Contacts of the helix formed by residues 276 - 290 (chain D) in PDB entry 2OQH
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 GLY 276 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D HIS* 4.6 2.2 - - - -
98D ALA* 4.6 0.2 - - - -
101D ASP* 3.3 17.5 - - - -
271D VAL* 2.9 20.0 + - - +
274D TRP 3.5 2.2 + - - -
275D GLY* 1.3 79.6 - - - +
277D ILE* 1.3 64.1 + - - -
278D ALA 3.5 1.6 - - - -
279D ALA* 3.7 6.5 + - - +
280D THR* 3.0 26.7 + - - -
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Residues in contact with ILE 277 (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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101D ASP* 2.9 12.5 + - - +
102D VAL* 4.3 20.2 - - + -
105D TRP* 3.6 39.3 - - + +
116D VAL* 4.2 12.1 - - + -
120D LEU* 3.6 39.0 - - + -
271D VAL* 4.3 16.4 - - + -
276D GLY* 1.3 70.9 - - - -
278D ALA* 1.3 67.5 + - - +
280D THR* 3.1 4.3 + - - -
281D LYS* 2.9 21.7 + - + +
308D ALA* 4.8 13.2 - - + +
312D VAL* 3.9 12.8 - - + -
353D LEU* 5.4 1.1 - - + -
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Residues in contact with ALA 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D LEU* 6.1 2.7 - - + -
76D GLU* 6.6 0.2 - - - -
79D HIS* 6.1 4.0 - - + +
101D ASP* 4.7 4.1 + - - +
105D TRP* 4.4 18.2 - - + +
120D LEU* 5.9 0.2 - - - -
276D GLY 3.5 0.4 - - - -
277D ILE* 1.3 80.3 - - - +
279D ALA* 1.3 58.3 + - - +
281D LYS* 3.1 10.1 + - - +
282D ALA* 2.8 30.1 + - - +
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Residues in contact with ALA 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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79D HIS* 6.2 2.0 - - + -
252D PHE* 3.3 26.8 - - + -
274D TRP* 3.7 28.5 - - + +
275D GLY 5.1 0.9 - - - -
276D GLY* 3.7 12.0 + - - +
277D ILE 3.2 0.4 - - - -
278D ALA* 1.3 78.1 - - - +
280D THR* 1.3 57.9 + - - +
282D ALA* 3.3 6.0 + - - -
283D LEU* 2.9 24.7 + - - +
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Residues in contact with THR 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D GLY* 4.9 0.4 - - - -
270D ASP 4.1 7.6 + - - +
271D VAL* 3.5 26.8 + - + +
274D TRP* 4.6 4.8 - - - +
276D GLY 3.0 14.8 + - - -
277D ILE* 3.1 9.9 + - - -
279D ALA* 1.3 74.5 - - - +
281D LYS* 1.3 65.8 - - - +
283D LEU* 3.2 8.7 + - - +
284D ALA* 3.0 20.8 + - - +
294D MSE 3.9 19.0 - - + +
296D LEU* 4.4 12.3 - - + -
312D VAL* 3.9 24.2 - - + -
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Residues in contact with LYS 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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120D LEU* 3.1 46.2 + - + +
277D ILE* 2.9 20.1 + - + +
278D ALA* 3.5 9.9 - - - +
280D THR* 1.3 76.5 - - - +
282D ALA* 1.3 62.6 + - - +
284D ALA* 3.3 9.2 + - - +
285D ALA* 3.2 18.7 + - - +
312D VAL* 4.4 10.3 - - + -
315D SER* 3.0 27.6 + - - +
316D THR* 2.9 33.4 + - - +
317D PRO* 5.5 0.2 - - - +
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Residues in contact with ALA 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D PHE* 3.9 13.0 - - + -
278D ALA 2.8 13.2 + - - +
279D ALA* 3.4 11.4 - - - +
281D LYS* 1.3 75.5 - - - +
283D LEU* 1.3 64.7 + - - +
285D ALA* 3.1 9.7 + - - +
286D HIS* 2.8 34.6 + - + +
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Residues in contact with LEU 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D PHE* 3.8 12.1 - - + -
