Contacts of the helix formed by residues 272 - 287 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B LYS* 5.2 1.4 - - - -
208B VAL* 3.8 18.0 + - - +
210B GLN* 5.0 0.8 - - - +
270B TYR 3.3 7.4 - - - -
271B ASP* 1.3 79.6 + - - +
273B LEU* 1.3 58.4 + - - +
274B SER* 3.8 8.3 - - - -
275B LYS* 2.9 49.9 + - - +
276B GLN* 3.7 11.4 + - - +
328B VAL* 3.0 33.3 - - + +
330B GLU* 4.0 17.7 - - - +
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 6.0 0.2 - - + -
249B PRO* 4.6 4.9 - - + -
270B TYR* 3.9 21.5 + - + -
272B ASP* 1.3 72.1 - - - +
274B SER* 1.3 64.2 + - - +
275B LYS 3.4 0.2 - - - -
276B GLN* 3.4 28.8 + - + +
277B ALA* 3.0 17.7 + - - +
304B HIS* 3.3 40.6 + - + +
307B LEU* 4.0 22.7 - - + -
308B LEU* 4.2 14.1 - - + -
327B PRO* 3.8 22.2 - - + -
328B VAL 2.7 9.7 + - - +
329B ILE* 3.7 13.2 - - + -
344B VAL* 4.6 5.4 - - + -
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ASP* 3.1 10.6 + - - -
273B LEU* 1.3 76.6 - - - +
275B LYS* 1.3 61.6 + - - +
277B ALA* 2.9 23.6 + - - +
278B VAL* 3.0 20.8 + - - +
296B TYR* 4.9 0.2 + - - -
329B ILE* 3.4 14.4 - - - +
330B GLU* 2.8 42.6 + - - -
340B ILE* 5.0 3.8 - - - -
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Residues in contact with LYS 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 3.5 28.9 - - - +
209B GLY* 3.5 24.0 - - - +
210B GLN* 4.9 7.9 - - + +
245B GLN* 4.7 3.0 - - - +
272B ASP* 2.9 33.4 + - - +
274B SER* 1.3 79.4 - - - +
276B GLN* 1.3 63.2 + - - +
278B VAL* 3.3 9.1 + - + +
279B ALA* 2.9 24.8 + - - +
330B GLU* 4.0 15.8 + - - -
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Residues in contact with GLN 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 3.8 14.7 - - + +
245B GLN 3.6 18.6 - - - +
246B TYR* 2.8 28.8 + - - +
249B PRO* 3.6 20.7 - - + +
250B PHE* 3.6 18.6 - - - -
272B ASP 3.7 4.9 + - - +
273B LEU* 3.4 21.8 + - + +
274B SER 3.2 0.4 - - - -
275B LYS* 1.3 78.1 - - - +
277B ALA* 1.3 56.0 + - - +
279B ALA* 3.2 7.0 + - - +
280B TYR* 2.9 27.4 + - - +
303B LEU* 3.7 12.8 - - - +
304B HIS* 2.9 31.6 + - - -
307B LEU* 5.0 1.3 - - - +
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU 3.0 12.4 + - - +
274B SER 2.9 10.4 + - - +
276B GLN* 1.3 75.9 + - - +
278B VAL* 1.3 53.1 + - - +
280B TYR* 3.1 7.2 + - - +
281B ARG* 2.8 34.7 + - - +
296B TYR* 3.7 20.5 - - + +
300B VAL* 4.3 6.9 - - + +
303B LEU* 4.5 6.3 - - - -
304B HIS* 4.1 13.9 - - + +
340B ILE* 4.2 16.8 - - + -
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Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B SER* 3.0 18.8 + - - +
275B LYS* 3.8 9.9 - - + +
276B GLN 3.3 0.2 - - - -
277B ALA* 1.3 75.6 - - - +
279B ALA* 1.3 57.7 + - - +
281B ARG* 3.3 29.6 + - - +
282B GLN* 2.9 26.7 + - - +
296B TYR* 3.6 19.7 - - - +
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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
----------------------------------------------------------
242B ALA* 3.4 26.4 - - + +
245B GLN* 3.8 34.3 - - + +
246B TYR 4.5 1.3 - - - +
275B LYS 2.9 13.8 + - - +
276B GLN 3.4 8.5 - - - +
278B VAL* 1.3 76.6 - - - +
