Contacts of the helix formed by residues 289 - 296 (chain B) in PDB entry 3LUE
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 ILE 289 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B THR* 5.2 2.0 - - + -
166B TYR* 3.8 46.9 - - + +
171B LEU* 3.7 29.8 - - + -
285B CYS* 4.4 6.3 - - + -
286B ASP* 2.8 41.3 + - + +
288B ASP* 1.4 76.8 - - + +
290B ARG* 1.3 55.5 + - - +
291B LYS 3.2 2.9 - - - -
292B ASP* 2.6 43.1 + - + +
293B LEU* 3.0 20.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLY 5.8 0.6 + - - -
270A GLU* 4.8 6.5 + - - -
282B ILE* 3.3 31.5 + - + +
283B MET* 2.8 49.6 + - - +
284B LYS 4.6 0.6 - - - -
285B CYS* 2.8 25.9 + - + +
286B ASP 3.5 9.5 + - - +
287B VAL* 4.0 34.1 - - - +
288B ASP 3.7 0.6 - - - -
289B ILE* 1.3 75.9 - - - +
291B LYS* 1.3 65.5 + - - +
293B LEU* 2.9 12.8 + - - +
294B TYR* 2.9 35.0 + - + -
325B MET* 6.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 2.5 31.7 + - - +
288B ASP* 3.5 25.4 - - - +
289B ILE* 3.0 0.4 + - - -
290B ARG* 1.3 80.8 - - - +
292B ASP* 1.3 70.7 + - - +
294B TYR* 3.9 7.7 + - - +
295B ALA* 3.5 20.3 + - - +
325B MET* 4.8 13.5 - - + -
326B LYS 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B THR* 4.4 25.3 - - + +
150B GLY* 5.0 1.1 - - - -
288B ASP 4.1 5.2 - - - +
289B ILE* 2.6 32.3 + - - +
291B LYS* 1.3 80.1 - - - +
293B LEU* 1.3 63.6 + - + +
295B ALA* 3.3 2.3 + - - +
296B ASN* 2.8 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B THR* 4.9 4.9 - - + -
150B GLY* 3.0 38.1 - - - +
151B ILE* 3.4 10.2 - - + +
164B PRO* 3.8 11.0 - - + -
165B ILE 4.1 7.2 - - - +
171B LEU* 5.9 0.2 - - + -
282B ILE* 4.0 25.6 - - + -
285B CYS* 3.6 38.4 - - + -
289B ILE* 3.6 19.3 - - + +
290B ARG* 2.9 12.6 + - - +
292B ASP* 1.3 76.0 - - - +
294B TYR* 1.4 60.4 + - - +
296B ASN 3.3 11.4 + - - +
297B THR* 3.2 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PHE* 3.7 26.3 - + - -
282B ILE* 3.4 43.6 - - + +
283B MET* 4.6 4.6 - - - -
290B ARG* 2.9 39.0 + - + +
291B LYS* 3.9 4.5 + - - +
293B LEU* 1.4 72.0 - - - +
295B ALA* 1.3 58.7 + - - +
296B ASN 3.2 1.6 + - - -
297B THR* 3.8 7.7 + - - -
317B ILE* 4.0 16.6 - - + -
321B ALA* 3.7 21.1 - - + -
322B PRO* 3.9 12.3 - - + +
325B MET* 4.1 22.7 - - + -
326B LYS 3.9 12.6 - - - +
327B ILE* 3.4 23.1 - - + +
328B LYS 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ARG* 5.6 0.2 + - - -
291B LYS 3.5 12.1 + - - +
292B ASP* 3.3 5.2 + - - +
294B TYR* 1.3 77.2 - - - +
296B ASN* 1.3 77.6 + - - +
326B LYS* 4.0 25.8 + - + +
328B LYS* 3.1 36.1 - - + +
330B ILE* 3.7 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ARG* 2.8 37.6 + - - +
149B THR* 3.7 10.3 + - - +
150B GLY* 3.4 14.0 - - - -
151B ILE 2.9 25.5 + - - +
292B ASP* 2.8 32.8 + - - +
293B LEU 3.3 5.5 - - - +
294B TYR 3.2 0.6 - - - -
295B ALA* 1.3 92.5 - - - +
297B THR* 1.3 61.0 + - - +
298B VAL* 3.7 2.9 + - - +
330B ILE* 3.7 7.9 - - - -
----------------------------------------------------------
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