Contacts of the helix formed by residues 267 - 282 (chain C) in PDB entry 2OFJ
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 SER 267 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C TRP* 4.0 6.4 - - - -
11C ILE* 3.4 29.2 - - - -
31C TYR* 2.5 30.7 + - - -
44C GLU* 2.5 34.3 + - - -
266C GLU* 1.3 74.8 - - - +
268C SER* 1.3 66.1 + - - +
269C LEU 3.6 2.4 + - - -
270C GLY 3.0 3.6 + - - -
271C LEU* 2.9 21.4 + - - +
292C LEU* 4.9 0.2 - - - -
295C MET* 4.4 4.2 - - - +
299C GLN* 4.9 0.7 - - - -
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Residues in contact with SER 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 5.3 0.2 - - - +
267C SER* 1.3 71.8 - - - +
269C LEU* 1.3 50.7 + - - +
271C LEU* 3.5 8.6 - - - +
272C THR* 2.7 40.4 + - - +
292C LEU* 3.9 21.9 - - - +
295C MET* 5.2 0.2 - - - -
297C ALA 5.4 0.2 + - - -
298C GLN* 3.3 21.8 - - - +
299C GLN 2.7 32.4 + - - +
301C ARG 2.8 21.9 + - - -
303C TRP* 4.5 4.5 - - - -
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TYR* 3.6 31.9 - - + -
42C TRP* 4.0 27.4 - - + -
43C GLY 4.5 9.9 - - - +
44C GLU 4.7 0.7 - - - +
267C SER* 3.0 10.6 + - - +
268C SER* 1.3 80.8 + - - +
270C GLY* 1.3 61.1 + - - +
272C THR* 2.7 20.4 + - - -
273C GLN* 3.1 19.6 + - - +
299C GLN 4.0 5.4 - - - +
300C VAL* 3.6 14.6 - - + -
301C ARG* 3.3 54.5 - - + +
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Residues in contact with GLY 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 2.9 34.1 + - - +
85C PHE* 5.4 4.4 - - - -
266C GLU* 4.0 11.2 - - - -
267C SER 3.0 0.6 + - - -
269C LEU* 1.3 75.4 - - - +
271C LEU* 1.3 56.9 + - - +
273C GLN* 3.4 10.7 + - - +
274C LEU* 2.9 35.2 + - - +
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Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C SER* 3.5 16.6 - - - +
266C GLU* 3.4 35.9 - - + +
267C SER 2.9 14.8 + - - +
268C SER* 3.5 9.2 - - - +
270C GLY* 1.3 73.6 - - - +
272C THR* 1.3 65.6 + - - +
274C LEU* 3.1 11.3 + - + +
275C ALA* 2.9 23.0 + - - +
289C LEU* 3.8 22.7 - - + +
291C THR* 3.9 8.5 - - - +
292C LEU* 3.7 40.4 - - + +
303C TRP* 3.7 16.1 - - + -
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Residues in contact with THR 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ALA* 4.6 0.9 - - - +
104C TYR* 4.7 9.5 + - + +
268C SER 2.7 26.2 + - - +
269C LEU* 2.7 24.3 + - - -
271C LEU* 1.3 73.1 - - - +
273C GLN* 1.3 60.6 + - - +
275C ALA* 3.3 10.9 - - - +
276C ARG* 3.1 28.7 + - - +
301C ARG* 3.8 19.7 - - + +
302C ARG 3.6 31.0 - - - +
303C TRP* 4.0 16.8 - - + -
304C PRO* 4.7 4.0 - - + -
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Residues in contact with GLN 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TRP 2.8 22.2 + - - +
43C GLY* 3.9 10.9 - - - -
44C GLU 4.0 6.9 - - - +
85C PHE* 5.8 2.7 - - + -
89C CYS* 3.8 25.3 - - - +
93C GLU* 2.7 24.9 - - - +
98C LEU* 4.3 8.0 - - + +
269C LEU* 3.1 24.6 + - - +
270C GLY* 3.7 10.2 - - - +
271C LEU 3.1 0.2 - - - -
272C THR* 1.3 76.4 + - - +
274C LEU* 1.3 58.6 + - - +
276C ARG* 3.1 13.9 + - - +
277C ILE* 2.8 38.4 + - + +
301C ARG* 3.7 18.3 + - - +
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Residues in contact with LEU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PHE* 3.6 22.4 - - + -
236C PRO* 3.5 34.3 - - + -
261C ILE* 4.0 9.8 - - + +
262C SER 4.3 1.6 - - - +
263C SER* 4.2 4.3 - - - -
266C GLU* 3.2 36.1 - - - +
270C GLY 2.9 22.6 + - - +
271C LEU* 3.1 8.9 + - + +
273C GLN* 1.3 72.7 - - - +
275C ALA* 1.3 56.9 + - - +
277C ILE* 3.6 6.9 - - + +
278C ALA* 2.8 35.7 + - - +
289C LEU* 3.5 31.9 - - + +
