Contacts of the helix formed by residues 267 - 282 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TRP* 3.9 5.8 - - - -
11B ILE* 3.5 24.7 - - - -
31B TYR* 2.6 29.6 + - - -
44B GLU* 2.9 26.3 + - - -
265B ILE 4.0 0.2 + - - -
266B GLU* 1.3 77.9 - - - +
268B SER* 1.3 68.1 + - - +
269B LEU 3.2 5.2 + - - -
270B GLY 3.2 2.1 + - - -
271B LEU* 3.0 16.6 + - - +
295B MET* 3.6 14.3 - - - +
299B GLN* 4.4 1.1 - - - -
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Residues in contact with SER 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B SER* 1.3 72.5 - - - +
269B LEU* 1.3 55.0 + - - +
271B LEU* 3.4 13.2 + - - +
272B THR* 2.9 35.9 + - - +
292B LEU* 4.3 14.6 - - - +
297B ALA 5.5 0.6 + - - -
298B GLN* 3.9 25.7 - - - +
299B GLN 2.9 30.7 + - - +
301B ARG 2.8 26.6 + - - -
303B TRP* 4.8 3.6 - - - -
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TYR* 3.9 15.5 - - + -
42B TRP* 4.0 26.7 - - + -
43B GLY 4.5 11.4 - - - +
44B GLU* 4.6 0.7 - - + -
267B SER* 3.2 10.5 + - - +
268B SER* 1.3 79.8 + - - +
270B GLY* 1.3 61.8 + - - +
272B THR* 2.7 22.5 + - - -
273B GLN* 3.2 42.1 + - + +
299B GLN 3.9 5.6 - - - +
300B VAL* 3.2 44.0 - - + -
301B ARG* 3.9 20.2 - - + +
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Residues in contact with GLY 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLU* 2.9 30.5 + - - -
85B PHE* 5.1 4.5 - - - -
266B GLU* 4.1 11.7 - - - -
267B SER 3.2 1.1 + - - -
269B LEU* 1.3 70.6 - - - +
271B LEU* 1.3 60.4 + - - +
273B GLN* 3.2 15.2 + - - +
274B LEU* 2.9 34.7 + - - +
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B SER* 3.8 7.9 - - - +
266B GLU* 3.3 38.5 - - - +
267B SER 3.0 18.6 + - - +
268B SER* 3.8 12.1 - - - +
270B GLY* 1.3 75.7 - - - +
272B THR* 1.3 57.6 + - - +
274B LEU* 3.3 8.8 + - + +
275B ALA* 2.9 28.8 + - - +
289B LEU* 3.8 13.4 - - + +
291B THR* 3.7 19.1 - - - +
292B LEU* 3.6 40.8 - - + +
303B TRP* 3.5 18.5 - - + -
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Residues in contact with THR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ALA* 4.5 1.0 - - - +
104B TYR* 4.7 11.2 - - + +
268B SER 2.9 20.7 + - - +
269B LEU* 2.7 23.2 + - - -
271B LEU* 1.3 74.3 - - - +
273B GLN* 1.3 57.4 + - - +
275B ALA* 3.4 9.6 - - - +
276B ARG* 3.0 34.5 + - - +
301B ARG* 4.0 17.1 + - + +
302B ARG 3.4 30.1 - - - +
303B TRP* 3.9 18.4 - - + -
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Residues in contact with GLN 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B TRP 2.8 24.9 + - - -
44B GLU* 4.0 9.9 + - - +
85B PHE* 5.2 3.3 - - + -
89B CYS* 3.7 27.5 - - - +
93B GLU* 2.7 30.2 + - - +
98B LEU* 4.4 8.7 - - + +
269B LEU* 3.2 30.3 + - - +
270B GLY* 3.6 11.3 - - - +
272B THR* 1.3 73.8 + - - +
274B LEU* 1.3 56.1 + - - +
276B ARG* 3.2 13.5 + - - +
277B ILE* 2.8 40.4 + - + +
301B ARG* 3.9 9.4 - - - +
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B PHE* 3.9 17.3 - - + -
236B PRO* 3.3 34.8 - - + -
261B ILE* 3.8 13.7 - - + +
262B SER 3.9 7.2 - - - +
266B GLU* 3.4 39.7 - - + +
270B GLY 2.9 18.0 + - - +
271B LEU* 3.5 8.5 - - - +
273B GLN* 1.3 70.9 - - - +
275B ALA* 1.3 57.4 + - - +
277B ILE* 3.2 7.6 + - + +
278B ALA* 2.7 35.3 + - - +
289B LEU* 3.5 29.2 - - + -
