Contacts of the helix formed by residues 269 - 286 (chain B) in PDB entry 2IAG
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 269 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLY 3.4 5.6 + - - -
268B VAL* 1.3 76.2 - - - +
270B GLU* 1.3 59.4 + - - +
271B GLU* 3.6 10.2 + - - +
272B MET* 3.1 24.5 + - - +
273B GLN* 2.8 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B SER* 5.5 0.2 - - - -
243B PRO* 3.5 36.4 - - + +
244B ALA* 4.2 13.7 + - - +
268B VAL 3.8 0.2 + - - -
269B SER* 1.3 73.5 - - - +
271B GLU* 1.3 60.4 + - - +
273B GLN* 3.8 20.6 - - - +
274B ALA* 3.1 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B TRP* 5.6 0.3 - - - +
269B SER* 3.1 9.5 - - - +
270B GLU* 1.3 76.7 - - - +
272B MET* 1.3 62.1 + - + +
274B ALA* 3.4 18.5 - - - +
275B ARG* 3.5 29.6 + - - +
701B NA 4.0 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASP 3.8 4.5 - - - +
110B VAL* 3.6 13.2 - - - -
111B GLN* 3.4 47.8 - - + +
112B LEU* 4.2 4.9 - - + -
268B VAL* 3.6 18.4 - - + -
269B SER* 3.1 16.5 + - - +
271B GLU* 1.3 78.1 - - + +
273B GLN* 1.3 65.6 + - - +
275B ARG* 3.0 32.0 + - - +
276B ALA* 2.9 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PRO* 3.8 14.1 - - + +
260B LEU* 3.6 27.0 - - - +
263B LEU* 3.9 21.5 - - + +
264B GLU* 4.0 24.3 + - - +
268B VAL* 2.7 37.0 + - + +
269B SER 2.8 17.3 + - - +
270B GLU* 3.7 19.2 + - - +
271B GLU 3.3 0.2 - - - -
272B MET* 1.3 75.4 - - - +
274B ALA* 1.3 51.6 + - - +
276B ALA* 3.0 8.7 + - - +
277B LEU* 2.8 42.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
238B TRP* 3.4 33.4 - - + +
241B LEU 4.1 12.4 - - - +
242B SER* 4.0 11.0 - - - -
243B PRO* 4.1 1.7 - - - +
270B GLU 3.1 14.4 + - - +
271B GLU* 3.4 13.5 - - - +
273B GLN* 1.3 76.5 - - - +
275B ARG* 1.3 57.5 + - - +
277B LEU* 3.3 3.8 + - - +
278B VAL* 3.1 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE* 4.2 2.7 - - - +
109B ASP* 2.9 34.5 + - - +
110B VAL* 3.4 21.4 - - + +
238B TRP* 3.5 60.9 + - + +
271B GLU* 3.5 29.7 + - - +
272B MET* 3.0 27.4 + - - +
274B ALA* 1.3 74.6 - - - +
276B ALA* 1.3 65.5 + - - +
278B VAL* 3.3 2.1 + - - +
279B LEU* 3.1 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 3.8 12.9 - - + +
112B LEU* 4.6 12.1 - - + -
259B TYR* 3.4 20.9 + - - +
263B LEU* 4.2 18.8 - - + -
272B MET 2.9 11.9 + - - +
273B GLN* 3.0 9.2 + - - +
275B ARG* 1.3 75.7 - - - +
277B LEU* 1.3 57.3 + - - +
279B LEU* 3.6 5.3 + - + +
280B GLN* 3.0 32.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
181B TYR* 2.7 37.7 + - + +
241B LEU* 3.3 27.6 - - + +
243B PRO* 4.3 8.7 - - + -
246B LEU* 3.6 15.3 - - + -
255B TRP* 5.6 0.9 - - + -
256B LEU* 3.6 28.0 - - + -
259B TYR* 4.0 21.8 - - + -
260B LEU* 4.1 18.6 - - + -
263B LEU* 4.9 1.8 - - + -
273B GLN 2.8 22.3 + - - +
274B ALA 3.5 7.4 - - - +
275B ARG 3.2 0.2 - - - -
276B ALA* 1.3 75.4 - - - +
278B VAL* 1.3 61.6 + - - +
280B GLN* 3.6 3.5 + - + -
281B LEU* 3.0 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE* 4.1 6.1 - - + -
207B PHE* 5.4 1.6 - - + -
210B LEU* 4.5 13.5 - - + -
234B LYS* 5.2 0.4 - - + +
237B LEU* 3.5 49.4 - - + +
238B TRP* 3.4 31.4 - - + +
241B LEU* 4.0 12.1 - - + -
274B ALA 3.1 14.4 + - - +
275B ARG 3.9 2.0 - - - +
