Contacts of the helix formed by residues 283 - 295 (chain B) in PDB entry 2OKC
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 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281B THR* 3.0 14.7 + - - +
282B LYS* 1.3 74.1 - - - +
284B ASN* 1.3 58.5 + - - +
285B GLN* 3.1 26.1 + - - +
286B LEU* 3.2 25.1 + - + +
287B ASN* 3.0 31.2 + - - -
309B ASN* 2.9 23.7 + - - +
313B GLU* 2.8 29.7 + - - +
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Residues in contact with ASN 284 (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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245B LEU* 3.7 19.8 - - - +
261B PRO* 3.7 22.2 - - - +
263B GLY 3.0 26.3 + - - +
264B THR* 3.7 5.3 + - - -
265B ARG* 3.5 38.7 + - + +
282B LYS 3.2 8.2 + - - +
283B ASN* 1.3 72.4 + - - +
285B GLN* 1.3 63.8 + - - +
287B ASN* 3.4 7.6 + - - +
288B PHE* 3.0 34.3 + - - -
500B SAM 5.2 3.1 + - - -
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Residues in contact with GLN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B PRO* 5.9 0.4 - - + -
261B PRO 2.8 26.5 + - - +
262B PHE 3.0 13.4 + - - +
263B GLY 2.8 29.9 + - - +
283B ASN* 3.1 12.8 + - - +
284B ASN* 1.3 82.5 + - - +
286B LEU* 1.3 60.1 + - - +
288B PHE* 3.5 7.0 + - - +
289B LEU* 3.0 27.5 + - - +
306B LEU* 4.1 12.3 - - + +
307B PRO* 3.8 28.0 - - + +
309B ASN* 5.2 4.6 - - - +
310B VAL* 3.7 19.5 - - + -
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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
----------------------------------------------------------
281B THR* 4.0 10.1 - - + +
283B ASN* 3.2 41.9 + - + +
285B GLN* 1.3 78.1 - - - +
287B ASN* 1.3 57.8 + - - +
289B LEU* 3.4 10.8 + - + +
290B GLN* 2.9 32.1 + - - +
310B VAL* 3.8 33.7 - - + +
313B GLU* 3.8 8.3 - - + +
316B ALA* 4.2 4.3 - - + -
317B GLY* 3.5 39.9 - - - +
320B ILE* 3.7 21.7 - - + +
321B ARG* 6.2 0.2 - - + -
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Residues in contact with ASN 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 3.8 17.7 - - + +
272B ILE* 3.7 19.7 - - - +
277B PHE* 3.4 17.9 - - + -
281B THR* 2.9 33.8 + - - +
282B LYS* 4.4 2.6 - - - +
283B ASN 3.0 20.0 + - - +
284B ASN* 3.7 7.3 - - - +
285B GLN 3.2 0.2 - - - -
286B LEU* 1.3 74.2 - - - +
288B PHE* 1.3 64.0 + - - +
290B GLN* 3.0 27.7 + - - +
291B HIS* 3.0 24.4 + - - +
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Residues in contact with PHE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PRO* 3.8 22.9 - - + -
178B ALA* 3.9 8.7 - - + -
244B SER* 4.0 11.9 - - - -
245B LEU* 3.9 21.8 - - + -
260B PRO* 3.8 27.8 - - + -
261B PRO* 3.7 27.6 - - + -
284B ASN* 3.0 29.3 + - - +
285B GLN* 3.8 5.6 - - - +
287B ASN* 1.3 77.4 - - - +
289B LEU* 1.3 56.1 + - - +
291B HIS* 3.4 2.6 + + - +
292B MSE 2.9 44.9 + - + +
500B SAM 3.5 44.4 - + - -
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Residues in contact with LEU 289 (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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285B GLN 3.0 18.4 + - - +
286B LEU* 3.6 9.2 - - + +
287B ASN 3.3 0.2 - - - -
288B PHE* 1.3 74.8 - - - +
290B GLN* 1.3 58.4 + - - +
292B MSE 3.3 12.6 + - + +
293B MSE 2.9 48.2 + - + +
306B LEU* 3.9 20.2 - - + -
310B VAL* 3.9 27.4 - - + -
