Contacts of the helix formed by residues 277 - 292 (chain B) in PDB entry 1LT8
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 277 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A PHE 3.9 10.3 - - - -
270A GLY* 4.0 9.6 - - - -
272A GLU* 3.7 23.8 - - + +
361A ARG* 4.0 4.7 - - - +
276B ALA* 1.3 78.8 - - - +
278B ARG* 1.3 65.5 + - - +
279B TRP* 3.2 13.3 + - + +
280B ASP* 3.0 35.5 + - - +
281B ILE* 3.3 12.3 + - - +
306B HIS* 4.5 1.3 - - - -
357B ILE* 3.5 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 3.0 39.8 + - - -
35A LYS* 4.9 4.8 - - - +
268A PRO 5.3 1.6 + - - -
269A PHE* 3.4 28.1 + - - +
272A GLU* 4.2 3.6 + - - -
277B THR* 1.3 73.8 - - - +
279B TRP* 1.3 96.6 + - + +
281B ILE* 3.3 4.4 + - - -
282B GLN* 3.0 26.4 + - - +
305B TYR* 3.7 45.9 - - + +
306B HIS* 4.8 0.4 - - - -
308B ARG* 3.5 9.9 - - - +
309B ALA* 3.4 25.2 - - + +
328B HIS* 3.0 32.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A PHE* 3.3 38.1 + + + -
270A GLY* 5.3 0.2 - - - -
277B THR* 3.0 13.6 - - + +
278B ARG* 1.3 97.1 - - + +
280B ASP* 1.3 67.4 + - - +
282B GLN* 3.2 29.0 + - - +
283B LYS* 3.1 21.7 + - - +
328B HIS* 4.6 7.0 - + - -
331B TRP* 3.2 69.7 - + + -
332B GLY 3.7 6.1 - - - -
352B TRP* 3.3 59.9 - + + +
353B GLU* 5.2 1.8 - - - -
357B ILE* 6.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ARG* 2.9 16.2 + - - -
221B PRO* 5.6 1.6 - - + +
252B HIS* 2.8 36.0 + - + +
276B ALA* 3.6 11.7 - - + -
277B THR* 3.0 28.7 + - - +
279B TRP* 1.3 76.4 - - - +
281B ILE* 1.3 58.7 + - - +
283B LYS* 3.2 12.1 + - - +
284B TYR* 3.0 26.2 + - - +
357B ILE* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PRO* 4.4 14.4 - - + -
250B ALA* 4.9 1.6 - - - -
276B ALA* 3.9 17.9 - - + -
277B THR 3.3 12.5 + - - +
278B ARG 3.6 7.9 - - - +
279B TRP 3.2 0.6 - - - -
280B ASP* 1.3 74.8 - - - +
282B GLN* 1.3 60.3 + - - +
284B TYR* 3.2 7.7 + - + +
285B ALA* 2.8 26.7 + - - +
302B PHE* 3.6 30.5 - - + -
306B HIS* 3.2 46.4 - - + +
309B ALA* 3.7 7.6 - - + -
310B ILE* 3.7 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ARG* 3.0 17.9 + - - +
279B TRP* 3.2 34.5 + - - +
281B ILE* 1.3 76.5 - - - +
283B LYS* 1.3 63.0 + - - +
285B ALA* 3.4 0.4 + - - -
286B ARG* 3.1 19.1 + - - +
309B ALA* 3.2 29.2 + - + +
312B GLU* 4.0 19.9 + - - +
313B GLU* 2.7 55.0 + - + +
328B HIS* 5.2 0.8 - - - -
331B TRP* 3.5 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B THR* 4.1 15.0 + - - -
279B TRP 3.1 11.9 + - - +
280B ASP* 3.4 13.0 + - - +
282B GLN* 1.3 75.1 - - - +
284B TYR* 1.3 64.9 + - - +
286B ARG* 3.5 5.8 + - - +
287B GLU* 3.1 57.5 + - + +
331B TRP* 5.8 1.5 - - + -
702B CIT 5.8 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PRO* 3.5 31.6 - - + -
224B SER* 5.9 0.2 - - - -