280B TYR* 1.3 56.5 + - - +
282B GLN* 3.2 9.7 + - - +
283B LEU* 3.0 24.1 + - - +
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Residues in contact with TYR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TYR* 3.5 38.3 - + + +
276B GLN 2.9 16.0 + - - +
277B ALA 3.7 2.9 - - - +
279B ALA* 1.3 72.8 - - - +
281B ARG* 1.3 56.1 + - - +
283B LEU* 3.9 19.1 - - + -
284B SER* 2.6 45.7 + - - -
289B ARG* 3.6 15.4 + - - -
297B PRO* 3.8 15.9 - - + -
299B ASP* 2.5 42.4 + - - -
300B VAL* 4.4 6.3 - - + -
303B LEU* 3.5 42.6 - - + -
306B ARG* 5.6 1.4 + - - -
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Residues in contact with ARG 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA 2.8 13.0 + - - +
278B VAL* 3.4 31.3 + - - +
280B TYR* 1.3 76.5 - - - +
282B GLN* 1.3 65.1 + - - +
284B SER* 3.7 0.2 - - - -
285B LEU* 2.9 43.2 + - + +
294B GLU* 3.0 21.4 + - - +
295B ALA* 3.3 31.8 - - - +
296B TYR* 3.3 40.8 + - + -
297B PRO* 3.9 10.7 - - + +
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Residues in contact with GLN 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ALA* 3.4 25.6 - - + +
243B PRO* 5.7 0.2 - - - +
278B VAL* 2.9 13.4 + - + +
279B ALA* 3.2 12.9 + - - +
281B ARG* 1.3 76.5 - - - +
283B LEU* 1.3 63.5 + - - +
285B LEU* 4.1 3.6 - - - +
286B LEU* 3.1 50.8 + - + +
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 4.9 2.8 - - + +
64B MET* 5.7 0.7 - - + -
66B LEU* 4.8 7.6 - - + -
76B VAL* 4.2 17.9 - - + -
242B ALA* 4.6 4.5 - - + +
243B PRO* 4.0 30.1 - - + -
246B TYR* 3.7 39.9 - - + -
279B ALA 3.0 13.7 + - - +
280B TYR* 3.7 20.0 - - + +
281B ARG 3.3 0.2 - - - -
282B GLN* 1.3 77.7 - - - +
284B SER* 1.3 62.9 + - - +
286B LEU* 3.6 5.8 + - - +
287B LEU* 3.1 44.7 + - + +
289B ARG* 5.3 1.8 - - - +
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Residues in contact with SER 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B TYR* 2.6 35.4 + - - -
281B ARG 3.2 4.2 + - - -
283B LEU* 1.3 77.0 - - - +
285B LEU* 1.3 59.9 + - - +
287B LEU* 3.1 19.8 + - - +
288B ARG 3.2 0.2 + - - -
289B ARG* 3.1 40.3 + - - +
297B PRO* 3.2 35.7 - - - +
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ARG* 2.9 29.7 + - + +
282B GLN* 4.1 4.0 - - - +
284B SER* 1.3 73.8 - - - +
286B LEU* 1.3 63.8 + - + +
287B LEU 3.1 2.0 - - - -
288B ARG* 2.9 20.5 + - - +
289B ARG 3.8 7.2 - - - +
291B PRO* 3.7 40.2 - - + -
295B ALA* 3.7 29.4 - - + +
297B PRO* 5.9 1.1 - - + -
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP* 3.8 56.6 - - + +
40B ILE* 4.3 10.8 - - + +
282B GLN* 3.1 45.0 + - + +
283B LEU* 4.0 5.6 - - - +
285B LEU* 1.3 76.2 - - + +
287B LEU* 1.3 58.9 + - - +
288B ARG* 3.2 6.4 + - - +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 3.8 29.6 - - + -
66B LEU* 4.2 10.5 - - + -
67B ILE* 3.8 29.2 - - + -
76B VAL* 4.5 3.4 - - + -
283B LEU* 3.1 30.7 + - + +
284B SER 3.1 11.3 + - - +
285B LEU 3.1 0.6 - - - -
286B LEU* 1.3 77.3 - - - +
288B ARG* 1.3 69.3 + - - +
289B ARG* 3.3 39.6 + - + +
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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