320B ILE* 3.8 21.3 - - + -
321B ARG* 6.2 3.1 - - + -
324B LEU* 4.7 11.2 - - + -
351B LEU* 4.7 5.6 - - + -
353B PHE* 4.3 24.0 - - + -
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Residues in contact with GLN 290 (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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277B PHE* 3.2 20.6 - - + -
278B TYR* 3.0 42.6 + - + -
279B VAL* 2.8 31.6 + - - +
281B THR* 3.9 8.9 - - - +
286B LEU 2.9 18.5 + - - +
287B ASN* 3.0 31.8 + - - +
289B LEU* 1.3 75.7 - - - +
291B HIS* 1.3 61.9 + - - +
293B MSE 3.2 12.7 + - - +
294B LEU* 3.0 30.3 + - + +
320B ILE* 4.1 12.5 - - + +
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Residues in contact with HIS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PRO* 4.6 4.8 - - + +
244B SER* 3.1 42.3 + - - -
245B LEU* 4.0 11.7 - - + -
247B LYS 3.8 8.7 - - - -
249B PRO* 4.4 8.7 - - + +
274B ARG* 3.1 27.9 + - - -
277B PHE* 4.0 10.9 - - + -
287B ASN 3.0 17.5 + - - +
288B PHE* 3.5 6.5 - + - +
290B GLN* 1.3 77.1 - - - +
292B MSE 1.3 59.6 + - + +
294B LEU* 3.0 8.6 + - - +
295B MSE 3.0 63.3 + - + +
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Residues in contact with MSE 292 (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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177B PRO* 4.0 23.1 - - + -
256B ILE* 3.3 32.0 - - + +
258B ALA* 3.9 19.7 - - - -
260B PRO* 3.7 25.4 - - + -
288B PHE* 2.9 31.3 + - + +
289B LEU* 3.8 11.7 - - + +
291B HIS* 1.3 75.4 - - + +
293B MSE 1.3 66.8 + - - +
295B MSE 3.3 10.6 + - - -
296B LEU* 3.7 8.1 + - - +
304B VAL* 3.8 38.6 - - + -
306B LEU* 4.6 4.7 - - + -
353B PHE* 5.0 7.7 - - + -
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Residues in contact with MSE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B TYR* 3.3 33.4 - - + +
289B LEU* 2.9 35.7 + - + +
290B GLN* 3.5 7.0 - - - +
291B HIS 3.2 0.2 - - - -
292B MSE 1.3 77.6 - - - +
294B LEU* 1.3 55.0 + - - +
295B MSE 3.2 1.1 + - - -
296B LEU* 3.8 5.2 + - - +
320B ILE* 4.0 16.6 - - - +
323B ARG* 4.1 2.9 - - + -
324B LEU* 3.7 46.9 - - + +
328B PHE* 3.5 36.8 - - + -
353B PHE* 4.1 13.5 - - + -
355B LYS* 2.6 29.6 + - - -
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B PRO* 3.6 13.5 - - + +
252B LEU* 3.3 20.1 - - - +
274B ARG* 4.3 0.7 - - - +
276B ASP* 3.6 52.9 - - + +
277B PHE* 3.7 23.8 - - + -
278B TYR* 3.7 24.7 - - + +
290B GLN* 3.0 20.1 + - + +
291B HIS* 3.0 8.7 + - - +
293B MSE 1.3 77.4 - - - +
295B MSE 1.3 55.4 + - - +
296B LEU 3.5 0.7 - - - +
355B LYS* 4.1 7.5 + - - +
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Residues in contact with MSE 295 (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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175B CYS* 3.4 40.4 - - + -
177B PRO* 3.9 20.0 - - + -
249B PRO* 4.0 18.6 - - + -
251B THR 4.3 2.0 - - - +
252B LEU* 3.2 13.0 - - - -
253B VAL* 3.0 32.2 + - + +
256B ILE* 3.6 28.3 - - + -
291B HIS* 3.0 46.6 + - - +
292B MSE 3.6 2.7 - - - +
293B MSE 3.2 0.6 - - - -
294B LEU* 1.3 79.3 - - - +
296B LEU* 1.3 58.6 + - - +
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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
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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