Contacts of the helix formed by residues 302 - 319 (chain B) in PDB entry 4OGB
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 ASN 302 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ASP* 1.3 102.5 + - - +
303B TYR* 1.3 64.6 + - - +
304B SER* 3.3 14.1 - - - +
305B ASP* 2.7 48.8 + - - +
306B ARG* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLU* 6.0 2.2 - - - -
259B SER* 5.0 7.6 - - - -
262B LYS* 3.6 29.4 - - + +
263B MET* 3.6 32.7 - - + +
266B ASP* 2.6 30.4 + - - -
302B ASN* 1.3 73.4 - - - +
304B SER* 1.3 62.0 + - - +
306B ARG* 3.0 11.3 + - + +
307B ILE* 2.8 59.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ASN* 3.3 10.5 + - - -
303B TYR* 1.3 80.5 - - - +
305B ASP* 1.3 68.4 + - - +
307B ILE* 3.5 8.0 - - - +
308B GLN* 3.1 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B MET* 4.0 19.1 - - - +
299B LEU 5.6 0.5 - - - +
300B LEU* 4.3 15.7 - - + -
301B ASP* 4.5 1.6 + - - +
302B ASN* 2.7 35.2 + - - +
304B SER* 1.3 78.7 + - - +
306B ARG* 1.3 64.7 + - - +
308B GLN* 3.5 21.7 + - - +
309B VAL* 3.1 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B VAL* 3.1 27.8 + - - +
185B PHE* 3.8 11.3 - - + +
186B THR* 4.0 9.9 - - - +
189B GLU* 2.9 44.5 + - - +
300B LEU* 2.5 58.6 + - + +
301B ASP 4.6 2.9 - - - -
302B ASN 3.1 22.6 + - - +
303B TYR* 3.0 11.9 + - + +
305B ASP* 1.3 76.5 - - - +
307B ILE* 1.3 62.2 + - - +
309B VAL* 3.3 6.6 + - - +
310B LEU* 3.1 27.0 + - + +
508B EDO 5.2 2.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
263B MET* 3.9 33.9 - - + +
266B ASP* 3.5 17.9 - - + +
267B ILE* 4.0 13.2 - - + -
303B TYR* 2.8 62.8 + - + +
304B SER* 3.5 9.0 - - - +
306B ARG* 1.3 73.9 - - - +
308B GLN* 1.3 55.8 + - - +
310B LEU* 3.0 12.7 + - + +
311B GLN* 2.6 48.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
279B LEU* 5.3 2.6 - - + +
282B ASP* 3.0 44.3 + - - +
283B LEU* 5.6 1.3 - - + -
286B MET* 3.4 34.0 - - - +
304B SER* 3.1 16.4 + - - +
305B ASP* 3.5 22.1 + - - +
307B ILE* 1.3 83.0 - - + +
309B VAL* 1.3 59.0 + - - +
311B GLN* 3.3 17.0 - - - +
312B ASN* 2.9 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 4.8 5.2 - - + -
185B PHE* 3.6 24.9 - - + -
283B LEU* 5.3 3.6 - - + -
286B MET* 3.5 32.3 - - + -
298B LEU* 5.0 0.7 - - + -
300B LEU* 3.8 14.1 - - + -
305B ASP 3.1 17.1 + - - +
306B ARG 3.6 7.0 - - - +
307B ILE 3.2 0.2 - - - -
308B GLN* 1.3 73.0 - - - +
310B LEU* 1.3 60.2 + - - +
312B ASN* 3.5 3.1 + - - -
313B MET* 2.9 28.2 + - + +
384B TRP* 3.9 22.2 - - + -
387B LEU* 4.3 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 4.7 3.4 - - + -
185B PHE* 3.5 38.1 - - + -
189B GLU* 4.0 34.8 - - + +
192B ALA* 5.6 0.2 - - + -
193B ALA* 4.6 12.8 - - + -
263B MET* 4.4 6.5 - - - -
267B ILE* 4.0 20.4 - - + -
306B ARG* 3.1 16.0 + - + +
307B ILE* 3.0 23.6 + - + +
309B VAL* 1.3 73.6 - - - +
311B GLN* 1.3 66.2 - - - +
313B MET* 3.2 13.0 + - + +
314B VAL* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ASP* 2.8 45.4 + - - +
267B ILE* 4.0 9.9 - - - +
270B ALA* 3.7 23.7 - - + +
271B THR* 6.0 0.5 - - - +
279B LEU* 3.8 17.0 - - + +
307B ILE* 2.6 29.1 + - + +
308B GLN* 3.3 25.2 + - - +
310B LEU* 1.3 74.4 - - - +
