Contacts of the helix formed by residues 273 - 287 (chain B) in PDB entry 5ULM
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 ARG 273 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 1.3 95.6 - - + +
274B GLU* 1.3 74.4 + - - +
276B ILE* 3.1 5.9 + - - +
277B LEU* 3.0 34.3 + - + +
306B ILE* 5.9 5.8 - - + +
310B THR* 3.4 33.7 - - - +
312B ASP* 3.5 20.4 + - - +
313B ILE* 4.0 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 3.3 20.4 - - + +
273B ARG* 1.3 96.8 + - - +
275B SER* 1.3 57.6 + - - +
277B LEU* 3.4 11.8 + - + +
278B ASN* 2.9 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 3.5 26.0 + - - +
273B ARG 3.3 0.2 - - - -
274B GLU* 1.3 75.5 - - - +
276B ILE* 1.3 63.9 + - - +
278B ASN* 3.5 5.2 + - - +
279B ASP* 3.1 35.7 + - - +
302B ARG* 3.3 17.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE 3.3 14.8 - - - +
273B ARG 3.1 7.2 + - - +
275B SER* 1.3 76.4 - - - +
277B LEU* 1.3 64.8 + - - +
279B ASP* 3.4 3.4 + - - +
280B ILE* 3.0 38.1 + - + +
299B ILE* 4.1 7.3 - - + +
302B ARG* 3.4 47.8 - - + +
303B VAL* 3.7 29.6 - - + +
306B ILE* 4.1 13.7 - - + -
313B ILE* 3.6 24.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
273B ARG* 3.0 27.4 + - + +
274B GLU* 3.7 11.7 - - + +
276B ILE* 1.3 77.4 - - - +
278B ASN* 1.3 62.8 + - - +
280B ILE* 3.4 7.3 + - + +
281B ARG* 3.1 24.2 + - - +
312B ASP* 3.6 55.2 - - + +
313B ILE* 3.9 12.6 - - + +
316B ASN* 3.8 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B GLU* 2.9 30.1 + - - +
275B SER* 4.0 6.1 - - - +
277B LEU* 1.3 77.1 - - - +
279B ASP* 1.3 61.8 + - - +
281B ARG* 2.8 37.3 + - - +
282B LYS* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B SER* 3.1 17.9 + - - +
276B ILE 3.8 3.1 - - - +
278B ASN* 1.3 81.1 - - - +
280B ILE* 1.3 59.4 + - - +
282B LYS* 3.9 13.3 - - - +
283B ALA* 2.9 29.1 + - - +
295B GLU* 5.1 3.3 - - - +
299B ILE* 3.5 11.4 - - + +
302B ARG* 2.8 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE* 3.0 40.1 + - + +
277B LEU* 3.7 7.9 - - - +
279B ASP* 1.3 75.9 - - - +
281B ARG* 1.3 60.0 + - - +
283B ALA* 3.3 3.5 + - - +
284B ARG* 2.9 32.8 + - - +
296B LEU* 4.9 2.9 - - + -
299B ILE* 3.9 21.3 - - + -
313B ILE* 4.3 12.1 - - + +
316B ASN* 3.5 35.9 - - + +
317B LEU* 4.1 29.8 - - + +
320B SER* 4.2 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU 3.1 13.0 + - - +
278B ASN* 2.8 34.6 + - - +
280B ILE* 1.3 77.3 - - - +
282B LYS* 1.3 62.7 + - - +
284B ARG* 3.3 10.4 + - - +
285B ASN* 3.1 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ASN 3.0 18.0 + - - +
279B ASP* 3.9 14.6 + - - +
281B ARG* 1.3 77.5 - - - +
283B ALA* 1.3 56.3 + - - +
285B ASN* 3.2 8.3 + - - +
286B LEU* 2.9 55.1 + - + +
----------------------------------------------------------
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 ASP 2.9 20.5 + - - +
280B ILE* 3.4 8.5 - - - +
282B LYS* 1.3 76.5 - - - +
284B ARG* 1.3 56.6 + - - +
287B TYR* 2.9 45.4 + - - +
292B LEU* 3.6 14.6 - - + +
295B GLU* 3.5 26.7 - - + -
296B LEU* 4.6 3.6 - - + -
299B ILE* 4.2 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE* 2.9 30.8 + - - +
281B ARG* 3.3 8.5 + - + +
283B ALA* 1.3 72.3 - - - +
285B ASN* 1.3 59.6 - - - +
287B TYR 3.6 10.4 - - - +
288B THR* 5.4 2.6 - - - +
292B LEU* 4.4 8.4 - - + +
316B ASN* 4.6 8.4 + - - -
319B LEU* 3.7 36.0 + - - +
320B SER* 3.8 26.3 - - - +
322B ARG* 6.0 0.6 - - - +
323B ASP* 2.6 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ARG* 3.1 13.7 + - + +
282B LYS* 3.2 9.8 + - - +
284B ARG* 1.3 77.9 - - - +
286B LEU* 1.3 70.8 + - - +
287B TYR 5.0 0.2 - - - +
288B THR* 6.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LYS* 2.9 52.3 + - + +
285B ASN* 1.3 83.3 - - - +
287B TYR* 1.3 98.6 + - + +
288B THR* 4.4 0.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ALA* 2.9 23.3 + - - +
284B ARG 3.6 10.9 - - - +
285B ASN 5.2 0.2 - - - -
286B LEU* 1.3 113.9 - - + +
288B THR* 1.3 70.4 + - - +
291B GLU* 3.9 20.2 - - + -
292B LEU* 3.5 32.1 - - - +
295B GLU* 3.9 41.7 + - + -
----------------------------------------------------------
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