Contacts of the helix formed by residues 302 - 315 (chain B) in PDB entry 6O81
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
----------------------------------------------------------
55B ARG* 3.1 39.9 - - + +
56B PHE* 3.2 23.6 - - - -
196B CYS* 4.1 17.4 - - - -
198B GLU* 4.2 12.1 + - - +
199B ASP* 6.1 0.2 - - - -
301B SER* 1.3 79.6 + - - +
303B LEU* 1.3 71.2 + - + +
304B HIS* 3.1 11.9 + - - +
305B MET* 3.1 25.2 + - - +
306B TYR* 3.1 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 4.4 5.9 - - + -
302B ASN* 1.3 83.6 - - + +
304B HIS* 1.3 65.4 + - + +
306B TYR* 3.7 8.6 - - + +
307B SER* 2.8 37.6 + - - +
412B LEU* 5.9 6.1 - - + -
428B ARG* 4.1 40.4 - - + -
430B VAL* 4.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PRO* 3.2 34.7 + - + +
194B THR 5.4 0.7 - - - -
195B ARG 5.1 0.7 - - - -
196B CYS* 3.4 32.1 - - + +
197B HIS* 6.4 1.6 - + - -
198B GLU* 6.0 0.2 - - - +
302B ASN* 3.1 12.4 + - - +
303B LEU* 1.3 83.7 - - + +
305B MET* 1.3 61.0 + - - +
307B SER* 3.3 5.9 + - - -
308B ALA* 2.9 27.4 + - + +
304C GLU* 5.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B THR* 3.2 32.3 - - + +
195B ARG* 4.7 0.4 - - - -
196B CYS* 3.6 22.9 - - - -
199B ASP* 4.4 18.6 - - + +
245B LEU* 5.1 12.8 - - + -
246B ASP 5.9 1.6 - - - +
298B ALA* 5.5 0.2 - - + -
299B ARG* 3.3 26.9 - - + +
300B VAL* 3.7 6.5 - - - -
301B SER* 3.5 29.6 - - - +
302B ASN* 3.1 17.8 + - - +
304B HIS* 1.3 72.2 - - - +
306B TYR* 1.3 59.2 + - - +
308B ALA* 4.5 4.5 - - - +
309B VAL* 2.9 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 4.4 16.8 - + + -
68B LEU* 4.8 11.7 - - + -
69B PRO 2.6 27.4 + - - -
70B LEU* 3.6 33.3 + - + +
75B LEU* 5.0 4.3 - - + -
300B VAL* 4.0 14.7 - - + +
302B ASN 3.1 20.3 + - - +
303B LEU* 3.7 10.1 - - + +
305B MET* 1.3 77.6 - - - +
307B SER* 1.3 63.0 + - - +
309B VAL* 4.2 0.5 - - - +
310B CYS* 2.9 33.4 + - + +
395B TYR* 4.1 20.7 - + - +
397B TRP* 2.9 26.3 + + - -
412B LEU* 4.1 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LEU* 2.8 26.1 + - - +
304B HIS* 3.8 8.5 - - - -
306B TYR* 1.3 78.0 - - - +
308B ALA* 1.3 58.9 + - - +
310B CYS 3.4 0.3 + - - -
311B ALA* 2.9 27.7 + - - +
395B TYR* 3.1 42.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PRO* 3.6 25.8 - - + +
194B THR* 3.7 20.9 - - + +
304B HIS* 2.9 18.9 + - + +
305B MET* 4.0 4.9 - - - +
307B SER* 1.3 77.5 - - - +
309B VAL* 1.3 57.3 + - - +
311B ALA* 3.4 5.4 + - - +
312B ASP* 2.9 36.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
70B LEU* 4.2 12.8 - - + -
156B ILE* 3.7 37.5 - - + -
194B THR* 5.1 4.3 - - + -
296B TYR* 4.2 10.1 - - + +
298B ALA* 4.1 18.6 - - + -
