Contacts of the helix formed by residues 285 - 299 (chain B) in PDB entry 3Q36
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 PRO 285 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B SER 3.8 6.1 - - - +
284B PHE* 1.3 87.1 - - + +
286B PRO* 1.4 75.8 - - + +
287B CYS* 3.3 1.3 - - - -
288B MET* 2.9 29.2 + - + -
289B ARG* 2.9 10.1 + - - -
312B PHE* 4.0 11.4 - - + -
444B PRO* 3.9 32.3 - - + +
447B PHE* 3.4 30.1 - - + -
458B SF4 3.6 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PHE 4.0 0.2 - - - -
285B PRO* 1.4 85.8 - - + +
287B CYS* 1.3 63.0 + - - +
289B ARG* 3.3 7.9 + - + +
290B GLN* 3.1 27.4 + - - +
385B PRO* 4.0 15.9 - - + -
386B PHE* 3.5 34.3 - - + -
398B LEU* 5.7 0.9 - - + -
401B TYR* 4.3 14.2 + - + -
424B CYS* 3.7 13.9 - - - -
427B TYR* 3.6 35.4 - - + -
458B SF4 4.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PRO* 3.0 7.2 + - - -
286B PRO* 1.3 78.4 - - - +
288B MET* 1.3 101.8 + - - +
290B GLN* 3.4 6.1 + - - +
291B LEU* 3.4 25.3 + - - +
308B GLN* 3.7 5.3 + - - +
381B TYR 4.7 1.2 - - - +
383B GLY 3.1 24.9 - - - +
385B PRO* 3.8 11.1 - - + +
444B PRO* 4.4 0.9 - - - -
458B SF4 2.3 42.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PHE* 4.1 6.5 - - + -
285B PRO* 2.9 15.1 + - + +
287B CYS* 1.3 92.4 - - - +
289B ARG* 1.3 67.3 + - - +
290B GLN 3.1 0.4 - - - -
291B LEU* 3.4 5.4 + - - +
292B HIS* 3.0 26.0 + - - +
308B GLN* 3.6 35.7 - - + +
309B TYR* 4.1 12.3 - - + -
312B PHE* 3.5 70.0 - - + -
365B PHE* 5.0 3.8 - - + +
370B ILE* 3.9 6.7 - - + -
444B PRO* 3.9 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B SER* 3.4 31.1 + - - +
281B THR* 3.4 39.8 + - - +
284B PHE* 4.2 8.2 - - + +
285B PRO 2.9 12.5 + - - +
286B PRO* 3.3 10.3 + - + +
288B MET* 1.3 79.2 - - - +
290B GLN* 1.3 60.6 + - - +
292B HIS* 4.1 1.6 - - - +
293B LYS* 3.2 26.2 + - + +
400B SER 5.0 2.4 + - - -
401B TYR* 3.1 61.0 + - + +
427B TYR* 3.1 24.7 + - - -
431B ILE* 5.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PRO 3.1 14.0 + - - +
287B CYS* 3.4 10.3 + - - +
288B MET 3.1 0.2 - - - -
289B ARG* 1.3 74.9 - - - +
291B LEU* 1.3 54.8 + - - +
293B LYS* 3.2 6.8 + - - +
294B ALA* 2.8 35.8 + - - +
381B TYR* 3.5 30.5 + - + +
382B HIS 5.0 2.6 + - - -
383B GLY 5.4 1.8 + - - -
385B PRO* 3.4 29.8 - - + +
389B SER* 4.1 0.9 + - - -
397B LYS* 3.0 38.1 + - + +
401B TYR* 4.0 14.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
287B CYS 3.4 7.8 + - - +
288B MET* 3.4 9.1 + - - +
290B GLN* 1.3 73.8 - - - +
292B HIS* 1.3 61.7 + - - +
294B ALA* 3.7 2.3 - - - +
295B LEU* 2.8 31.9 + - - +
301B LEU* 3.9 11.0 - - + +
305B GLY* 3.9 16.6 - - - +
308B GLN* 3.7 34.5 - - + +
309B TYR* 3.9 36.6 - - + +
381B TYR* 3.1 39.9 - - + +
382B HIS* 3.6 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE* 3.3 20.3 - - + +
277B ASP* 2.8 24.0 + - - -
280B SER* 2.8 33.0 + - - +
284B PHE* 4.6 0.9 - - + -
288B MET 3.0 14.7 + - - +
289B ARG 4.1 2.9 - - - +
291B LEU* 1.3 77.1 - - - +
293B LYS* 1.3 60.5 + - - +
295B LEU* 3.3 2.7 + - - +
296B ARG* 2.9 67.4 + - + +
309B TYR* 2.6 36.6 + - + +
326B PHE* 3.9 9.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ARG* 3.2 21.0 + - + +
290B GLN* 3.3 7.4 - - - +
292B HIS* 1.3 83.6 - - + +
294B ALA* 1.3 62.2 + - - +
296B ARG* 3.3 7.8 + - + +
297B GLU* 3.1 53.7 + - + +
401B TYR* 6.3 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLN 2.8 19.5 + - - +
291B LEU 3.7 4.3 - - - +
293B LYS* 1.3 70.6 - - - +
295B LEU* 1.3 68.1 + - - +
297B GLU* 3.2 8.1 + - - -
298B ASN* 2.8 32.9 + - + +
300B HIS 4.4 1.3 - - - -
301B LEU* 4.0 7.9 - - + -
381B TYR* 3.6 44.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LEU 2.8 23.0 + - - +
292B HIS* 3.5 5.2 - - + +
294B ALA* 1.3 72.1 - - - +
296B ARG* 1.3 56.4 + - + +
299B HIS* 2.7 34.1 + - - -
300B HIS 3.8 26.0 - - - +
301B LEU* 3.9 4.9 - - + +
309B TYR* 3.8 8.1 - - + -
326B PHE* 3.4 38.8 - - + -
327B TRP* 3.6 29.8 - - + -
330B GLU* 3.5 23.8 - - + +
331B PHE* 3.8 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU 5.1 5.5 + - - -
276B ILE* 5.1 4.2 - - - +
277B ASP* 3.4 29.2 + - - +
292B HIS* 2.9 55.5 + - + +
293B LYS* 3.5 9.2 - - + +
294B ALA 3.1 0.2 - - - -
295B LEU* 1.3 77.7 - - + +
297B GLU* 1.3 58.8 + - + +
299B HIS* 3.1 26.2 - - - -
326B PHE* 4.1 14.5 - - - -
330B GLU* 3.4 30.7 + - - +
333B LYS* 4.0 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B LYS* 3.1 44.8 + - + +
294B ALA* 4.1 6.5 - - - +
296B ARG* 1.3 79.1 - - + +
298B ASN* 1.3 75.4 + - - +
299B HIS* 3.5 12.4 + - - -
381B TYR* 5.6 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ALA* 2.8 15.6 + - - +
297B GLU* 1.3 96.6 + - - +
299B HIS* 1.3 62.4 + - - +
300B HIS* 2.6 34.2 + - + +
381B TYR* 3.2 34.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 2.7 24.6 + - - -
296B ARG 3.1 20.5 + - - -
297B GLU* 3.8 12.8 + - - -
298B ASN* 1.3 73.5 - - - +
300B HIS* 1.3 58.6 + - - +
330B GLU* 3.2 32.7 + - - +
331B PHE* 3.5 22.2 - - - +
333B LYS* 3.5 38.9 + - + +
334B GLY* 3.6 16.7 - - - -
----------------------------------------------------------
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