.6 9.9 - - - +
288B HIS* 4.5 12.1 - - + -
290B GLY* 4.4 6.7 + - - +
291B ALA* 4.2 21.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
241B VAL* 5.1 0.9 - - + -
243B ALA* 3.6 4.8 - - + -
244B VAL 2.7 29.9 + - - -
245B ASP 3.1 20.2 + - - -
246B PRO* 4.4 6.3 - - + -
249B ALA* 4.2 5.4 - - + -
278B GLY 3.1 21.7 + - - +
279B ALA 3.9 2.9 - - - +
281B VAL* 1.3 77.3 - - - +
283B ALA* 1.3 53.7 + - - +
284B SER 3.1 1.1 + - - -
1303B ADP 3.8 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B VAL* 3.5 28.3 - - + -
242B GLU 3.7 10.3 - - - +
244B VAL* 3.0 18.3 - - - +
279B ALA 2.9 21.0 + - - +
280B SER* 3.2 6.9 + - - +
282B ALA* 1.3 74.4 - - - +
284B SER* 1.3 61.8 + - - +
----------------------------------------------------------
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