Contacts of the helix formed by residues 328 - 342 (chain B) in PDB entry 1OLU
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 328 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B HIS* 5.0 11.0 - - + +
233B VAL* 4.0 6.7 - - - -
323B PRO 4.1 13.9 - - - +
326B ILE* 2.8 30.9 + - + +
327B PRO* 1.3 74.2 - - - +
329B LYS* 1.3 60.4 + - + +
330B TRP* 2.9 19.3 + - - +
331B LYS* 2.9 33.1 + - - +
332B CYS* 2.9 27.4 + - - -
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Residues in contact with LYS 329 (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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3B HIS 5.2 9.9 + - - +
233B VAL* 3.7 15.2 - - + +
236B GLU* 2.6 41.2 + - - +
237B VAL* 3.4 24.2 - - + +
240B MET* 3.9 14.7 - - - +
328B ASP* 1.3 78.4 - - + +
330B TRP* 1.3 92.2 + - + +
333B TYR* 2.7 36.5 + - - +
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Residues in contact with TRP 330 (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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240B MET* 3.4 24.7 - - + -
244B LYS* 4.3 20.4 - - + -
328B ASP* 2.9 14.8 + - - +
329B LYS* 1.3 105.4 - - + +
331B LYS* 1.3 62.7 + - + +
333B TYR* 3.9 16.6 - + - +
334B ASP* 2.9 30.3 + - - +
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Residues in contact with LYS 331 (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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310B VAL* 4.1 14.1 - - + +
313B TYR* 2.9 28.9 + - - +
323B PRO 5.6 0.7 - - - -
324B PHE* 2.8 31.6 + - - +
325B TYR 3.9 2.4 + - - -
326B ILE 3.3 22.7 + - - +
327B PRO* 4.4 1.3 - - + -
328B ASP* 2.9 29.2 + - - +
330B TRP* 1.3 75.7 - - + +
332B CYS* 1.3 64.9 + - - +
334B ASP* 3.9 4.2 - - - +
335B ALA* 3.2 23.4 + - - +
704B GOL 4.3 12.3 + - - +
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Residues in contact with CYS 332 (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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230B GLN* 3.7 5.2 - - - -
233B VAL* 4.5 4.0 - - - -
234B ILE* 4.7 6.1 - - + -
237B VAL* 3.6 22.4 - - + -
276B LEU* 3.7 9.2 - - + +
278B SER* 3.4 31.4 - - - -
310B VAL* 3.7 17.9 - - + -
327B PRO 3.5 9.9 - - - -
328B ASP 2.9 20.7 + - - +
331B LYS* 1.3 78.5 - - - +
333B TYR* 1.3 62.3 + - - +
335B ALA* 3.2 3.8 + - - +
336B LEU* 3.0 23.6 + - - +
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Residues in contact with TYR 333 (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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237B VAL* 4.1 13.4 - - + +
240B MET* 3.7 41.7 - - + -
241B ALA* 4.0 8.7 - - + -
244B LYS* 3.4 32.0 - - + +
245B LEU* 3.3 44.9 - - + +
329B LYS 2.7 23.7 + - - +
330B TRP* 3.9 16.2 - + - +
332B CYS* 1.3 73.8 - - - +
334B ASP* 1.3 61.1 + - + +
336B LEU* 3.1 5.4 + - + +
337B ARG* 2.8 43.7 + - - +
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Residues in contact with ASP 334 (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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330B TRP 2.9 20.2 + - - +
331B LYS* 3.9 5.2 - - - +
333B TYR* 1.3 80.9 - - + +
335B ALA* 1.3 61.0 + - - +
337B ARG* 3.0 33.5 + - - +
338B LYS* 3.1 52.7 + - - +
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Residues in contact with ALA 335 (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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276B LEU* 4.0 6.3 - - + -
308B SER* 4.2 10.7 + - - +
310B VAL* 3.4 33.0 - - + -
331B LYS 3.2 10.1 + - - +
332B CYS 3.2 4.2 + - - +
334B ASP* 1.3 76.3 - - - +
336B LEU* 1.3 57.1 + - - +
338B LYS* 3.3 10.6 + - - +
339B MET* 2.9 29.1 + - - +
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Residues in contact with LEU 336 (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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222B VAL* 3.7 34.5 - - + -
224B LEU* 4.3 9.6 - - + -
237B VAL* 3.8 21.8 - - + -
241B ALA* 3.8 28.0 - - + -
245B LEU* 5.4 2.5 - - + -
247B VAL* 5.2 0.4 - - + -
249B CYS* 3.9 13.0 - - - -
276B LEU* 3.7 10.0 - - + +
332B CYS 3.0 13.6 + - - +
333B TYR* 3.4 10.1 - - + +
335B ALA* 1.3 75.3 - - - +
337B ARG* 1.3 59.3 + - - +
339B MET* 3.2 10.8 + - + +
340B ILE* 2.8 46.9 + - + +
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Residues in contact with ARG 337 (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* 4.2 31.8 - - + +
333B TYR* 2.8 30.9 + - + +
334B ASP* 3.0 32.6 + - - +
336B LEU* 1.3 76.9 - - - +
338B LYS* 1.3 89.1 + - - +
340B ILE* 3.3 2.5 + - - +
341B ASN* 2.9 59.8 + - - +
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Residues in contact with LYS 338 (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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334B ASP* 3.1 36.1 + - - +
335B ALA* 3.7 7.6 - - - +
337B ARG* 1.3 101.0 - - - +
339B MET* 1.3 64.4 + - - +
341B ASN* 3.3 10.3 + - - +
342B TYR* 3.0 22.2 + - - +
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Residues in contact with MET 339 (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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222B VAL* 3.4 32.1 - - + -
274B ARG* 4.0 16.6 + - + -
275B LEU 3.3 33.4 - - - +
276B LEU* 4.0 8.5 - - + -
305B ALA* 4.0 17.2 - - + +
306B PRO* 3.5 24.2 - - + +
308B SER* 4.1 13.0 - - - +
335B ALA 2.9 16.3 + - - +
336B LEU* 3.7 14.1 - - + +
338B LYS* 1.3 72.7 - - - +
340B ILE* 1.3 66.6 + - - +
342B TYR* 3.1 22.6 + - - +
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Residues in contact with ILE 340 (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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221B ASP* 4.8 5.8 - - + +
222B VAL* 4.5 5.8 - - + -
245B LEU* 4.9 6.5 - - + -
247B VAL* 3.9 41.1 - - + -
274B ARG* 4.1 30.9 + - - +
336B LEU* 2.8 37.6 + - + +
337B ARG* 3.5 7.2 - - - +
339B MET* 1.3 77.2 - - - +
341B ASN* 1.3 68.7 + - - +
342B TYR 3.2 7.1 + - - +
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Residues in contact with ASN 341 (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* 6.2 0.2 - - - +
337B ARG* 2.9 51.2 + - - +
338B LYS* 3.6 8.4 - - - +
339B MET 3.2 0.4 - - - -
340B ILE* 1.3 82.6 - - - +
342B TYR* 1.3 65.3 + - - +
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Residues in contact with TYR 342 (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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274B ARG* 6.0 0.2 + - - -
304B GLU 3.9 11.5 - - - +
305B ALA* 3.8 21.8 - - + -
306B PRO* 3.6 31.6 - - + +
338B LYS 3.0 10.9 + - - +
339B MET* 3.1 19.8 + - - +
340B ILE 3.1 6.4 - - - +
341B ASN* 1.3 83.9 - - - +
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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