Contacts of the helix formed by residues 268 - 286 (chain A) in PDB entry 4IBR
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 268 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLN 3.9 1.1 + - - +
267A ALA* 1.3 80.1 - - - +
269A MET* 1.3 64.7 + - - +
270A ASP* 3.4 11.9 + - - +
271A GLU* 3.2 25.0 + - + +
272A ARG* 3.1 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ALA* 3.7 24.0 - - + -
237A SER 6.2 0.2 - - - +
242A ARG* 3.2 35.9 - - - -
268A THR* 1.3 73.2 - - - +
270A ASP* 1.3 57.8 + - - +
272A ARG* 3.4 25.2 + - - +
273A ASN* 2.9 49.8 + - - +
302A MES 3.9 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 3.1 10.4 + - - +
269A MET* 1.3 79.8 - - - +
271A GLU* 1.3 73.6 + - - +
273A ASN* 3.4 9.3 + - - +
274A ARG* 2.8 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 5.8 0.2 - - - +
39A LEU* 4.4 4.1 - - + +
267A ALA* 4.1 17.9 - - + -
268A THR* 3.2 18.4 + - + +
270A ASP* 1.3 85.9 + - - +
272A ARG* 1.3 61.2 + - - +
274A ARG* 3.3 39.5 + - - +
275A GLN* 2.9 49.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.0 15.5 - - + -
237A SER 4.7 4.8 + - - -
240A GLY* 2.8 50.5 + - - -
241A SER 3.2 14.3 + - - -
242A ARG* 4.0 16.5 - - + +
262A MET* 3.2 28.5 - - + +
265A SER* 4.6 7.4 - - - +
267A ALA* 3.1 23.6 + - + -
268A THR* 3.1 9.0 + - - +
269A MET* 3.4 42.7 - - - +
271A GLU* 1.3 74.9 - - - +
273A ASN* 1.3 64.8 + - - +
275A GLN* 3.5 2.9 + - - +
276A ILE* 3.2 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PRO* 3.8 31.7 - - + +
219A LEU* 3.4 19.1 - - + +
242A ARG* 2.9 36.0 + - - +
269A MET* 2.9 38.2 + - - +
270A ASP* 3.5 7.7 - - - +
272A ARG* 1.3 76.6 - - - +
274A ARG* 1.3 63.8 + - - +
276A ILE* 3.1 5.7 + - - +
277A ALA* 2.9 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PRO 5.3 0.4 - - - -
270A ASP* 2.8 22.4 + - - +
271A GLU* 3.4 38.1 + - - +
273A ASN* 1.3 78.4 - - - +
275A GLN* 1.3 67.7 + - - +
277A ALA* 3.1 9.1 + - + +
278A GLU* 2.8 64.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 2.9 31.2 + - - +
35A ALA* 3.8 16.8 - - + -
38A GLN* 3.4 32.7 - - - +
39A LEU* 3.7 31.4 - - + +
262A MET* 5.2 1.8 - - - -
271A GLU* 2.9 35.2 + - - +
272A ARG 3.9 2.9 - - - +
273A ASN 3.3 0.2 - - - -
274A ARG* 1.3 86.4 - - - +
276A ILE* 1.3 57.5 + - - +
278A GLU* 3.3 5.8 + - - +
279A ILE* 2.9 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LEU* 4.1 33.4 - - + -
220A LEU* 3.8 7.6 - - + +
242A ARG* 3.8 27.1 - - + +
243A GLY* 4.6 9.9 - - - +
244A ILE* 4.2 18.2 - - + -
260A ILE* 4.2 22.0 - - + -
262A MET* 3.9 17.9 - - - -
272A ARG 3.2 13.6 + - - +
273A ASN 3.1 7.7 + - - +
275A GLN* 1.3 77.1 - - - +
277A ALA* 1.3 58.3 + - - +
279A ILE* 3.3 9.9 + - + +
280A GLY* 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PRO 3.7 5.4 - - - +
219A LEU 3.6 13.2 + - - +
222A SER* 3.4 24.9 - - - +
223A ALA* 3.7 6.2 - - + +
273A ASN 2.9 11.9 + - - +
274A ARG* 3.1 11.9 + - + +
276A ILE* 1.3 78.4 - - - +
