Contacts of the helix formed by residues 273 - 285 (chain B) in PDB entry 1L8A
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 LYS 273 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 3.5 33.7 + - + -
269B THR* 3.9 1.2 + - - -
272B GLY* 1.3 79.9 - - - +
274B ILE* 1.3 66.5 + - - +
275B ILE 3.1 2.2 - - - +
276B ASN* 3.0 35.1 + - + +
277B GLU* 2.9 20.1 + - - +
314B MET 3.1 18.0 + - - -
315B ASN* 3.1 22.4 + - - +
316B GLU 5.1 1.3 - - - +
317B THR 2.8 29.6 + - - +
318B VAL* 4.2 5.6 - - + -
319B ASP* 3.4 10.3 - - - +
322B TYR* 3.9 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG* 4.4 8.5 - - - +
230B ASP* 3.6 26.2 - - + +
259B CYS* 4.8 1.1 - - + -
261B LEU* 3.3 37.0 - - + -
268B VAL* 3.5 37.0 - - + -
269B THR* 3.4 18.1 + - + +
273B LYS* 1.3 72.3 - - - +
275B ILE* 1.3 64.8 + - + +
277B GLU* 3.5 11.3 - - - +
278B LEU* 2.7 49.5 + - + +
319B ASP* 2.9 14.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 3.6 28.9 - - + +
259B CYS* 3.6 31.2 - - + -
261B LEU* 4.0 3.4 - - + -
273B LYS 3.1 0.8 - - - -
274B ILE* 1.3 82.1 - - + +
276B ASN* 1.3 58.5 + - - +
278B LEU* 4.4 5.4 - - - -
279B GLU* 2.8 28.4 + - - +
291B LYS* 3.5 26.9 - - - -
293B MET* 3.7 19.5 - - + -
319B ASP* 5.2 0.4 + - - -
387B LEU* 3.6 16.9 - - + +
389B HIS* 3.7 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 3.1 42.4 - - + +
57B SER 4.3 1.7 + - - +
59B TYR* 3.7 11.0 - - - +
273B LYS* 3.0 42.2 + - + +
275B ILE* 1.3 77.3 - - - +
277B GLU* 1.3 59.9 + - - +
279B GLU* 4.4 2.5 - - - -
280B GLY* 2.8 25.3 + - - -
291B LYS* 3.2 24.1 + - - -
315B ASN* 5.0 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 2.8 41.8 + - + +
247A ARG* 2.9 44.5 + - - +
284A GLY 4.8 1.8 - - - +
285A ALA* 6.0 0.3 - - - -
239B LYS* 4.3 7.0 + - - -
269B THR* 4.3 5.7 - - - +
273B LYS 2.9 12.0 + - - +
274B ILE* 3.2 14.8 + - - +
276B ASN* 1.3 76.7 - - - +
278B LEU* 1.3 69.5 + - + +
280B GLY* 3.2 2.4 + - - -
281B ILE* 3.1 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ASP* 4.4 11.0 - - + -
233B MET* 4.0 25.8 - - + -
239B LYS* 4.2 18.4 - - + +
257B ILE* 4.0 24.9 - - + -
259B CYS* 4.1 25.1 - - - -
274B ILE* 2.7 34.3 + - + +
275B ILE 3.6 3.4 - - - +
277B GLU* 1.3 81.4 - - + +
279B GLU* 1.3 63.3 + - - +
281B ILE* 3.5 1.7 - - - +
282B PHE* 3.0 36.3 + - + +
387B LEU* 4.0 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 3.3 16.2 - - - +
57B SER* 2.6 41.6 + - - -
275B ILE 2.8 21.2 + - - +
276B ASN* 3.8 2.8 - - - +
278B LEU* 1.3 72.6 - - - +
280B GLY* 1.3 58.6 + - - +
283B GLU* 2.9 41.8 + - + +
289B VAL* 4.1 20.2 - - + +
291B LYS* 2.7 35.6 + - - +
387B LEU* 3.8 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLY* 3.2 26.0 - - - -
56B ILE* 3.7 17.5 - - - -
276B ASN 2.8 17.4 + - - -
277B GLU* 3.6 1.3 - - - -
278B LEU 3.2 0.2 - - - -
279B GLU* 1.3 77.6 - - - +
281B ILE* 1.3 57.7 + - - +
283B GLU* 4.0 2.7 - - - +
284B GLY 3.0 20.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
239A LYS 4.8 3.4 - - - +
242A ILE* 4.3 9.6 - - + -
243A THR* 3.8 26.9 - - + -
281A ILE* 3.5 33.0 - - + +
284A GLY* 3.5 13.1 + - - +
285A ALA* 4.2 7.9 - - + -
239B LYS* 4.0 37.5 - - + +
242B ILE* 4.4 4.3 - - + -
277B GLU* 3.1 17.9 + - + +
278B LEU* 3.5 7.6 - - + +
280B GLY* 1.3 72.9 - - - +
282B PHE* 1.3 68.0 + - + +
284B GLY* 3.3 1.6 + - - -
285B ALA* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B MET* 3.8 29.6 - - + -
239B LYS* 4.1 16.2 - - + -
242B ILE* 3.5 38.4 - - + -
255B PHE* 3.7 19.5 - + - -
257B ILE* 4.3 3.8 - - + -
278B LEU* 3.0 38.0 + - + +
279B GLU* 4.9 0.2 - - - -
281B ILE* 1.3 80.5 - - + +
283B GLU* 1.3 64.5 + - - +
285B ALA* 3.1 7.6 + - - +
286B GLY 3.2 0.2 + - - -
287B TRP* 2.9 43.1 + + - +
289B VAL* 4.1 7.2 - - + -
385B VAL* 3.3 37.0 - - + -
387B LEU* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 5.8 4.6 + - - +
279B GLU* 2.9 27.6 + - + +
280B GLY* 4.0 3.6 - - - +
282B PHE* 1.3 76.4 - - - +
284B GLY* 1.3 62.1 + - - +
286B GLY* 2.9 20.1 + - - -
287B TRP 4.0 16.0 - - - +
289B VAL* 3.9 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 5.5 2.3 - - - +
277A GLU* 4.7 1.7 - - - +
280A GLY* 3.1 44.6 - - - -
281A ILE 3.3 2.1 + - - -
284A GLY* 4.4 1.8 - - - -
280B GLY 3.0 18.9 + - - -
281B ILE 3.6 2.9 - - - -
282B PHE 3.2 0.2 - - - -
283B GLU* 1.3 81.1 + - - +
285B ALA* 1.3 58.2 + - - +
286B GLY 3.1 1.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
277A GLU* 5.8 1.1 - - - -
281A ILE* 4.1 9.4 - - + +
242B ILE* 3.5 30.3 - - + -
243B THR* 4.0 21.0 - - + +
246B THR* 2.6 31.4 + - - +
281B ILE 2.9 17.2 + - - +
282B PHE 3.6 4.7 - - - +
283B GLU 3.1 0.8 - - - -
284B GLY* 1.3 75.8 - - - +
286B GLY* 1.3 51.5 + - - +
287B TRP* 3.5 5.1 - - + +
----------------------------------------------------------
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