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Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ALA* 3.9 11.2 - - + -
103B ASN 3.1 38.2 + - - +
104B TYR* 4.2 3.6 - - + -
271B LEU 2.9 17.2 + - - +
272B THR* 3.4 7.9 - - - +
274B LEU* 1.3 75.4 - - - +
276B ARG* 1.3 58.5 + - - +
278B ALA* 3.3 4.6 - - - +
279B ALA 3.2 12.0 + - - -
289B LEU* 3.3 11.1 - - + +
303B TRP* 3.8 17.7 - - + -
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Residues in contact with ARG 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B GLU* 3.2 31.3 + - - +
98B LEU* 2.6 50.1 + - + +
99B PRO* 2.7 21.4 + - - +
100B GLN* 3.7 27.2 - - - +
101B ALA 3.4 24.8 - - - +
102B ALA* 3.7 9.9 - - + -
104B TYR* 5.1 0.4 - - - +
272B THR* 3.0 24.1 + - - +
273B GLN* 3.4 11.5 - - - +
274B LEU 3.1 0.6 - - - -
275B ALA* 1.3 74.6 - - - +
277B ILE* 1.3 59.4 + - - +
279B ALA 3.6 0.3 + - - -
280B TRP* 3.1 28.1 + - - +
301B ARG* 3.4 13.7 - - - +
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Residues in contact with ILE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B PHE* 4.0 24.7 - - + -
89B CYS* 4.3 9.0 - - - -
98B LEU* 3.8 17.3 - - + -
236B PRO* 5.5 1.3 - - + -
242B LEU* 3.5 28.9 - - + -
245B VAL* 4.5 4.3 - - + -
261B ILE* 4.2 21.3 - - + -
273B GLN* 2.8 29.4 + - + +
274B LEU* 3.6 10.1 - - + +
276B ARG* 1.3 69.5 - - - +
278B ALA* 1.3 60.2 + - - +
280B TRP* 4.3 3.1 - - - -
281B LEU* 2.8 54.1 + - + +
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ASN* 4.3 4.3 - - + -
261B ILE* 4.1 7.4 - - + +
274B LEU 2.7 17.5 + - - +
275B ALA 3.3 11.2 - - - +
276B ARG 3.2 0.2 - - - -
277B ILE* 1.3 72.5 - - - +
279B ALA* 1.3 60.3 + - - +
282B THR* 2.6 52.3 + - - +
285B THR 4.6 1.3 - - - +
287B PRO* 3.8 33.7 - - + -
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ALA* 4.0 15.0 - - + +
102B ALA* 3.9 15.7 - - - +
103B ASN* 3.8 27.3 - - + +
275B ALA 3.2 3.2 + - - +
276B ARG 3.6 0.4 + - - +
278B ALA* 1.3 78.1 - - - +
280B TRP* 1.3 61.2 + - - +
283B PRO* 3.3 30.2 - - - +
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Residues in contact with TRP 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ALA* 6.2 0.7 - - + -
97B THR* 3.9 26.7 + - - -
98B LEU* 3.8 23.8 - - + -
99B PRO* 4.0 25.5 - - + +
242B LEU* 4.2 26.2 - - + -
246B ARG* 3.4 42.5 - - - +
276B ARG 3.1 17.6 + - - +
277B ILE* 3.7 3.6 - - - +
279B ALA* 1.3 80.5 - - - +
281B LEU* 1.3 81.3 + - + +
283B PRO* 4.2 5.2 - - - +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B LEU* 4.4 8.5 - - + -
245B VAL* 4.1 12.3 - - + -
246B ARG* 3.7 58.3 - - + +
249B VAL* 3.8 20.1 - - + +
250B GLN* 6.1 0.2 - - + -
253B HIS* 3.5 17.3 - - - -
261B ILE* 5.1 0.4 - - + -
277B ILE* 2.8 42.0 + - + +
280B TRP* 1.3 92.1 - - + +
282B THR* 1.3 60.8 + - + +
283B PRO* 3.1 13.2 - - - +
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Residues in contact with THR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ASN* 5.1 0.2 - - - +
249B VAL* 3.9 25.1 - - + -
253B HIS* 4.3 7.0 - - - +
259B ALA* 3.3 32.7 + - + +
261B ILE* 3.8 15.6 + - + +
278B ALA* 2.6 32.5 + - - +
281B LEU* 1.3 75.1 - - - +
283B PRO* 1.3 66.5 - - - +
284B ASP 3.4 2.0 - - - -
285B THR* 2.8 34.4 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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