278A GLU* 1.3 57.5 + - + +
280A GLY* 3.1 3.2 + - - +
281A ALA* 2.8 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 2.9 41.7 + - + +
274A ARG* 2.8 65.4 + - + +
275A GLN* 3.7 4.2 - - - +
277A ALA* 1.3 75.0 - - + +
279A ILE* 1.3 65.5 + - - +
281A ALA* 3.8 7.4 - - - +
282A SER* 3.1 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 4.3 5.2 - - + +
31A LYS* 3.8 21.3 - - + +
32A VAL* 3.7 39.7 - - + -
35A ALA* 4.2 11.4 - - + -
43A VAL* 4.4 12.1 - - + -
45A TYR* 4.0 11.9 - - + -
220A LEU* 5.6 0.2 - - + -
260A ILE* 3.7 32.3 - - + -
262A MET* 6.3 1.3 - - - -
275A GLN 2.9 21.4 + - - +
276A ILE* 3.6 9.2 - - + +
277A ALA 3.3 0.2 - - - -
278A GLU* 1.3 75.0 - - - +
280A GLY* 1.3 58.0 + - - +
282A SER* 3.3 3.6 + - - -
283A LEU* 2.9 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU* 3.5 26.0 - - - +
223A ALA* 3.9 10.8 - - - -
276A ILE 2.9 10.9 + - - -
277A ALA 3.1 4.9 + - - -
279A ILE* 1.3 74.9 - - - +
281A ALA* 1.3 58.2 + - - +
283A LEU* 3.2 9.3 + - - +
284A ILE* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ALA* 3.6 14.4 - - + +
277A ALA 2.8 18.1 + - - +
278A GLU* 3.8 9.0 - - - +
279A ILE 3.4 0.2 - - - -
280A GLY* 1.3 72.0 - - - +
282A SER* 1.3 57.6 + - - +
284A ILE* 3.3 3.8 + - - -
285A LYS* 2.9 53.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A HIS* 5.8 2.7 - - - +
26A PRO* 2.4 31.4 + - - -
27A GLU 3.2 13.2 + - - -
28A THR* 3.3 10.3 + - - -
31A LYS* 4.2 9.4 - - - -
278A GLU 3.1 17.9 + - - -
279A ILE 3.5 4.7 - - - -
281A ALA* 1.3 77.2 - - - +
283A LEU* 1.3 62.1 + - - +
285A LYS* 4.8 1.8 - - - -
286A HIS* 2.9 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 3.7 15.8 + - + +
45A TYR* 3.8 5.6 - - + +
47A GLU* 3.6 33.0 - - - +
220A LEU* 5.0 5.2 - - + -
248A LEU* 4.2 19.7 - - + -
256A ARG* 4.3 2.0 + - - +
258A VAL* 3.7 32.8 - - + -
279A ILE* 2.9 15.6 + - + +
280A GLY* 3.2 15.2 + - - +
282A SER* 1.3 76.2 - - - +
284A ILE* 1.3 62.4 + - + +
286A HIS 3.8 1.2 - - - -
287A TRP* 3.2 41.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU 5.9 0.4 - - - +
223A ALA* 3.7 22.4 - - + +
224A LEU* 4.8 3.1 - - + -
225A PRO* 3.7 28.7 - - + -
228A TRP* 3.6 37.0 - - + -
248A LEU* 4.2 16.8 - - + -
280A GLY 2.9 21.9 + - - +
281A ALA* 3.7 4.9 - - - +
283A LEU* 1.3 81.7 - - + +
285A LYS* 1.3 65.0 + - + +
287A TRP* 3.0 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A HIS* 2.6 49.2 + - + +
281A ALA* 2.9 38.6 + - + +
282A SER* 4.2 2.9 - - - +
284A ILE* 1.3 81.9 - - + +
286A HIS* 1.3 68.6 + - + +
287A TRP 3.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A HIS* 3.1 30.7 + - - +
26A PRO 3.5 5.8 + - - -
27A GLU* 4.0 23.5 - - + +
28A THR* 4.5 8.7 - - - +
256A ARG* 5.1 0.7 + - - -
282A SER* 2.9 40.0 + - - +
283A LEU 3.8 2.5 - - - +
285A LYS* 1.3 84.6 + - + +
287A TRP* 1.3 69.5 + - - +
----------------------------------------------------------
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