Contacts of the helix formed by residues 270 - 275 (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 ASP 270 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D TYR* 3.9 7.1 + - - -
246D ASN* 4.7 0.7 - - - +
269D GLY* 1.3 76.0 - - - +
271D VAL* 1.3 66.1 + - - +
272D TYR* 3.0 27.3 + - - +
273D LYS* 2.9 26.3 + - + +
274D TRP* 2.8 29.3 + - + +
280D THR* 4.1 5.8 + - - -
296D LEU* 4.1 1.8 - - - +
297D HIS* 3.3 38.6 - - + +
299D GLY* 5.0 1.4 + - - -
301D GLU* 4.5 5.4 - - - +
309D HIS* 3.5 11.6 + - - -
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Residues in contact with VAL 271 (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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98D ALA* 3.5 3.3 - - + +
102D VAL* 3.9 24.2 - - + -
270D ASP* 1.3 70.5 - - - +
272D TYR* 1.3 69.4 + - + +
275D GLY* 2.9 26.7 + - - -
276D GLY* 2.9 32.8 + - - +
277D ILE* 3.9 11.2 - - + +
280D THR* 3.5 26.1 + - + +
308D ALA 5.4 0.9 - - - +
309D HIS* 3.0 30.9 - - + +
312D VAL* 4.4 12.1 - - + -
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Residues in contact with TYR 272 (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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33D ARG* 5.2 1.3 - - - -
49D GLU 3.2 22.4 + - - -
50D THR* 3.8 21.1 - - - +
51D MSE 5.3 7.6 - - + +
91D TYR* 3.7 7.5 - - + +
95D ALA* 3.2 30.9 + - + +
98D ALA* 3.6 16.4 - - + -
102D VAL* 4.2 13.2 - - + +
270D ASP* 3.0 16.6 + - - +
271D VAL* 1.3 87.6 - - + +
273D LYS* 1.3 57.6 + - - +
275D GLY 4.3 1.3 - - - -
301D GLU* 3.7 31.6 - - + +
305D ALA* 2.7 36.2 + - + -
308D ALA* 3.3 15.6 - - - +
309D HIS* 3.7 17.5 - + - -
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Residues in contact with LYS 273 (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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87B PHE* 4.0 21.0 - - - -
91D TYR* 3.8 41.1 + - + +
94D TYR* 3.4 24.5 - - - +
246D ASN* 2.7 56.7 + - - +
247D MSE 4.9 0.6 - - - +
250D VAL* 3.9 28.4 - - + +
270D ASP* 2.9 25.9 + - + +
272D TYR* 1.3 78.7 - - - +
274D TRP* 1.3 70.6 + - + +
275D GLY 3.4 0.9 - - - -
297D HIS* 4.4 3.2 + - - -
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Residues in contact with TRP 274 (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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94D TYR* 4.0 14.1 - - - -
246D ASN* 5.8 0.4 + - - -
249D VAL* 3.6 24.8 + - + -
250D VAL* 3.6 16.6 + - - +
251D ARG* 3.4 30.1 - - - +
252D PHE* 3.3 58.3 - + - -
255D PHE* 5.5 1.8 - + - -
267D ILE* 4.8 2.0 - - + -
268D HIS 3.9 13.7 + - - -
269D GLY* 4.6 0.9 - - - -
270D ASP* 2.8 30.0 + - + +
271D VAL 4.5 0.7 - - - +
273D LYS* 1.3 91.2 - - + +
275D GLY* 1.3 62.1 + - - +
276D GLY 3.5 1.8 + - - -
279D ALA* 3.7 21.5 - - + +
280D THR* 4.6 8.3 - - - +
283D LEU* 3.6 34.5 - - + +
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Residues in contact with GLY 275 (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* 3.0 26.4 - - - -
94D TYR* 3.4 30.7 + - - +
97D ILE* 3.4 11.4 - - - +
98D ALA* 3.6 8.9 - - - -
101D ASP* 3.9 0.5 - - - +
271D VAL 2.9 9.1 + - - -
273D LYS 3.4 3.6 + - - -
274D TRP* 1.3 78.4 - - - +
276D GLY* 1.3 55.1 + - - -
279D ALA* 5.1 0.9 - - - -
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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