Contacts of the helix formed by residues 283 - 290 (chain C) in PDB entry 2BHT
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 283 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251C PHE* 2.6 42.4 + - - -
252C CYS* 3.3 19.9 - - - +
253C GLY 3.9 1.1 - - - -
282C ARG* 1.3 72.4 - - - +
284C ASP* 1.3 64.4 + - - +
285C ARG 3.1 1.1 - - - -
286C TYR* 2.8 25.3 + - - +
287C LEU 3.8 1.6 + - - -
292C PHE* 4.2 2.0 - - - -
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Residues in contact with ASP 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C GLU* 3.6 6.8 - - - +
251C PHE* 3.2 24.5 - - - -
282C ARG* 2.9 31.3 + - - +
283C GLY* 1.3 77.1 - - - +
285C ARG* 1.3 58.8 + - - +
286C TYR 3.2 0.7 + - - -
287C LEU* 3.3 21.1 - - - +
37D ALA 5.7 0.3 - - - -
38D GLY* 5.5 2.9 - - - -
99D ARG* 5.5 0.7 + - - -
282D ARG* 5.3 5.9 - - - +
284D ASP* 3.6 39.1 - - + +
285D ARG* 3.4 32.6 + - + +
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Residues in contact with ARG 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ALA 2.7 29.9 + - - -
38C GLY* 3.9 17.5 + - - -
39C SER* 4.2 1.4 - - - -
71C ASN* 2.8 32.5 + - - +
74C ILE* 3.3 30.7 - - + +
96C SER* 3.6 1.0 + - - -
98C GLU* 2.8 53.1 - - + +
99C ARG* 3.3 34.5 + - - +
102C ALA* 4.8 4.9 - - - -
281C ASP* 5.0 3.1 - - - +
282C ARG 4.1 3.7 + - - +
283C GLY 2.9 1.0 + - - -
284C ASP* 1.3 75.6 - - - +
286C TYR* 1.3 59.5 + - + +
251D PHE* 5.9 3.4 - - - -
284D ASP* 3.1 37.5 + - + +
287D LEU* 5.0 1.8 - - + -
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Residues in contact with TYR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C ARG* 3.0 32.2 + - - +
207C PRO* 3.5 36.4 + - + +
253C GLY* 3.5 23.3 - - - -
254C VAL* 3.6 29.4 + - + -
255C SER* 4.9 1.2 + - - -
281C ASP* 3.3 23.7 + - - -
282C ARG 4.1 2.7 - - - -
283C GLY 2.8 18.9 + - - +
285C ARG* 1.3 82.7 - - + +
287C LEU* 1.3 51.2 + - - +
288C SER 2.8 5.5 + - - -
289C THR* 2.5 53.6 + - + -
290C GLY 3.7 1.0 + - - -
291C VAL* 3.7 15.8 - - + +
292C PHE* 4.2 4.7 - - + -
320C PLP 3.8 8.1 - - - +
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLU* 3.7 0.4 + - - +
251C PHE* 3.8 24.9 - - + -
283C GLY 4.3 0.2 - - - +
284C ASP* 3.3 28.7 + - - +
285C ARG 3.5 2.4 - - - -
286C TYR* 1.3 76.9 - - - +
288C SER* 1.3 58.5 + - - +
290C GLY* 3.2 15.8 + - - +
292C PHE* 4.1 10.3 - - + -
98D GLU* 3.0 39.3 - - + +
99D ARG* 4.2 21.9 - - - +
101D ALA* 3.7 17.8 - - + +
102D ALA* 3.6 27.1 - - + +
285D ARG* 4.2 7.0 - - + -
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Residues in contact with SER 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C SER* 4.3 3.3 - - - -
97C GLN* 3.5 29.9 - - - +
98C GLU* 2.4 29.5 + - - -
286C TYR 2.8 1.2 + - - -
287C LEU* 1.3 78.8 - - - +
289C THR* 1.3 65.6 + - - +
290C GLY 3.3 0.2 - - - -
99D ARG* 4.1 15.6 - - - +
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Residues in contact with THR 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C SER* 4.7 14.6 - - - -
99C ARG* 5.5 0.9 - - - +
286C TYR* 2.5 43.0 + - + +
288C SER* 1.3 81.0 - - - +
290C GLY* 1.3 60.4 + - - +
291C VAL* 2.8 27.6 + - - +
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Residues in contact with GLY 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C ARG* 5.5 0.3 + - - -
286C TYR 3.7 0.4 + - - -
287C LEU 3.2 14.9 + - - -
288C SER 3.3 1.0 - - - -
289C THR* 1.3 81.1 + - - +
291C VAL* 1.3 58.3 + - - +
292C PHE* 3.0 13.8 + - - -
101D ALA* 5.8 4.0 - - - -
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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