Contacts of the helix formed by residues 275 - 293 (chain A) in PDB entry 2LBP
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 275 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 4.6 7.2 - - + -
249A PRO* 4.9 24.5 - - + -
250A LYS 5.7 2.0 - - - +
252A TYR* 5.4 6.1 - - + -
273A SER 3.6 5.8 - - - +
274A GLY* 1.3 83.1 - - - +
276A TYR* 1.3 76.2 + - + +
277A VAL 3.0 0.7 + - - -
278A TRP* 3.0 11.0 + - + +
279A ILE* 3.0 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 4.1 27.4 - + + +
21A MET* 3.6 33.0 - - + -
22A GLU* 4.0 10.9 - - + +
77A LEU* 3.8 19.3 - - + -
99A PRO 3.6 5.8 - - - -
100A GLY* 3.7 23.0 + - - -
274A GLY 3.1 1.2 - - - -
275A PRO* 1.3 88.7 - - + +
277A VAL* 1.3 60.0 + - - +
279A ILE* 3.5 28.5 - - + -
280A THR* 2.6 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 3.4 29.7 + - + +
24A ASN* 4.3 6.3 - - - +
25A GLY* 3.3 21.0 - - - +
261A ILE* 5.3 1.8 - - + -
265A LEU* 3.8 28.3 - - + -
271A ASP 3.7 23.8 - - - +
272A PRO 4.4 2.5 - - - +
274A GLY 2.9 19.8 + - - +
276A TYR* 1.3 78.3 - - - +
278A TRP* 1.3 74.0 - - + +
281A TYR* 3.3 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TYR* 3.7 31.9 - + + -
253A ASP* 3.7 28.8 - - + +
258A ASN* 3.5 39.7 - - + -
261A ILE* 3.8 35.4 - - + -
262A VAL* 3.8 15.0 - - + -
272A PRO* 2.6 33.0 + - + -
273A SER 4.6 1.7 - - - -
274A GLY 3.3 18.8 + - - -
275A PRO* 3.0 7.5 + - + +
277A VAL* 1.3 81.6 - - + +
279A ILE* 1.3 64.0 + - - +
280A THR 3.2 1.8 - - - -
281A TYR* 3.3 2.6 + - + -
282A ALA* 3.2 23.7 + - - +
314A VAL* 3.7 27.1 - - + +
315A ILE* 4.5 2.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
99A PRO* 2.4 37.9 - - + +
100A GLY* 4.1 3.1 - - - -
117A THR* 2.8 43.3 + - - +
118A ALA* 4.2 9.9 - - + -
252A TYR* 4.6 11.2 - - + +
275A PRO* 3.0 22.2 + - + +
276A TYR* 3.5 26.5 - - + -
278A TRP* 1.3 73.1 - - - +
280A THR* 1.3 57.5 + - - +
282A ALA* 3.6 6.4 - - - +
283A ALA 3.2 11.1 + - - -
315A ILE* 4.2 16.2 - - + -
329A PHE* 6.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 5.0 0.9 - - + -
22A GLU* 3.0 43.1 - - + +
25A GLY 4.8 0.4 - - - -
26A ALA* 4.0 13.9 - - + -
74A ILE* 3.9 22.5 - - + +
99A PRO* 3.5 21.1 + - + +
276A TYR* 2.6 24.3 + - - -
277A VAL 4.3 2.0 - - - -
279A ILE* 1.3 74.6 - - - +
281A TYR* 1.3 65.7 + - - +
282A ALA 3.2 1.1 - - - -
283A ALA* 3.3 2.6 + - - +
284A VAL* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY* 3.6 24.0 + - - +
28A GLN* 3.9 5.2 - - + -
29A ALA* 3.7 22.4 - - + -
32A ASP* 1.8 41.5 + - - +
33A ILE* 5.6 2.6 - - + +
261A ILE* 4.0 34.0 - - + +
277A VAL* 3.3 19.1 + - + +
278A TRP* 3.3 6.9 + + + +
280A THR* 1.3 78.3 - - - +
282A ALA* 1.3 58.0 - - - +
284A VAL* 2.6 29.9 - - - +
285A GLN* 3.0 40.5 + - + +
314A VAL* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR* 4.1 4.4 - - - +
278A TRP 3.2 17.1 + - - +
279A ILE* 3.6 8.1 - - - +
281A TYR* 1.3 74.5 - - - +
283A ALA* 1.3 56.6 + - - +
285A GLN* 3.7 6.8 + - - +
286A SER* 2.5 33.8 + - - -
313A THR* 2.8 37.8 + - + -
315A ILE* 3.8 12.8 - - + -
318A LEU* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 3.8 26.6 - - + +
97A ILE* 4.1 17.8 - - + +
99A PRO* 4.5 4.3 - - + -
117A THR* 3.6 25.1 - - - +
279A ILE 3.2 6.8 + - - +
280A THR* 3.4 13.2 - - - +
282A ALA* 1.3 74.0 - - - +
284A VAL* 1.3 65.3 + - - +
286A SER* 3.2 4.4 + - - -
287A LEU 3.2 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 5.7 4.5 - - + -
26A ALA* 4.6 4.7 - - + +
29A ALA* 2.8 38.1 - - + -
30A ILE* 4.1 21.8 - - + +
33A ILE* 4.2 10.8 - - + -
