Contacts of the helix formed by residues 283 - 290 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A PHE* 3.3 28.9 - - - -
252A CYS 3.4 18.8 - - - -
282A ARG* 1.3 77.3 - - - +
284A ASP* 1.3 64.2 + - - +
285A ARG 3.6 1.1 - - - -
286A TYR* 3.5 11.5 + - - +
287A LEU* 3.3 21.5 + - - +
292A PHE* 4.1 6.2 - - - -
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Residues in contact with ASP 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLU* 3.5 9.5 - - - +
251A PHE* 2.8 24.0 - - - -
282A ARG* 3.1 22.1 + - + +
283A GLY* 1.3 77.1 + - - +
285A ARG* 1.3 60.3 + - + +
286A TYR 3.0 9.8 + - - -
287A LEU* 3.1 34.5 + - + +
37B ALA 5.0 0.5 - - - +
102B ALA* 5.8 0.2 - - - +
284B ASP* 4.2 25.3 - - + +
285B ARG* 3.2 35.4 + - + +
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Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ALA 3.0 30.2 + - - -
38A GLY* 3.6 21.9 + - - -
39A SER* 4.1 2.2 - - - -
71A ASN* 3.5 21.0 + - - -
74A ILE* 3.5 37.9 - - - +
96A SER* 3.4 21.1 + - - -
98A GLU* 4.0 31.0 - - + +
99A ARG* 4.3 12.9 + - + +
102A ALA* 4.7 1.7 - - - +
281A ASP* 4.3 7.9 + - - +
282A ARG 5.1 0.4 - - - -
283A GLY 3.6 0.4 - - - -
284A ASP* 1.3 75.3 - - + +
286A TYR* 1.3 72.1 + - + +
287A LEU 3.7 0.4 - - - -
251B PHE* 5.0 3.0 - - - -
284B ASP* 3.1 47.2 + - + +
287B LEU* 4.9 0.4 - - + -
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Residues in contact with TYR 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLU* 4.0 0.2 - - - -
99A ARG* 3.7 25.0 + - - -
207A PRO* 4.7 15.6 + - + -
253A GLY* 3.5 16.6 - - - -
254A VAL* 4.1 22.2 - - + -
255A SER* 5.2 1.6 - - - -
281A ASP* 2.4 37.6 + - - -
282A ARG 2.8 29.8 - - - -
283A GLY 3.8 11.9 - - - +
284A ASP 3.0 0.8 - - - -
285A ARG* 1.3 86.3 - - + +
287A LEU* 1.3 64.3 + - - +
288A SER 3.3 0.9 - - - -
289A THR* 2.5 30.6 + - - +
291A VAL* 3.7 25.5 - - + +
292A PHE* 4.9 2.5 - - + -
320A PLP 3.7 13.9 - - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLU* 3.4 4.7 + - - +
251A PHE* 3.9 15.9 - - + -
283A GLY 3.3 13.4 + - - +
284A ASP* 3.1 39.8 + - + +
286A TYR* 1.3 79.7 - - - +
288A SER* 1.3 59.0 + - - +
289A THR 2.9 6.6 + - - -
290A GLY* 3.6 9.4 + - - -
291A VAL 4.7 1.2 + - - -
292A PHE* 4.6 19.8 + - + +
293A GLY 5.5 0.7 + - - -
294A GLU 4.4 6.6 - - - +
101B ALA* 4.6 13.3 - - + +
102B ALA* 4.1 32.1 - - + +
105B ALA* 5.7 0.2 - - + -
285B ARG* 4.8 14.8 - - + -
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Residues in contact with SER 288 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A SER* 5.2 2.8 - - - -
97A GLN* 5.7 0.5 + - - +
98A GLU* 2.3 45.5 + - - +
287A LEU* 1.3 71.0 - - - +
289A THR* 1.3 60.2 + - - +
290A GLY 3.5 1.6 - - - -
294A GLU 5.5 2.5 - - - -
288B SER* 4.9 14.4 - - - -
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Residues in contact with THR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ASN 6.0 2.0 - - - +
96A SER* 4.4 24.7 - - - -
286A TYR* 2.5 28.5 + - - +
287A LEU 2.9 1.4 + - - -
288A SER* 1.3 77.9 + - - +
290A GLY* 1.3 58.6 + - - +
291A VAL* 3.2 9.5 + - - +
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Residues in contact with GLY 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LEU 3.6 4.4 + - - -
288A SER 3.5 2.4 - - - -
289A THR* 1.3 78.1 - - - +
291A VAL* 1.3 63.3 + - - +
292A PHE 3.3 3.7 + - - -
293A GLY 3.5 11.6 + - - +
294A GLU* 3.8 32.0 + - - +
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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