Contacts of the helix formed by residues 300 - 314 (chain B) in PDB entry 4O6M
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 THR 300 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B TYR* 6.0 4.0 - - + -
147B TYR 6.1 1.6 - - - +
149B GLY* 4.3 11.1 - - - -
275B ILE* 4.3 2.7 - - + -
297B ILE 5.7 2.0 - - - +
298B PRO* 3.7 1.1 - - + +
299B ILE* 1.3 84.5 + - - +
301B ARG* 1.3 67.0 + - - +
302B ASP* 2.7 20.9 + - - -
303B PHE* 2.9 22.9 + - - +
304B ARG* 3.0 10.3 + - - +
335B ARG* 4.1 22.7 - - - +
419B SO4 3.3 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B HIS* 3.0 33.9 + - - -
211B SER* 5.2 0.2 - - - +
214B ASP* 3.6 15.7 + - - +
239B ASP* 3.5 32.3 + - - +
240B ARG* 3.6 17.7 - - - +
242B SER* 3.3 18.2 - - - -
243B ASP* 2.8 30.3 + - - +
246B ILE* 5.0 0.4 - - - +
300B THR* 1.3 72.4 - - - +
302B ASP* 1.3 62.7 + - - +
304B ARG* 3.2 19.7 + - - +
305B LEU* 3.0 46.7 + - + +
419B SO4 2.8 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLY* 3.2 18.7 + - - -
150B TRP 3.6 0.3 + - - -
151B ILE* 3.2 21.3 + - + +
152B ALA* 2.9 42.6 + - + +
156B ASN* 4.1 7.5 + - - +
208B GLN* 5.0 0.5 - - - +
211B SER* 4.3 12.1 + - - -
300B THR* 2.7 28.3 + - - -
301B ARG* 1.3 73.3 - - - +
303B PHE* 1.3 65.3 + - - -
305B LEU* 4.3 1.0 - - - +
306B LEU* 3.2 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLY* 4.9 0.4 - - - -
150B TRP* 3.9 28.9 - + + -
151B ILE* 3.6 25.1 - - + -
298B PRO* 3.3 52.7 - - + +
299B ILE* 4.0 2.0 - - - -
300B THR* 2.9 17.7 + - - +
302B ASP* 1.3 91.8 + - - +
304B ARG* 1.3 66.6 + - - +
306B LEU* 3.3 6.9 + - + +
307B ILE* 2.9 37.8 + - + +
417B MPG 4.0 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ARG* 4.0 1.6 - - - +
243B ASP* 2.9 27.7 + - - -
272B SER* 3.6 38.9 + - - +
275B ILE* 3.6 14.1 - - - +
299B ILE* 2.9 50.7 + - + +
300B THR 3.0 6.2 + - - +
301B ARG* 3.5 28.1 - - - +
303B PHE* 1.3 76.6 - - - +
305B LEU* 1.3 61.9 + - + +
307B ILE* 3.3 8.2 + - - +
308B ILE* 3.0 33.4 + - + +
324B ILE* 3.9 24.5 - - + +
419B SO4 2.8 30.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
207B ILE* 3.8 26.4 - - + +
208B GLN* 4.0 2.3 - - - +
210B HIS* 3.9 7.4 - - + -
211B SER* 3.4 40.4 - - - +
243B ASP* 4.2 12.6 - - - +
246B ILE* 4.2 16.8 - - + -
301B ARG* 3.0 50.2 + - + +
302B ASP 4.4 0.2 - - - +
304B ARG* 1.3 75.1 - - + +
306B LEU* 1.3 61.1 + - - +
308B ILE* 3.3 14.4 + - + +
309B PHE* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ILE* 3.4 38.8 - - + -
155B ILE* 5.7 5.4 - - + -
208B GLN* 3.6 25.5 + - + +
302B ASP 3.2 20.5 + - - +
303B PHE* 3.3 6.9 + - + +
305B LEU* 1.3 76.7 - - - +
307B ILE* 1.3 58.5 + - + +
309B PHE* 3.2 22.4 + - + +
310B ALA* 2.8 32.6 + - + +