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Residues in contact with ALA 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ALA* 3.8 3.8 - - + -
103C ASN 3.2 31.3 + - - +
104C TYR* 3.9 13.9 - - + -
271C LEU 2.9 12.4 + - - +
272C THR 3.3 11.0 - - - +
274C LEU* 1.3 77.8 - - - +
276C ARG* 1.3 55.7 + - - +
278C ALA* 3.6 3.9 - - - +
279C ALA 3.1 20.4 + - - -
289C LEU* 3.4 8.6 - - - +
303C TRP* 3.8 20.2 - - + -
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Residues in contact with ARG 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C GLU* 2.9 31.2 + - - +
98C LEU* 3.1 47.7 + - + +
99C PRO 3.1 16.2 + - - +
100C GLN* 3.6 37.4 + - - +
101C ALA 3.5 13.9 - - - +
102C ALA* 3.5 19.3 - - + -
104C TYR* 5.3 3.4 - - - -
272C THR* 3.1 15.0 + - - +
273C GLN* 3.1 13.4 + - - +
275C ALA* 1.3 75.1 - - - +
277C ILE* 1.3 60.7 + - - +
279C ALA* 3.4 2.9 + - - +
280C TRP* 3.0 28.6 + - - +
301C ARG* 3.4 14.5 - - - +
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Residues in contact with ILE 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PHE* 4.0 19.7 - - + -
89C CYS* 4.0 9.9 - - - -
98C LEU* 3.7 18.8 - - + -
236C PRO* 5.3 1.8 - - + -
242C LEU* 3.4 30.5 - - + -
245C VAL* 4.5 6.7 - - + -
261C ILE* 4.3 20.2 - - + -
273C GLN* 2.8 29.3 + - + +
274C LEU* 3.7 8.1 - - + +
276C ARG* 1.3 69.3 - - - +
278C ALA* 1.3 61.6 + - - +
280C TRP* 3.2 8.1 + - + +
281C LEU* 2.9 50.1 + - + +
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Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ASN* 4.8 3.6 - - + -
261C ILE* 4.2 9.1 - - + +
274C LEU 2.8 21.3 + - - +
275C ALA 3.6 6.1 - - - +
277C ILE* 1.3 73.1 - - - +
279C ALA* 1.3 60.1 + - - +
280C TRP 3.0 0.2 + - - -
282C THR* 2.7 51.8 + - - +
285C THR 4.8 1.1 - - - +
287C PRO* 3.7 34.1 - - + -
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Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C PRO* 5.9 0.2 - - - -
101C ALA* 3.3 33.7 - - + +
102C ALA* 3.6 2.9 - - - -
103C ASN* 3.4 29.0 - - + +
275C ALA 3.1 4.0 + - - -
276C ARG 3.4 2.2 + - - +
278C ALA* 1.3 77.5 - - - +
280C TRP* 1.3 61.2 + - - +
283C PRO* 3.3 28.1 - - - +
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Residues in contact with TRP 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ALA* 5.8 0.4 - - + -
97C THR* 3.9 26.2 + - - -
98C LEU* 4.0 21.1 - - + -
99C PRO* 3.8 24.3 - - + +
242C LEU* 4.1 31.2 - - + -
243C GLU* 5.8 1.6 - - - -
246C ARG* 3.5 36.8 - - - -
276C ARG 3.0 17.1 + - - +
277C ILE* 3.4 7.6 - - + +
278C ALA 3.1 0.2 - - - -
279C ALA* 1.3 79.1 - - - +
281C LEU* 1.3 83.3 + - + +
283C PRO* 3.5 8.3 - - - +
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Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU* 4.7 3.1 - - + +
245C VAL* 3.7 30.7 - - + -
246C ARG* 3.9 39.5 - - + +
249C VAL* 3.5 25.8 - - + +
253C HIS* 3.5 8.7 - - - -
261C ILE* 5.0 1.1 - - + -
277C ILE* 2.9 27.3 + - + +
280C TRP* 1.3 110.7 - - + +
282C THR* 1.3 66.4 + - + +
283C PRO* 3.3 8.3 - - - +
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Residues in contact with THR 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ASN* 5.0 0.5 + - - -
249C VAL* 4.1 17.5 - - + -
253C HIS* 4.3 4.3 - - + +
259C ALA* 3.2 32.4 + - + +
261C ILE* 3.9 17.8 + - + +
278C ALA* 2.7 34.0 + - - +
281C LEU* 1.3 79.9 - - - +
283C PRO* 1.3 63.1 - - - +
284C ASP* 2.9 20.9 + - - -
285C THR* 2.9 24.1 + - - +
287C PRO* 5.7 0.2 - - - +
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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) + - + + + + + -
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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