Contacts of the helix formed by residues 291 - 308 (chain B) in PDB entry 3H8E
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 MET 291 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 4.4 18.8 - - + +
190B GLY* 5.3 5.8 - - - -
197B CYS* 2.8 35.4 - - - +
198B HIS* 5.9 0.2 - - - -
199B PRO* 6.3 0.7 - - - -
202B LEU* 2.6 56.8 - - + -
267B LYS* 3.5 14.0 - - - +
268B GLY* 3.8 17.0 - - - -
269B ILE* 3.0 32.6 + - - +
292B CYS* 1.3 63.9 + - - +
293B GLY 3.2 3.4 - - - -
294B ALA* 3.2 5.0 + - + +
295B ALA* 2.8 29.2 + - + +
298B PHE* 5.7 0.2 - - + -
376B THR* 4.6 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B THR* 4.7 5.4 - - + +
190B GLY* 4.3 22.2 - - - -
291B MET* 1.3 75.8 - - - +
293B GLY* 1.4 61.0 + - - +
295B ALA* 3.6 9.2 - - + +
296B SER* 2.8 31.0 + - - -
376B THR* 4.0 10.6 + - + +
465B ILE* 3.9 3.6 - - + +
469B ALA* 3.8 40.2 - - + -
470B TRP* 4.7 11.0 - - - -
479B ALA* 4.6 8.1 - - - -
483B PRO* 4.3 0.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B GLY* 3.8 7.2 - - - -
267B LYS 3.6 5.1 + - - -
291B MET 3.2 1.4 - - - -
292B CYS* 1.4 73.5 - - - +
294B ALA* 1.3 64.5 + - - +
296B SER* 2.9 22.3 + - - -
297B VAL* 3.1 13.2 + - - +
374B ILE* 3.4 26.6 - - - +
375B ALA* 4.5 1.6 - - - -
376B THR* 4.6 5.3 + - - +
465B ILE* 3.8 8.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
202B LEU* 4.9 7.4 - - + -
266B GLY* 3.7 14.9 - - - +
267B LYS 3.0 8.9 + - - +
268B GLY* 3.6 24.7 - - - +
291B MET 3.2 6.9 + - - +
293B GLY* 1.3 74.4 - - - +
295B ALA* 1.3 63.8 + - - +
297B VAL* 3.2 4.0 + - - +
298B PHE* 3.0 27.1 + - + -
317B LEU* 3.8 23.2 - - + +
319B CYS* 4.7 3.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
186B THR* 2.8 43.2 + - + +
189B LEU* 4.1 25.1 - - + -
190B GLY* 4.5 4.3 - - - +
291B MET* 2.8 23.7 + - + +
292B CYS* 3.7 11.9 - - - +
293B GLY 3.3 0.2 - - - -
294B ALA* 1.3 74.6 - - - +
296B SER* 1.3 57.8 + - - +
298B PHE* 3.4 4.1 + - - +
299B GLY 3.0 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B THR* 3.6 13.0 - - - +
292B CYS 2.8 13.6 + - - -
293B GLY 2.9 17.2 + - - -
295B ALA* 1.3 70.7 - - - +
297B VAL* 1.3 60.2 + - - +
300B THR* 2.8 34.4 + - - -
374B ILE* 3.5 11.6 - - - +
483B PRO* 2.7 50.0 - - - +
484B VAL* 4.0 3.9 - - - +
487B LEU* 4.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 3.9 28.7 - - + +
266B GLY 4.0 15.7 - - - +
293B GLY 3.1 13.9 + - - +
294B ALA 3.2 7.8 + - - +
296B SER* 1.3 72.4 - - - +
298B PHE* 1.3 58.2 + - - +
300B THR* 3.3 5.3 + - - -
301B LEU* 2.8 30.7 + - - +
315B CYS* 3.5 36.2 - - + -
317B LEU* 3.7 13.2 - - + -
374B ILE* 3.9 19.1 - - + -
487B LEU* 5.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 2.5 41.4 - + + -
189B LEU* 3.5 14.4 - - + -
202B LEU* 3.4 46.4 - - + -
205B GLN* 4.0 6.5 - - + -
206B ALA* 3.8 27.8 - - + -
209B LEU* 4.2 13.8 - - + +
250B LEU* 4.0 12.8 - - + -
291B MET* 5.9 0.2 - - + -
294B ALA 3.0 22.0 + - - -
295B ALA* 3.4 6.5 - - - +
297B VAL* 1.3 75.3 - - - +
299B GLY* 1.4 57.8 + - - +
301B LEU* 3.4 6.8 + - - +
302B ARG* 2.9 24.9 + - - +
317B LEU* 3.2 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLY* 3.2 27.6 - - - -
185B PHE* 3.8 6.3 - - - -
186B THR* 3.3 18.8 - - - -
