Contacts of the helix formed by residues 277 - 291 (chain B) in PDB entry 1OHV
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 277 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B LEU* 4.7 1.9 - - - +
238B GLU* 2.6 38.1 + - - -
276B ALA* 1.3 76.8 - - - +
278B ASP* 1.3 64.6 + - - +
279B ASP* 3.6 10.9 + - - +
280B PHE* 3.0 27.4 + - - +
281B PHE* 3.3 9.0 - - - -
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Residues in contact with ASP 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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276B ALA 4.9 0.7 - - - +
277B SER* 1.3 73.0 - - - +
279B ASP* 1.3 63.2 + - - +
281B PHE* 3.1 4.5 + - - +
282B ARG* 3.0 48.6 + - - +
315B HIS 3.3 17.0 - - - +
316B TRP* 3.5 22.6 + - + -
408B ARG* 2.8 45.0 + - - -
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Residues in contact with ASP 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLU* 4.7 3.8 - - - +
277B SER* 3.1 11.6 + - - +
278B ASP* 1.3 78.8 - - - +
280B PHE* 1.3 62.4 + - - +
282B ARG* 3.3 25.9 + - - +
283B LYS* 2.7 63.8 + - - +
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Residues in contact with PHE 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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185B PHE* 4.3 19.1 - + - -
220B PHE* 4.1 5.6 - + - -
221B PRO* 3.5 37.7 - - + -
238B GLU* 3.6 30.5 - - + +
241B CYS* 4.2 5.8 - - + -
242B LEU* 3.5 33.9 - - + +
276B ALA* 3.5 19.5 - - + -
277B SER* 3.0 15.5 + - - +
279B ASP* 1.3 79.5 + - - +
281B PHE* 1.3 79.5 + + - +
283B LYS* 3.4 5.1 + - - +
284B LEU* 2.9 42.8 + - + +
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Residues in contact with PHE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PHE* 3.9 16.8 - + - -
264B VAL* 3.8 23.8 - - + -
265B GLU 3.5 19.7 - - - -
266B PRO* 3.3 28.0 - - + -
276B ALA* 3.6 25.6 - - + -
277B SER 3.3 19.9 + - - -
278B ASP* 3.1 5.4 + - - +
280B PHE* 1.3 86.9 - + - +
282B ARG* 1.3 60.2 + - - +
284B LEU* 3.2 6.5 + - + +
285B ARG* 2.9 30.7 + - - +
295B PHE* 4.4 4.1 - + - -
316B TRP* 3.3 55.6 - + + +
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Residues in contact with ARG 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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278B ASP* 3.0 33.1 + - - +
279B ASP* 3.7 36.3 + - - +
281B PHE* 1.3 75.6 - - - +
283B LYS* 1.3 59.2 - - + +
285B ARG* 3.4 4.9 + - - +
286B ASP* 3.0 32.5 + - - +
315B HIS 4.5 1.6 + - - -
316B TRP* 2.8 40.7 + - + +
318B LEU* 3.6 38.3 - - + +
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Residues in contact with LYS 283 (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* 3.7 32.0 - - + +
279B ASP* 2.7 52.7 + - - +
280B PHE 3.7 0.7 - - - +
282B ARG* 1.3 73.9 - - + +
284B LEU* 1.3 61.1 + - - +
286B ASP* 3.1 12.1 + - - +
287B ILE* 2.9 33.1 + - + +
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Residues in contact with LEU 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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185B PHE* 3.6 33.7 - - + -
242B LEU* 3.8 15.2 - - + +
245B VAL* 3.9 31.2 - - + -
262B ILE* 4.7 8.3 - - + -
264B VAL* 4.1 11.4 - - + -
280B PHE* 2.9 31.5 + - + +
281B PHE* 3.2 8.5 + - + +
283B LYS* 1.3 76.5 - - - +
285B ARG* 1.3 58.2 + - - +
287B ILE* 3.2 7.6 + - + +
288B SER* 2.9 27.0 + - - -
295B PHE* 3.8 23.6 - - + -
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Residues in contact with ARG 285 (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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281B PHE 2.9 17.0 + - - +
282B ARG 3.5 6.5 - - - +
284B LEU* 1.3 77.3 - - - +
286B ASP* 1.3 62.2 + - - +
288B SER* 3.2 3.7 + - - -
289B ARG* 3.1 56.2 + - - +
295B PHE* 3.4 31.5 - - + +
316B TRP* 5.6 0.2 - - + -
318B LEU* 4.4 11.4 - - + -
320B ASP* 2.7 51.9 + - - +
321B PRO 3.4 19.7 - - - +
322B ALA* 3.7 8.8 - - - -
323B ASP* 3.1 30.9 + - - -
339B LYS* 3.6 1.0 - - - +
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Residues in contact with ASP 286 (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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282B ARG* 3.0 18.7 + - - +
283B LYS* 3.1 16.3 + - - +
285B ARG* 1.3 75.3 - - - +
287B ILE* 1.3 59.1 + - + +
289B ARG* 2.9 29.8 + - - +
290B LYS* 2.9 29.7 + - - +
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Residues in contact with ILE 287 (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* 3.7 45.5 - - + +
245B VAL* 4.2 10.5 - - + -
246B GLU* 4.0 22.2 - - + +
249B ILE* 3.9 24.7 - - + -
262B ILE* 5.0 0.9 - - + -
283B LYS* 2.9 19.8 + - + +
284B LEU* 3.2 10.7 + - + +
286B ASP* 1.3 74.0 - - + +
288B SER* 1.3 67.3 + - - +
290B LYS* 3.1 9.1 + - + -
291B HIS* 3.1 32.8 + - + +
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Residues in contact with SER 288 (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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262B ILE* 3.7 16.8 - - - +
284B LEU 2.9 12.5 + - - -
285B ARG* 3.4 10.8 - - - -
287B ILE* 1.3 78.3 - - - +
289B ARG* 1.3 60.5 + - - +
291B HIS 3.4 0.5 + - - -
292B GLY 3.2 2.6 + - - -
293B CYS* 2.8 55.4 + - - +
294B ALA 3.4 13.5 + - - -
295B PHE* 3.5 24.4 - - - +
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Residues in contact with ARG 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 ARG* 3.1 38.3 + - - +
286B ASP* 2.9 36.1 + - - +
287B ILE 3.2 0.2 - - - -
288B SER* 1.3 74.3 - - - +
290B LYS* 1.3 65.8 + - - +
292B GLY* 3.1 13.5 + - - -
293B CYS 4.6 2.2 - - - -
320B ASP* 3.2 33.5 + - - +
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Residues in contact with LYS 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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246B GLU* 2.7 35.1 + - - +
286B ASP 2.9 17.5 + - - +
287B ILE* 3.1 10.3 + - + +
289B ARG* 1.3 78.1 - - - +
291B HIS* 1.3 70.8 + - + +
292B GLY 3.7 0.3 + - - -
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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
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151B TYR* 4.2 10.4 + - - -
246B GLU* 2.6 41.4 + - + +
249B ILE* 3.8 28.4 - - + +
250B VAL* 4.2 18.1 - - + +
259B VAL 5.2 0.3 - - - +
287B ILE* 3.1 31.5 + - + +
290B LYS* 1.3 90.0 + - + +
292B GLY* 1.3 63.8 + - - +
293B CYS* 3.2 11.8 + - - -
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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