408B MPG 5.6 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PRO 5.1 1.6 - - - +
299B ILE* 3.9 22.4 - - + -
303B PHE* 2.9 30.7 + - + +
304B ARG* 3.5 5.8 - - - +
306B LEU* 1.3 76.6 - - + +
308B ILE* 1.3 57.2 + - - +
310B ALA* 3.4 5.1 + - - +
311B CYS* 2.9 37.7 + - - -
320B ALA* 4.0 24.7 - - + +
323B ILE* 3.9 33.2 - - + -
324B ILE* 4.7 3.4 - - + -
327B LEU* 5.0 3.6 - - + -
408B MPG 4.5 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PHE* 4.0 26.2 - - + -
204B GLY* 5.3 0.2 - - - -
207B ILE* 4.2 15.0 - - + -
246B ILE* 3.9 21.8 - - + -
247B VAL* 5.3 7.0 - - + -
250B ILE* 4.3 12.1 - - + -
304B ARG* 3.0 19.8 + - + +
305B LEU* 3.3 24.2 + - + +
307B ILE* 1.3 75.9 - - - +
309B PHE* 1.3 58.9 + - - +
311B CYS* 3.9 0.9 - - - +
312B SER* 2.6 34.3 + - - +
317B PRO* 6.4 0.2 - - + -
320B ALA* 3.9 14.7 - - + +
321B LEU* 6.2 1.3 - - + -
324B ILE* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B GLY* 3.3 35.7 - - - +
205B VAL* 3.9 20.2 - - + -
207B ILE* 5.2 0.2 - - - +
208B GLN* 3.9 22.0 - - + -
305B LEU 2.9 14.4 + - - +
306B LEU* 3.3 28.9 - - + +
308B ILE* 1.3 75.8 - - - +
310B ALA* 1.3 78.7 + - + +
312B SER* 3.2 3.3 + - - -
313B VAL* 3.0 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU* 2.8 21.6 + - + +
307B ILE 4.0 1.6 - - - +
309B PHE* 1.3 82.5 - - + +
311B CYS* 1.3 62.7 + - - +
313B VAL* 3.1 26.1 + - + +
314B VAL* 3.5 10.7 + - - +
408B MPG 3.6 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ILE* 2.9 24.0 + - - +
308B ILE 4.1 0.2 - - - +
310B ALA* 1.3 78.2 - - - +
312B SER* 1.3 56.5 + - - +
314B VAL* 3.2 14.2 - - - +
316B LEU 2.8 47.5 + - - +
317B PRO* 4.4 0.2 - - + -
319B LEU* 3.8 23.6 - - - -
320B ALA* 3.6 32.1 - - + -
323B ILE* 4.4 0.4 - - - -
408B MPG 3.9 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PHE* 3.4 25.3 - - - -
197B TYR* 4.0 4.7 - - - -
200B THR* 3.5 36.2 - - - +
201B LEU* 4.2 2.1 - - - -
204B GLY* 3.8 9.6 - - - -
308B ILE* 2.6 23.7 + - - +
309B PHE 3.2 4.7 + - - -
311B CYS* 1.3 76.0 - - - +
313B VAL* 1.3 60.5 + - - +
315B ASN* 2.9 19.3 + - - +
316B LEU 4.6 1.1 - - - +
317B PRO* 4.3 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B TYR* 2.6 26.7 + - - -
201B LEU* 3.5 32.5 - - + +
205B VAL* 4.9 0.2 - - + -
309B PHE* 3.0 43.2 + - + +
310B ALA* 3.1 22.9 - - + +
312B SER* 1.3 76.6 - - - +
314B VAL* 1.3 64.5 + - + +
315B ASN 3.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B TYR* 4.5 0.4 - - - -
310B ALA 3.6 13.2 - - - +
311B CYS* 3.2 18.2 - - - +
313B VAL* 1.3 84.4 - - + +
315B ASN* 1.3 68.0 + - - +
316B LEU* 3.3 24.1 + - + +
319B LEU* 5.8 0.2 - - + -
408B MPG 4.3 22.0 - - + -
----------------------------------------------------------
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