295B ALA 3.0 12.7 + - - -
298B PHE* 1.4 71.7 - - - +
300B THR* 1.4 66.5 - - - +
302B ARG* 3.3 1.3 + - - -
303B ALA* 3.0 19.4 + - - +
484B VAL* 4.2 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 3.9 12.8 - - + -
296B SER 2.8 22.5 + - - -
297B VAL 3.8 3.1 - - - -
299B GLY* 1.4 69.1 - - - +
301B LEU* 1.3 61.5 + - - +
303B ALA* 3.1 3.3 + - - +
304B VAL* 2.8 33.2 + - + +
313B LEU* 5.2 0.2 - - + -
484B VAL* 3.9 10.8 - - - +
487B LEU* 3.5 34.2 - - + +
488B THR* 3.9 17.9 - - - +
491B LEU* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 3.9 13.9 - - + -
216B LEU* 4.1 7.4 - - + -
250B LEU* 3.5 41.5 - - + -
252B TYR* 4.1 20.4 - - + -
264B LEU* 5.5 0.2 - - - +
297B VAL 2.8 21.3 + - - +
298B PHE* 3.7 5.4 - - - +
300B THR* 1.3 73.7 - - - +
302B ARG* 1.4 62.4 + - - +
304B VAL* 3.2 5.9 + - + +
305B LEU* 2.9 42.2 + - + +
313B LEU* 4.0 21.4 - - + +
315B CYS* 4.1 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B THR* 3.6 40.3 + - + +
182B GLY* 4.2 4.5 - - - +
185B PHE* 3.3 42.4 - - + +
209B LEU* 3.9 28.8 - - + +
213B HIS* 5.7 2.2 + - - -
298B PHE 2.9 18.3 + - - +
299B GLY* 3.3 10.1 + - - +
301B LEU* 1.4 72.6 - - - +
303B ALA* 1.3 57.3 + - - +
305B LEU* 3.4 11.7 + - - +
306B GLU* 3.0 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ALA* 3.4 34.0 + - + +
179B ILE* 4.3 2.2 - - - +
182B GLY* 4.8 0.7 - - - -
299B GLY 3.0 12.7 + - - +
300B THR 3.4 7.4 - - - +
302B ARG* 1.3 75.7 - - - +
304B VAL* 1.3 58.4 + - - +
306B GLU* 3.2 2.9 + - - +
307B LEU* 3.0 34.9 + - - +
484B VAL* 4.9 0.7 - - + -
488B THR* 3.8 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B TYR* 3.6 34.4 + - + -
300B THR* 2.8 21.7 + - + +
301B LEU* 3.6 4.3 - - + +
303B ALA* 1.3 73.0 - - + +
305B LEU* 1.3 62.1 + - - +
307B LEU* 3.4 1.4 + - - -
308B GLN* 2.8 24.3 + - - -
309B LEU* 3.3 34.4 + - + -
311B VAL* 4.6 4.0 - - + -
313B LEU* 4.0 14.1 - - + -
488B THR* 5.3 4.3 - - + -
491B LEU* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 4.4 5.8 - - + -
213B HIS* 3.8 56.1 + - + +
215B ALA* 5.6 1.1 - - + -
216B LEU* 4.3 14.8 - - + +
252B TYR* 3.7 33.0 - - + -
301B LEU* 2.9 42.7 + - + +
302B ARG* 3.7 8.7 - - - +
304B VAL* 1.3 75.3 - - - +
306B GLU* 1.3 65.8 + - - +
308B GLN* 3.2 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LYS* 4.9 7.3 + - - +
177B SER* 4.1 10.4 - - - +
178B ALA* 2.7 38.0 + - + +
181B THR* 3.7 22.0 + - + +
213B HIS* 6.4 0.2 - - - -
302B ARG* 3.0 14.4 + - + +
303B ALA* 3.5 8.1 - - - +
305B LEU* 1.3 76.6 - - - +
307B LEU* 1.3 61.9 + - + +
308B GLN* 4.4 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LYS* 4.0 35.9 + - + +
175B HIS* 3.8 26.0 - - + +
178B ALA* 3.5 23.8 - - + -
303B ALA 3.0 20.3 + - - +
304B VAL 3.9 2.5 - - - +
306B GLU* 1.3 77.0 - - + +
308B GLN* 1.3 70.1 + - - +
309B LEU* 3.3 22.8 + - + +
488B THR* 4.3 15.9 - - + -
492B LEU* 4.0 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B TYR* 3.3 12.1 + - + +
304B VAL 2.8 10.8 + - - -
305B LEU 3.2 15.6 + - - +
306B GLU 4.4 4.5 - - - +
307B LEU* 1.3 80.0 - - - +
309B LEU* 1.4 67.2 + - - +
310B PRO* 3.5 5.2 - - - +
----------------------------------------------------------
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