255D PHE* 4.4 19.3 - - + -
267D ILE* 4.2 12.1 - - + -
269D GLY* 3.9 12.6 - - - -
274D TRP* 3.6 49.4 - - + -
279D ALA 2.9 13.6 + - - +
280D THR* 3.2 11.8 + - - +
282D ALA* 1.3 75.8 - - - +
284D ALA* 1.3 62.9 + - - +
286D HIS* 3.1 4.4 + - + +
287D CYS* 2.9 35.3 + - - -
294D MSE 3.7 21.3 - - + -
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Residues in contact with ALA 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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280D THR 3.0 10.5 + - - +
281D LYS* 3.3 12.1 - - - +
283D LEU* 1.3 75.9 - - - +
285D ALA* 1.3 62.0 + - - +
287D CYS* 3.1 4.9 + - - +
288D GLU* 3.1 28.0 + - - +
294D MSE 3.5 21.7 - - - -
312D VAL* 6.5 0.4 - - + -
316D THR* 3.3 33.7 - - + -
318D VAL* 3.8 4.5 - - + +
319D LEU* 5.7 0.4 - - + -
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Residues in contact with ALA 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 LYS 3.2 7.8 + - - +
282D ALA* 3.1 12.7 + - - +
284D ALA* 1.3 80.1 - - - +
286D HIS* 1.3 63.8 + - - +
288D GLU* 3.2 15.7 + - - +
289D THR* 3.0 27.4 + - - +
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Residues in contact with HIS 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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252D PHE* 3.7 32.2 - + - -
255D PHE* 3.6 44.0 - + + -
282D ALA* 2.8 32.2 + - + -
283D LEU* 3.3 10.8 - - + +
285D ALA* 1.3 78.8 - - - +
287D CYS* 1.3 62.0 + - - +
289D THR* 3.2 9.1 + - - -
290D PHE* 3.0 29.6 + + - +
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Residues in contact with CYS 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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255D PHE* 5.1 0.2 - - - -
267D ILE* 4.1 18.4 - - - -
283D LEU* 2.9 27.2 + - - -
284D ALA 3.5 8.1 - - - +
286D HIS* 1.3 75.4 - - - +
288D GLU* 1.3 62.6 + - - +
290D PHE 3.4 0.3 + - - -
291D GLY* 3.1 3.5 + - - -
292D LEU* 2.7 58.3 + - + +
293D GLY 4.1 7.2 - - - -
294D MSE 3.9 31.6 - - + -
318D VAL* 4.7 2.7 - - + -
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Residues in contact with GLU 288 (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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284D ALA* 3.1 15.2 + - - +
285D ALA* 3.2 16.0 + - - +
287D CYS* 1.3 75.1 - - - +
289D THR* 1.3 64.2 + - - +
291D GLY* 3.3 11.9 + - - -
292D LEU 5.0 1.3 - - - -
316D THR* 6.3 0.7 - - - -
317D PRO* 4.3 12.7 - - - +
318D VAL* 4.0 33.1 + - + +
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Residues in contact with THR 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D ALA* 3.0 15.1 + - - +
286D HIS* 3.5 10.8 - - - -
288D GLU* 1.3 79.3 - - - +
290D PHE* 1.3 79.2 + - + +
291D GLY 3.5 0.7 + - - -
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Residues in contact with PHE 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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255D PHE* 3.6 23.3 - + + -
259D MSE 3.7 44.6 - - + +
286D HIS* 3.0 19.8 + + - +
288D GLU 3.3 0.2 - - - -
289D THR* 1.3 93.0 - - + +
291D GLY* 1.3 64.3 + - - +
292D LEU* 3.2 15.8 + - + +
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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