276B ALA 3.3 0.2 - - - -
277B LEU* 1.3 76.8 - - - +
279B LEU* 1.3 65.2 + - - +
280B GLN 3.3 0.2 - - - -
281B LEU* 3.2 9.8 + - + +
282B TRP* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B MET* 4.0 38.8 - - + -
108B PHE* 3.5 42.5 - - + -
110B VAL* 4.1 15.7 - - + -
112B LEU* 6.1 0.7 - - + -
259B TYR* 5.4 1.8 - - - +
275B ARG 3.1 14.2 + - - +
276B ALA* 3.6 9.9 - - - +
278B VAL* 1.3 76.8 - - - +
280B GLN* 1.3 73.9 + - - +
282B TRP* 3.1 8.6 + - + +
283B ALA* 2.8 32.6 + - + +
600B HEM 6.0 1.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
124B MET* 4.1 21.3 - - - +
181B TYR* 3.6 5.6 - - - +
255B TRP* 3.6 31.4 - - + -
259B TYR* 3.6 34.2 + - + -
276B ALA 3.0 20.0 + - - +
277B LEU* 3.8 3.6 - - - +
278B VAL 3.3 0.2 - - - -
279B LEU* 1.3 89.9 - - - +
281B LEU* 1.3 59.8 + - - +
283B ALA* 3.7 15.1 - - - +
284B THR* 2.9 34.8 + - - -
600B HEM 4.6 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 5.2 3.1 - - + -
177B TYR* 4.1 18.6 - - + -
181B TYR* 3.1 27.6 + - + +
203B VAL* 4.1 20.9 - - + -
207B PHE* 3.7 25.3 - - + -
237B LEU* 4.2 12.8 - - + -
241B LEU* 4.0 16.8 - - + -
277B LEU 3.0 11.0 + - - +
278B VAL* 3.2 11.6 + - + +
280B GLN* 1.3 75.0 - - - +
282B TRP* 1.3 59.1 + - - +
284B THR* 4.0 1.6 - - - -
285B GLN* 2.8 58.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE* 3.4 41.1 - + + -
207B PHE* 3.6 30.7 - + + -
210B LEU* 4.5 5.6 - - + -
211B ASP* 3.4 19.5 + - - -
214B LEU* 3.6 32.2 - - + +
278B VAL 3.1 5.5 + - - +
279B LEU* 3.1 8.5 + - + +
281B LEU* 1.3 74.9 - - - +
283B ALA* 1.3 70.8 + - + +
284B THR 3.1 4.5 - - - -
286B GLY* 2.9 33.6 + - - -
287B ASN* 5.9 3.8 - - - -
480B ARG* 5.7 2.7 - - - -
483B PHE* 4.0 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
----------------------------------------------------------
279B LEU* 2.8 23.3 + - + +
280B GLN* 3.2 19.5 + - - +
282B TRP* 1.3 90.4 - - + +
284B THR* 1.3 58.7 + - - +
286B GLY 5.1 0.3 + - - -
287B ASN* 5.3 4.7 + - - +
600B HEM 3.5 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 3.4 14.8 - - + +
181B TYR* 4.8 4.3 - - + -
255B TRP* 4.2 8.9 - - + -
280B GLN* 2.9 21.5 + - - +
281B LEU* 3.6 4.7 - - - +
283B ALA* 1.3 80.6 - - - +
285B GLN* 1.3 94.3 + - + +
286B GLY 3.8 0.4 - - - -
287B ASN 5.3 0.6 + - - -
288B MET* 3.9 3.5 - - - +
600B HEM 2.8 65.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B TYR* 3.5 18.2 - - - -
173B LEU* 3.7 36.7 - - + +
176B GLY* 3.6 28.8 - - - -
177B TYR* 4.0 1.1 - - - +
180B LEU* 3.5 16.0 - - - +
181B TYR* 5.4 0.2 - - - -
207B PHE* 4.5 2.5 - - + -
281B LEU* 2.8 37.4 + - + +
284B THR* 1.3 107.1 + - + +
286B GLY* 1.3 61.7 + - - +
287B ASN 3.3 4.9 + - - -
288B MET* 3.4 28.0 + - - +
289B GLY 4.5 1.7 + - - -
446B TYR* 4.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B TYR* 3.5 21.4 + - - -
207B PHE* 4.1 8.5 - - - -
211B ASP* 5.0 1.2 - - - +
281B LEU 4.1 0.2 + - - -
282B TRP* 2.9 31.2 + - - -
283B ALA 4.8 0.4 - - - -
284B THR 3.8 0.6 - - - -
285B GLN* 1.3 77.3 - - - +
287B ASN* 1.3 67.5 + - - +
290B PRO* 3.6 10.9 - - - +
485B LEU* 5.0 0.9 - - - +
487B GLN* 4.4 4.9 + - - -
----------------------------------------------------------
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