Contacts of the helix formed by residues 272 - 287 (chain A) in PDB entry 3OFN
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 ASP 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A LYS* 5.5 2.1 - - - -
208A VAL* 3.9 13.2 + - - +
270A TYR 3.3 5.6 - - - -
271A ASP* 1.3 86.9 + - - +
273A LEU* 1.3 63.3 + - - +
274A SER* 3.2 10.3 + - - -
275A LYS* 2.8 64.4 + - - +
276A GLN* 3.4 13.5 + - - +
328A VAL* 3.2 21.9 - - + +
329A ILE* 4.8 0.2 - - - -
330A GLU* 4.7 9.8 - - - +
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A PRO* 4.0 11.9 - - + -
270A TYR* 3.8 21.1 + - + -
272A ASP* 1.3 71.9 - - - +
274A SER* 1.3 64.2 + - - +
276A GLN* 3.5 23.8 - - + +
277A ALA* 3.3 16.6 + - - +
304A HIS* 3.3 32.2 + - + +
307A LEU* 3.7 27.1 - - + -
308A LEU* 4.3 11.7 - - + -
327A PRO* 3.7 25.8 - - + -
328A VAL 2.8 8.0 + - - +
329A ILE* 3.5 15.7 - - + -
344A VAL* 4.8 6.3 - - + -
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Residues in contact with SER 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ASP* 3.2 8.7 - - - -
273A LEU* 1.3 80.5 - - - +
275A LYS* 1.3 63.7 + - - +
277A ALA* 3.4 5.8 + - - +
278A VAL* 3.3 25.2 + - - +
296A TYR* 5.2 0.7 + - - -
328A VAL 3.9 0.4 + - - -
329A ILE* 3.4 15.7 - - - +
330A GLU* 3.1 44.2 + - - -
340A ILE* 5.1 5.5 - - - +
341A PRO* 5.9 0.3 - - - +
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A VAL* 3.0 33.1 - - + +
209A GLY* 3.5 24.2 - - - +
210A GLN* 4.6 5.8 - - + +
245A GLN* 4.8 2.1 - - - +
272A ASP* 2.8 34.6 + - - +
274A SER* 1.3 77.4 - - - +
276A GLN* 1.3 62.1 + - - +
277A ALA 3.3 0.2 - - - -
278A VAL* 3.5 11.0 + - + +
279A ALA* 3.1 20.3 + - - +
330A GLU* 4.9 13.7 + - - -
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Residues in contact with GLN 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A VAL* 3.8 17.1 - - + +
245A GLN 3.6 15.3 - - - +
246A TYR* 3.2 24.5 + - + +
249A PRO* 3.2 26.7 - - + +
250A PHE* 3.4 23.8 - - - -
272A ASP 3.4 9.5 + - - +
273A LEU* 3.5 9.9 - - - +
274A SER 3.4 0.4 - - - -
275A LYS* 1.3 77.5 - - - +
277A ALA* 1.3 57.1 + - - +
279A ALA* 2.9 7.1 + - - +
280A TYR* 2.8 26.2 + - - +
303A LEU* 3.5 11.1 - - + +
304A HIS* 3.0 32.7 + - - -
307A LEU* 4.9 1.0 - - - +
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A LEU 3.3 15.8 + - - +
274A SER 3.5 6.1 - - - +
275A LYS 3.3 0.2 - - - -
276A GLN* 1.3 78.3 + - - +
278A VAL* 1.3 56.3 + - - +
280A TYR* 3.3 2.5 + - - +
281A ARG 2.9 24.1 + - - -
296A TYR* 3.5 24.6 - - + -
300A VAL* 4.5 6.7 - - + +
303A LEU* 4.2 13.5 - - + -
304A HIS* 3.9 15.9 - - + -
340A ILE* 4.5 11.7 - - + -
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A SER 3.3 17.7 + - - +
275A LYS* 3.6 11.0 - - + +
276A GLN 3.2 0.6 - - - -
277A ALA* 1.3 75.7 - - - +
279A ALA* 1.3 63.9 + - - +
281A ARG* 3.3 24.5 + - - +
282A GLN* 3.0 22.0 + - + +
296A TYR* 4.1 20.2 - - - +
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ALA* 3.6 21.8 - - - +
245A GLN* 3.7 35.4 - - + +
246A TYR* 4.0 6.3 - - - +
275A LYS 3.1 11.9 + - - +
