Contacts of the helix formed by residues 259 - 274 (chain B) in PDB entry 3QN3
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 SER 259 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B GLY 4.6 7.6 - - - -
250B LYS* 4.5 14.1 - - - +
251B TYR* 4.4 2.0 - - - -
257B ALA 4.0 2.0 + - - -
258B PHE* 1.3 75.0 - - - +
260B SER* 1.3 65.2 + - - +
261B GLU* 3.5 13.2 + - - +
262B ALA* 3.0 26.6 + - - +
263B LEU* 2.9 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PHE* 5.0 0.7 - - - -
249B GLY 4.7 7.1 + - - -
251B TYR* 3.7 16.7 - - - -
259B SER* 1.3 73.5 - - - +
261B GLU* 1.3 69.7 + - - +
263B LEU* 3.3 3.1 + - - +
264B ILE* 3.0 34.2 + - - +
283B LEU* 4.1 3.7 - - - +
287B ASP* 2.6 33.3 + - - -
290B GLY* 4.3 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B SER* 3.2 10.5 + - - +
260B SER* 1.3 88.5 + - - +
262B ALA* 1.3 57.7 + - - +
264B ILE* 3.5 14.8 - - + +
265B GLU* 3.1 34.8 + - + +
290B GLY* 6.1 0.3 - - - -
293B LYS* 3.4 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PHE* 4.1 16.0 - - + -
259B SER* 3.0 29.1 + - - +
261B GLU* 1.3 76.0 - - - +
263B LEU* 1.3 59.8 + - - +
265B GLU* 3.1 10.7 + - - +
266B ARG* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B SER* 4.9 0.2 - - - -
245B PHE* 4.6 3.6 - - + -
251B TYR* 3.7 36.8 - - + -
253B MET* 3.9 27.8 - - + -
258B PHE* 3.9 11.3 - - + -
259B SER 2.9 16.6 + - - +
260B SER 3.7 4.0 - - - +
262B ALA* 1.3 73.6 - - - +
264B ILE* 1.3 65.3 + - - +
266B ARG* 3.1 17.1 + - + +
267B TYR* 3.0 62.0 + - + +
282B GLY 3.6 10.1 - - - +
283B LEU* 4.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B SER 3.0 23.3 + - - +
261B GLU* 3.5 17.7 - - + +
262B ALA 3.2 0.2 - - - -
263B LEU* 1.3 75.4 - - - +
265B GLU* 1.3 66.8 + - - +
267B TYR* 3.0 20.7 + - + +
268B VAL* 3.1 14.5 + - + +
283B LEU* 4.1 15.7 - - + -
290B GLY* 3.9 7.2 - - - +
293B LYS* 3.7 30.7 - - + -
294B LEU* 3.8 23.8 - - + +
297B LYS* 4.2 35.4 - - + -
298B LEU* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B GLU* 3.1 18.4 + - + +
262B ALA* 3.1 11.0 + - - +
264B ILE* 1.3 79.4 - - - +
266B ARG* 1.3 62.4 + - - +
268B VAL* 3.2 11.8 + - - +
269B GLU* 3.0 27.2 + - - +
297B LYS* 3.7 32.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PHE* 5.8 0.2 - - + -
213B ASN* 6.4 0.4 - - - +
214B ASN* 5.5 0.2 - - - +
215B THR* 3.7 22.0 - - - +
253B MET* 4.7 4.0 - - + -
254B GLU* 3.0 40.3 + - - +
258B PHE* 4.3 14.8 - - + -
262B ALA 2.9 12.5 + - - +
263B LEU* 3.1 25.5 + - + +
265B GLU* 1.3 76.9 - - - +
267B TYR* 1.3 57.2 + - + +
269B GLU* 3.2 34.2 + - - +
270B LEU* 2.9 64.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PHE* 4.3 11.7 - + - -
238B LEU* 5.8 0.9 - - + -
240B VAL* 3.6 26.1 - - + +
263B LEU* 3.0 50.7 + - + +
264B ILE* 3.0 12.5 + - - +
266B ARG* 1.3 74.2 - - + +
268B VAL* 1.3 56.5 + - - +
270B LEU* 3.8 14.5 - - + +
271B CYS* 2.8 41.7 + - - -
279B ILE* 3.9 23.3 - - + -
282B GLY* 2.4 49.5 + - - -
283B LEU* 4.9 2.2 - - + -
294B LEU* 4.2 16.8 - - + -
298B LEU* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE 3.1 15.6 + - - +
265B GLU* 3.5 16.6 - - - +
267B TYR* 1.3 75.7 - - - +
269B GLU* 1.3 57.9 + - - +
271B CYS* 3.4 2.9 + - - +
272B ALA* 3.0 29.9 + - + +
297B LYS* 4.0 32.1 - - + -
298B LEU* 3.9 28.5 - - + -
301B LYS* 4.9 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLU* 3.0 14.0 + - - +
266B ARG* 3.2 38.8 + - - +
268B VAL* 1.3 77.5 - - - +
270B LEU* 1.3 63.7 + - + +
272B ALA* 3.1 16.6 + - - +
273B LYS* 3.2 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PHE* 4.2 29.2 - - + -
214B ASN* 6.0 1.1 - - + -
215B THR* 3.7 24.5 - - + -
218B ILE* 4.7 5.2 - - + -
238B LEU* 4.9 7.4 - - + -
254B GLU* 5.8 0.7 - - - +
266B ARG* 2.9 51.6 + - + +
267B TYR* 3.8 14.6 - - + +
269B GLU* 1.3 74.3 - - - +
271B CYS* 1.3 59.8 + - - +
273B LYS* 3.2 2.1 + - - +
274B TYR* 3.0 49.1 + - + +
276B ILE* 3.8 14.5 - - + +
279B ILE* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B TYR* 2.8 29.7 + - - +
268B VAL* 3.8 5.8 - - - +
270B LEU* 1.3 73.4 - - - +
272B ALA* 1.3 60.8 + - - +
274B TYR 3.2 16.1 - - - +
276B ILE* 4.0 24.9 - - + +
279B ILE* 4.1 7.6 - - - -
298B LEU* 4.7 6.5 - - + -
301B LYS* 3.5 28.1 + - - +
302B ILE* 3.8 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B VAL* 3.0 15.0 + - + +
269B GLU* 3.1 10.9 + - - +
271B CYS* 1.3 77.7 - - - +
273B LYS* 1.3 61.0 + - + +
274B TYR 3.7 0.2 - - - -
301B LYS* 4.2 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B THR* 5.7 0.8 - - - +
219B ASP* 4.4 3.6 + - - -
269B GLU 3.2 14.5 + - - +
270B LEU* 3.2 3.1 + - - +
272B ALA* 1.3 78.3 - - + +
274B TYR* 1.3 105.5 + - + +
275B PRO* 4.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B THR* 3.7 17.6 - - + +
218B ILE* 3.4 41.7 - - + -
219B ASP* 2.8 30.9 + - - -
222B MET* 4.3 15.0 - - + -
236B ILE* 5.4 0.4 - - + -
270B LEU* 3.0 40.0 + - + +
271B CYS* 3.2 18.4 - - - +
272B ALA 3.7 0.4 - - - -
273B LYS* 1.3 121.4 + - + +
275B PRO* 1.4 60.9 - - + +
276B ILE* 2.8 23.8 + - + -
----------------------------------------------------------
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