Contacts of the helix formed by residues 277 - 291 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223D LEU* 4.7 3.2 - - - +
238D GLU* 2.5 39.3 + - - -
276D ALA* 1.3 76.8 - - - +
278D ASP* 1.3 64.2 + - - +
279D ASP* 3.6 10.8 + - - +
280D PHE* 3.0 27.2 + - - +
281D PHE* 3.3 9.0 + - - -
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Residues in contact with ASP 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D ALA 3.8 1.1 + - - +
277D SER* 1.3 73.7 - - - +
279D ASP* 1.3 62.0 + - - +
281D PHE* 3.1 5.0 + - - +
282D ARG* 3.0 47.9 + - - +
315D HIS 3.3 18.1 - - - +
316D TRP* 3.5 21.6 + - + -
408D ARG* 2.8 46.3 + - - -
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Residues in contact with ASP 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D GLU* 4.7 3.8 - - - +
277D SER* 3.1 11.6 + - - +
278D ASP* 1.3 78.9 - - - +
280D PHE* 1.3 63.6 + - - +
282D ARG* 3.3 25.5 + - - +
283D LYS* 2.7 64.9 + - - +
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Residues in contact with PHE 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D PHE* 4.2 19.3 - + - -
220D PHE* 4.2 5.8 - + - -
221D PRO* 3.6 36.6 - - + -
238D GLU* 3.6 32.1 - - + +
241D CYS* 4.2 6.3 - - + -
242D LEU* 3.6 32.6 - - + +
276D ALA* 3.5 20.2 - - + -
277D SER* 3.0 16.2 + - - +
279D ASP* 1.3 79.1 + - - +
281D PHE* 1.3 78.0 + + - +
283D LYS* 3.3 6.1 + - - +
284D LEU* 2.9 42.3 + - + +
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Residues in contact with PHE 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D PHE* 3.9 15.9 - + - -
264D VAL* 3.8 24.2 - - + -
265D GLU 3.4 20.6 - - - -
266D PRO* 3.2 32.8 - - + -
276D ALA* 3.6 25.8 - - + -
277D SER 3.3 18.6 + - - -
278D ASP* 3.1 5.3 + - - +
280D PHE* 1.3 86.6 - + - +
282D ARG* 1.3 59.6 + - - +
284D LEU* 3.6 6.8 - - + +
285D ARG* 2.9 30.3 + - - +
295D PHE* 4.5 4.2 - + - -
316D TRP* 3.3 51.7 - + + +
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Residues in contact with ARG 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D ASP* 3.0 30.2 + - - +
279D ASP* 3.3 38.5 + - - +
281D PHE* 1.3 75.6 - - - +
283D LYS* 1.3 59.1 + - + +
285D ARG* 3.4 4.2 + - - +
286D ASP* 3.0 33.4 + - - +
315D HIS 4.6 1.6 + - - -
316D TRP* 2.8 41.1 + - + +
318D LEU* 3.6 38.8 - - + +
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Residues in contact with LYS 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D LEU* 3.7 32.9 - - + +
279D ASP* 2.7 50.2 + - - +
280D PHE 3.7 0.4 - - - +
282D ARG* 1.3 74.9 - - + +
284D LEU* 1.3 61.4 + - - +
286D ASP* 3.2 13.8 + - - +
287D ILE* 3.0 31.8 + - + +
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Residues in contact with LEU 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D PHE* 3.6 33.4 - - + -
242D LEU* 3.8 14.8 - - + +
245D VAL* 3.9 30.7 - - + -
262D ILE* 4.7 8.5 - - + -
264D VAL* 4.1 11.2 - - + -
280D PHE* 2.9 32.9 + - + +
281D PHE* 3.2 8.5 + - + +
283D LYS* 1.3 75.4 - - - +
285D ARG* 1.3 59.6 + - - +
287D ILE* 3.2 6.5 + - + +
288D SER* 2.9 27.2 + - - -
295D PHE* 3.8 24.0 - - + -
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Residues in contact with ARG 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D PHE 2.9 17.3 + - - +
282D ARG 3.5 5.8 - - - +
284D LEU* 1.3 77.1 - - - +
286D ASP* 1.3 61.5 + - - +
288D SER* 3.4 2.4 + - - -
289D ARG* 3.1 54.1 + - - +
293D CYS 5.1 0.2 + - - -
295D PHE* 3.4 42.7 - - + +
316D TRP* 5.6 0.2 - - + -
318D LEU* 4.4 10.5 - - + -
320D ASP* 2.8 51.5 + - - -
321D PRO 3.4 9.1 - - - +
322D ALA* 3.7 9.3 - - - -
323D ASP* 3.0 32.5 + - - -
339D LYS* 3.4 1.0 - - - +
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Residues in contact with ASP 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D ARG* 3.0 19.3 + - - +
283D LYS* 3.2 17.1 + - + +
285D ARG* 1.3 76.5 - - - +
287D ILE* 1.3 59.8 + - + +
289D ARG* 3.0 28.1 + - - +
290D LYS* 2.9 29.7 + - - +
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Residues in contact with ILE 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D LEU* 3.7 45.3 - - + +
245D VAL* 4.2 11.4 - - + -
246D GLU* 4.0 22.0 - - + +
249D ILE* 3.9 23.6 - - + -
262D ILE* 4.9 0.9 - - + -
283D LYS* 3.0 20.3 + - + +
284D LEU* 3.2 10.7 + - + +
286D ASP* 1.3 72.3 - - + +
288D SER* 1.3 67.4 + - - +
290D LYS* 3.2 9.1 + - + -
291D HIS* 3.1 32.7 + - + +
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Residues in contact with SER 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D ILE* 3.7 17.0 - - - +
284D LEU 2.9 12.9 + - - -
285D ARG* 3.5 10.3 - - - -
286D ASP 3.3 0.2 - - - -
287D ILE* 1.3 79.2 - - - +
289D ARG* 1.3 60.8 + - - +
291D HIS 3.4 0.3 + - - -
292D GLY 3.2 2.1 + - - -
293D CYS* 2.7 56.9 + - - +
294D ALA 3.4 13.3 + - - -
295D PHE* 3.5 24.2 - - - +
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Residues in contact with ARG 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D ARG* 3.1 36.0 + - - +
286D ASP* 3.0 35.7 + - - +
288D SER* 1.3 78.3 - - - +
290D LYS* 1.3 64.8 + - - +
292D GLY* 3.1 14.1 + - - +
293D CYS 4.6 2.5 - - - +
320D ASP* 3.2 34.1 + - - +
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Residues in contact with LYS 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D GLU* 2.7 34.6 + - - +
286D ASP 2.9 18.2 + - - +
287D ILE* 3.2 9.6 + - + +
289D ARG* 1.3 77.7 - - - +
291D HIS* 1.3 68.9 + - + +
292D GLY 3.7 0.3 + - - -
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Residues in contact with HIS 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D TYR* 4.3 10.0 + - - -
246D GLU* 2.6 41.1 + - + +
249D ILE* 3.7 30.7 - - + +
250D VAL* 4.1 19.9 - - + +
259D VAL 5.2 0.5 - - - +
287D ILE* 3.1 36.3 + - + +
290D LYS* 1.3 89.8 + - + +
292D GLY* 1.3 62.7 + - - +
293D 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