44A LEU* 4.5 11.0 - - + -
74A ILE* 4.0 15.7 - - + +
280A THR 3.2 7.4 + - - +
281A TYR* 2.6 17.9 - - + +
283A ALA* 1.3 75.4 - - - +
285A GLN* 1.3 77.1 + - + +
286A SER 3.0 0.3 + - - -
287A LEU* 4.9 1.6 - - + -
288A ALA* 3.0 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 4.1 8.7 - - + -
281A TYR* 3.0 33.8 + - + +
282A ALA* 3.7 7.8 - - - +
283A ALA 3.3 0.2 - - - -
284A VAL* 1.3 85.1 - - + +
286A SER* 1.3 53.6 + - - +
288A ALA 3.3 8.5 - - - -
289A THR* 2.7 31.2 - - + +
290A ALA* 3.3 6.8 + - - +
311A ALA* 4.8 0.6 - - - +
312A ASN 4.3 16.2 + - - +
313A THR* 3.4 11.2 - - - +
314A VAL* 3.0 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 4.7 4.3 - - - -
117A THR* 4.4 0.8 - - - +
282A ALA 2.5 24.2 + - - -
283A ALA* 3.6 5.2 - - - -
284A VAL 3.1 0.8 - - - -
285A GLN* 1.3 73.9 - - - +
287A LEU* 1.3 59.8 + - - +
290A ALA* 2.1 32.3 - - - +
306A LEU* 3.0 18.6 - - - +
311A ALA* 3.3 28.7 - - - +
313A THR* 4.2 0.3 + - - -
318A LEU* 4.2 4.0 - - - +
320A TRP* 3.9 18.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 3.7 33.2 - - + -
44A LEU* 5.3 0.2 - - + -
72A TYR* 3.7 18.8 - - + -
74A ILE* 4.1 8.3 - - + -
95A LEU* 3.4 30.3 - - + -
97A ILE* 3.9 19.9 - - + +
283A ALA 3.2 8.8 + - - +
284A VAL* 4.0 2.7 - - + +
286A SER* 1.3 80.3 - - - +
288A ALA* 1.3 70.4 + - + +
290A ALA 2.7 11.1 - - - +
291A LEU* 3.7 2.9 - - - +
292A GLU* 3.0 42.1 + - - +
302A LEU* 3.8 7.8 - - + +
306A LEU* 4.2 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 4.0 3.7 - - + +
39A ILE* 4.2 2.9 - - + -
44A LEU* 3.3 35.4 - - + -
284A VAL* 3.0 23.7 + - + +
285A GLN* 3.3 1.7 - - - +
287A LEU* 1.3 89.2 - - + +
289A THR* 1.3 82.1 - - - +
290A ALA 3.5 0.4 - - - -
292A GLU* 3.5 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 4.4 11.7 - - + -
39A ILE* 4.5 2.8 - - - +
285A GLN* 2.7 33.7 - - + +
287A LEU 3.4 1.6 + - - -
288A ALA* 1.3 83.0 - - - +
290A ALA* 1.3 75.2 + - - +
291A LEU* 2.1 12.6 + - - -
292A GLU* 3.4 5.5 + - - +
293A ARG* 2.3 66.8 + - - +
312A ASN 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLN 3.3 4.6 + - - +
286A SER 2.1 30.8 - - - +
287A LEU 2.7 10.9 - - - +
289A THR* 1.3 93.6 + - - +
291A LEU* 1.3 47.4 + - - +
305A ASP* 5.5 0.4 - - - -
306A LEU* 3.7 18.6 - - + -
310A GLY 3.9 5.6 - - - +
311A ALA* 3.8 27.6 - - + -
312A ASN 4.8 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A SER 4.2 0.4 - - - +
289A THR 2.1 5.3 + - - -
290A ALA* 1.3 65.4 - - - +
292A GLU* 1.3 55.3 - - - +
293A ARG* 2.7 6.0 - - - +
294A THR* 2.5 44.8 + - + +
296A SER* 4.7 2.7 - - - -
301A ALA 3.3 4.9 - - - +
302A LEU* 2.4 86.4 - - + +
305A ASP* 3.0 44.5 + - + +
306A LEU* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.6 31.2 - - + +
39A ILE* 3.6 34.1 - - + +
40A LYS* 4.1 4.2 + - - -
44A LEU* 4.0 1.0 - - - +
72A TYR* 4.0 9.5 - - + +
287A LEU* 3.0 48.6 + - - +
288A ALA* 3.5 17.9 - - - +
289A THR 3.4 1.6 + - - +
291A LEU* 1.3 76.1 - - - +
293A ARG* 1.3 56.2 + - - +
294A THR 3.0 0.7 - - - -
295A GLY* 3.1 20.7 + - - -
296A SER 4.1 17.1 - - - +
297A ASP* 5.7 0.2 - - - +
302A LEU* 4.3 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 4.4 10.3 + - - +
36A LYS* 6.0 4.0 - - - +
38A GLY 3.4 26.1 + - - -
39A ILE* 4.2 10.8 - - + +
40A LYS* 4.5 26.5 - - - +
289A THR* 2.3 54.7 + - - +
291A LEU* 2.7 1.5 - - - -
292A GLU* 1.3 80.0 - - - +
294A THR* 1.3 51.2 - - - +
295A GLY 3.3 3.9 + - - -
----------------------------------------------------------
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