225B LEU* 4.0 22.0 - - + -
246B SER* 2.9 31.3 + - - -
248B PRO* 3.1 20.5 - - + +
280B ASP 3.0 13.2 + - - +
281B ILE* 3.2 22.9 + - + +
283B LYS* 1.3 78.5 - - - +
285B ALA* 1.3 65.6 + - - +
287B GLU* 3.3 12.1 + - - +
288B ALA* 2.8 29.4 + - + +
296B ILE* 3.4 21.0 - - + +
297B GLY 2.7 28.2 + - - -
302B PHE* 4.2 6.3 - + - -
310B ILE* 4.2 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ILE 2.8 16.8 + - - +
282B GLN 3.6 4.9 - - - +
283B LYS 3.3 0.2 - - - -
284B TYR* 1.3 83.0 - - - +
286B ARG* 1.3 63.3 + - - +
288B ALA* 3.4 6.1 + - - +
289B TYR* 3.0 24.3 + - - +
296B ILE* 4.1 7.4 - - - +
310B ILE* 3.9 37.9 - - + +
313B GLU* 4.1 9.9 - - + -
314B LEU* 4.1 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLN 3.1 17.2 + - - +
283B LYS* 3.8 6.1 - - - +
285B ALA* 1.3 74.4 - - - +
287B GLU* 1.3 61.4 + - + +
289B TYR* 3.0 22.4 + - - +
290B ASN* 2.8 49.5 + - - +
313B GLU* 2.8 51.2 + - - +
314B LEU* 3.6 8.9 - - - +
316B PRO* 4.9 3.6 - - - +
317B GLU* 3.1 36.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PRO 5.9 0.5 - - - -
222B THR* 4.9 8.1 + - - +
225B LEU* 3.7 16.7 - - + +
283B LYS* 3.1 52.5 + - + +
284B TYR* 3.6 9.5 - - - +
286B ARG* 1.3 81.3 - - + +
288B ALA* 1.3 56.9 + - - +
290B ASN* 3.3 11.3 + - - +
291B LEU* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 3.5 20.6 - - + +
246B SER* 4.3 1.1 - - - +
284B TYR* 2.8 31.1 + - + +
285B ALA 3.6 5.2 - - - +
287B GLU* 1.3 72.2 - - - +
289B TYR* 1.3 64.4 + - - +
291B LEU* 3.0 10.4 + - - +
292B GLY 3.1 0.2 + - - -
293B VAL* 2.9 41.0 + - + +
296B ILE* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.4 28.7 - - + -
285B ALA 3.0 13.6 + - - +
286B ARG* 3.2 25.6 - - - +
288B ALA* 1.3 76.8 - - - +
290B ASN* 1.3 73.6 + - - +
292B GLY* 2.9 16.6 + - - -
293B VAL 3.8 9.6 - - - -
294B ARG* 3.0 41.0 + - - -
296B ILE* 4.1 1.7 - - + +
314B LEU* 4.0 14.8 - - + -
317B GLU* 3.3 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ARG* 2.8 41.5 + - - +
287B GLU* 3.7 9.2 - - - +
289B TYR* 1.3 92.1 - - - +
291B LEU* 1.3 60.9 + - - +
292B GLY* 3.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 3.7 34.3 - - + +
228B VAL* 3.7 27.1 - - + -
229B LYS* 4.1 32.1 - - + +
232B LYS* 3.4 35.1 - - + +
244B LEU* 4.4 0.3 - - - +
287B GLU 2.9 13.3 + - - +
288B ALA* 3.0 10.7 + - - +
290B ASN* 1.3 76.7 - - - +
292B GLY* 1.3 57.3 + - - +
293B VAL* 4.0 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LYS* 5.2 2.2 - - - -
244B LEU* 4.2 16.5 + - - +
289B TYR 2.9 6.8 + - - -
290B ASN 3.2 1.2 + - - -
291B LEU* 1.3 80.4 - - - +
293B VAL* 1.3 63.9 + - - +
294B ARG* 3.2 26.5 + - - +
----------------------------------------------------------
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