312B ASN* 1.3 58.2 + - - +
314B VAL* 3.4 1.7 + - - +
315B HIS* 2.9 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 3.3 50.8 + - - +
280B LEU* 4.4 0.5 + - - -
283B LEU* 3.7 39.5 - - + +
308B GLN* 2.9 32.2 + - - +
309B VAL 4.2 2.5 - - - +
311B GLN* 1.3 74.4 - - - +
313B MET* 1.3 61.3 + - - +
315B HIS* 3.5 5.5 - - - +
316B CYS* 2.8 34.2 + - - -
380B LEU* 4.0 13.7 - - + +
384B TRP* 4.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B THR* 4.2 10.8 - - + +
175B LEU* 3.5 24.2 - - + +
176B LEU* 3.6 52.5 - - + -
181B LEU* 4.3 8.1 - - + -
185B PHE* 4.0 21.8 - - + -
193B ALA* 5.3 2.2 - - - -
309B VAL* 2.9 17.0 + - + +
310B LEU* 3.5 12.8 - - + +
312B ASN* 1.3 78.1 - - - +
314B VAL* 1.3 57.8 + - - +
316B CYS* 3.4 5.4 + - - +
317B ALA* 3.1 22.9 + - - +
384B TRP* 3.6 28.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
168B VAL* 4.6 6.7 - - + +
172B THR* 3.9 17.3 - - + +
193B ALA* 3.8 16.8 - - + +
196B ALA 5.3 0.4 - - - -
197B SER* 3.7 33.2 - - - +
200B HIS* 5.4 2.5 - - + -
267B ILE* 3.6 31.4 - - + -
271B THR* 4.3 15.3 - - + -
310B LEU 3.0 13.3 + - - +
311B GLN 4.1 0.9 - - - +
313B MET* 1.3 74.6 - - + +
315B HIS* 1.3 60.8 + - - +
317B ALA* 3.1 1.9 + - - +
318B ASP* 2.8 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA 4.1 14.3 + - - +
271B THR* 4.6 13.9 + - - +
273B MET* 3.8 18.4 - - - -
276B HIS* 2.8 36.8 + + + +
279B LEU* 4.1 22.0 - - + -
311B GLN 2.9 18.6 + - - +
312B ASN* 3.3 9.8 + - - +
314B VAL* 1.3 77.3 - - - +
316B CYS* 1.3 50.9 + - - +
318B ASP* 3.1 11.6 + - - +
319B LEU* 2.8 54.1 + - + +
380B LEU* 3.6 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 4.1 4.9 - - + -
312B ASN 2.8 25.7 + - - +
313B MET* 3.5 6.5 - - - +
315B HIS* 1.3 73.6 - - - +
317B ALA* 1.3 61.3 + - - +
319B LEU 3.1 4.6 - - - +
320B SER* 3.0 23.6 + - - -
380B LEU* 3.7 35.0 - - - +
381B TRP* 3.3 29.2 - - + +
384B TRP* 3.8 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASP* 5.3 0.2 - - - +
168B VAL* 3.7 25.1 - - + +
171B SER* 3.9 6.8 - - - -
172B THR* 3.3 37.2 - - - +
175B LEU* 4.2 5.1 - - + +
313B MET 3.1 11.6 + - - +
314B VAL 3.4 7.0 - - - +
316B CYS* 1.3 75.8 - - - +
318B ASP* 1.3 62.2 + - - +
320B SER* 2.8 28.8 + - - -
321B ASN* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TYR* 4.3 2.3 + - - -
164B HIS* 3.2 12.0 - - - -
168B VAL* 4.0 7.6 - - + +
200B HIS* 3.3 8.7 + - - +
271B THR* 4.0 26.3 - - + +
273B MET* 6.1 0.2 - - - +
314B VAL* 2.8 13.4 + - + +
315B HIS* 3.2 16.6 + - - +
317B ALA* 1.3 77.8 - - - +
319B LEU* 1.3 63.2 + - + +
320B SER 3.5 2.4 + - - -
321B ASN* 3.5 9.5 - - - +
501B 2SR 4.1 19.0 - - - +
502B ZN 2.3 35.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B MET* 4.2 8.7 - - - -
315B HIS* 2.8 43.6 + - + +
316B CYS 3.1 4.9 - - - +
318B ASP* 1.3 75.9 - - + +
320B SER* 1.3 58.4 + - - +
321B ASN* 3.6 6.1 - - - -
322B PRO* 3.7 10.4 - - - +
372B PHE* 4.0 10.5 - - + -
376B ILE* 3.7 30.5 - - + -
377B VAL* 3.7 14.7 - - + +
380B LEU* 3.8 18.4 - - + -
381B TRP* 3.2 13.3 + - - +
501B 2SR 3.5 37.2 - - + -
510B DMS 5.6 1.1 - - + -
----------------------------------------------------------
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