276A GLN 2.9 10.7 + - - +
278A VAL* 1.3 76.0 - - - +
280A TYR* 1.3 62.6 + - - +
282A GLN* 3.2 20.7 + - - +
283A LEU* 3.4 8.0 + - - +
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Residues in contact with TYR 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A TYR* 3.4 40.6 - + + +
276A GLN 2.8 12.7 + - - +
277A ALA 3.6 6.5 - - - +
278A VAL 3.2 0.2 - - - -
279A ALA* 1.3 73.8 - - - +
281A ARG* 1.3 66.9 + - - +
282A GLN 3.1 0.7 + - - -
283A LEU* 3.3 16.2 + - + +
284A SER* 3.2 32.7 + - - -
289A ARG* 3.6 22.0 + - - -
297A PRO* 3.0 33.4 - - + -
299A ASP* 3.1 30.9 + - - -
300A VAL* 4.6 5.8 - - + -
303A LEU* 3.7 36.6 - - + -
306A ARG* 5.4 3.2 + - - -
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Residues in contact with ARG 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ALA 2.9 14.1 + - - +
278A VAL* 3.3 31.1 + - - +
280A TYR* 1.3 76.1 - - - +
282A GLN* 1.3 63.0 + - - +
284A SER* 3.3 1.2 + - - -
285A LEU* 2.9 40.1 + - + +
294A GLU* 2.8 30.7 + - - +
295A ALA* 3.3 34.1 - - - +
296A TYR* 3.6 35.5 + - + -
297A PRO* 3.7 12.7 - - + +
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Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ALA* 3.5 26.3 + - + +
278A VAL* 3.0 13.8 + - + +
279A ALA* 3.4 12.6 - - - +
280A TYR 3.1 0.6 - - - -
281A ARG* 1.3 80.6 - - - +
283A LEU* 1.3 65.6 + - - +
285A LEU* 4.0 4.9 - - - +
286A LEU* 3.1 42.7 + - + +
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 4.7 1.5 - - - +
66A LEU* 3.9 21.8 - - + -
76A VAL* 4.5 9.4 - - + -
242A ALA* 3.9 5.8 - - + +
243A PRO* 3.4 46.4 - - + -
246A TYR* 4.0 25.8 - - + -
279A ALA 3.4 5.6 + - - +
280A TYR* 3.6 24.0 - - + +
282A GLN* 1.3 76.4 - - - +
284A SER* 1.3 56.3 + - - +
286A LEU* 3.0 8.3 + - - +
287A LEU* 2.7 48.9 + - + +
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A TYR* 3.2 17.9 + - - -
281A ARG 3.3 6.4 + - - -
282A GLN 3.2 0.6 - - - -
283A LEU* 1.3 74.6 - - - +
285A LEU* 1.3 67.8 + - - +
287A LEU* 3.3 4.3 + - - -
288A ARG 3.1 3.5 + - - -
289A ARG* 3.0 57.3 + - - +
290A PRO 5.9 0.9 - - - -
297A PRO* 3.6 33.2 - - - +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ARG* 2.9 43.4 + - + +
282A GLN* 4.0 4.5 - - - +
284A SER* 1.3 76.1 - - - +
286A LEU* 1.3 62.0 + - + +
288A ARG* 3.3 20.4 + - - +
289A ARG 5.0 2.9 - - - +
291A PRO* 4.3 18.6 - - + -
295A ALA* 3.7 30.5 - - + +
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP* 3.0 59.4 - - + +
40A ILE* 3.9 16.4 - - + +
282A GLN* 3.1 45.4 + - + +
283A LEU* 3.0 6.3 + - - +
285A LEU* 1.3 78.6 - - + +
287A LEU* 1.3 59.2 + - - +
288A ARG* 3.0 12.5 + - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 3.8 35.7 - - + -
66A LEU* 4.2 19.7 - - + -
67A ILE* 3.7 38.2 - - + +
74A GLY* 4.9 8.7 - - - -
76A VAL* 4.0 19.7 - - + -
283A LEU* 2.7 26.9 + - + +
284A SER* 4.0 7.2 - - - +
286A LEU* 1.3 71.6 - - - +
288A ARG* 1.3 68.3 + - - +
289A ARG* 3.3 16.0 + - + +
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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