299B ARG 3.9 19.7 - - - +
300B VAL* 4.4 6.1 - - + -
305B MET* 2.9 22.1 + - + +
306B TYR 4.2 2.0 - - - +
308B ALA* 1.3 74.4 - - + +
310B CYS* 1.3 59.8 + - - +
312B ASP* 3.3 6.0 + - - +
313B VAL* 2.9 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 3.3 43.0 - - + +
71B ALA* 5.4 0.4 - - - -
306B TYR* 2.9 23.4 + - + +
307B SER 3.8 0.4 - - - +
309B VAL* 1.3 77.3 - - - +
311B ALA* 1.3 56.8 + - - +
313B VAL* 3.3 4.9 + - - +
314B ILE* 2.9 42.0 + - - +
378B VAL* 3.8 7.6 - - - -
395B TYR* 3.6 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B SER 2.9 18.9 + - - +
308B ALA* 3.8 6.1 - - - +
310B CYS* 1.3 75.5 - - - +
312B ASP* 1.3 59.2 + - - +
314B ILE* 4.2 5.1 - - - +
315B ARG* 3.1 51.2 + - - +
376B ASN 6.1 1.6 - - - +
395B TYR* 4.6 6.7 + - + +
304C GLU* 5.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B HIS* 4.9 4.0 - - - -
194B THR* 3.5 14.3 + - - -
296B TYR* 2.4 41.2 + - + +
308B ALA 2.9 18.5 + - - +
309B VAL 3.7 3.8 - - - +
310B CYS 3.2 0.2 - - - -
311B ALA* 1.3 76.2 - - - +
313B VAL* 1.3 62.7 + - - +
315B ARG* 3.2 23.6 + - - -
316B ARG 3.2 3.8 + - - -
317B TRP* 2.8 51.8 + - + +
318B VAL* 4.5 2.2 - - + -
297C PHE* 4.0 5.1 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
70B LEU* 4.3 13.7 - - + -
71B ALA* 4.9 6.7 - - + -
78B TYR* 3.5 29.4 - - + +
156B ILE* 4.1 18.2 - - + -
309B VAL* 2.9 20.6 + - + +
310B CYS* 3.3 6.3 + - - +
312B ASP* 1.3 72.7 - - - +
314B ILE* 1.3 66.5 + - + +
316B ARG* 3.2 12.2 + - - +
317B TRP 4.8 0.4 - - - +
318B VAL* 3.7 24.9 - - + +
321B LEU 4.7 7.1 - - - +
322B THR* 5.5 0.3 - - - +
323B PRO* 4.2 27.0 - - + +
343B TYR* 4.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA* 4.1 14.4 - - + -
310B CYS* 2.9 31.1 + - - +
311B ALA* 4.2 6.5 - - - +
313B VAL* 1.3 76.8 - - + +
315B ARG* 1.3 56.5 + - - +
316B ARG 3.3 0.2 + - - -
323B PRO* 4.7 2.0 - - + -
341B ASN* 4.0 3.6 - - - +
343B TYR* 2.3 49.1 + - + -
359B ASN* 3.7 41.3 - - + +
361B LEU* 3.7 37.0 - - + +
376B ASN 5.9 0.9 - - - -
377B SER 5.4 2.0 - - - +
378B VAL* 4.6 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B HIS* 5.6 4.0 - - - -
311B ALA* 3.1 29.6 + - + +
312B ASP* 3.2 23.0 + - - -
313B VAL 3.3 0.4 - - - -
314B ILE* 1.3 73.9 - - + +
316B ARG* 1.3 69.0 + - - +
317B TRP* 3.2 30.5 + - + +
341B ASN* 4.0 12.6 + - - +
358B GLU* 5.1 0.2 - - - -
359B ASN* 3.4 36.8 - - - +
291C PRO* 3.9 9.0 - - - +
303C LEU* 2.4 32.5 + - - +
304C GLU* 3.0 30.7 + - - +
306C VAL 3.2 16.2 + - - -
307C SER* 5.2 3.8 - - - +
308C VAL 4.8 6.4 - - - +
----------------------------------------------------------
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