Contacts of the helix formed by residues 282 - 290 (chain B) 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 ARG 282 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLY 3.3 12.5 + - - -
34A ASN* 3.0 27.1 + - - +
35A ASN 3.3 19.5 + - - -
36A PRO* 4.1 12.9 + - - +
37A ALA 6.2 0.2 - - - -
38A GLY* 3.6 9.1 - - - -
282A ARG* 3.6 26.8 - - - +
33B GLY* 3.5 24.8 + - - -
34B ASN* 3.2 30.3 - - - +
38B GLY* 4.0 4.7 + - - +
251B PHE* 3.5 17.0 - - + +
252B CYS* 3.7 0.4 - - - -
253B GLY 3.9 0.4 - - - -
279B ILE* 5.6 1.1 - - + -
281B ASP* 1.3 79.0 - - - +
283B GLY* 1.3 59.9 + - - +
284B ASP* 3.1 25.5 + - + +
285B ARG* 4.3 5.7 + - - +
286B TYR* 3.8 12.1 - - - -
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Residues in contact with GLY 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B PHE* 3.3 25.3 + - - -
252B CYS* 3.2 31.8 - - - +
253B GLY 3.7 1.3 - - - -
282B ARG* 1.3 73.1 - - - +
284B ASP* 1.3 58.2 + - - +
285B ARG 3.3 1.6 - - - -
286B TYR* 3.0 29.5 + - - +
287B LEU 3.5 4.7 + - - -
292B PHE* 3.6 3.7 - - - -
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Residues in contact with ASP 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLY* 5.9 0.7 - - - -
98A GLU* 3.9 12.0 - - - +
102A ALA* 4.8 0.5 - - - +
284A ASP* 4.2 24.3 - - + +
285A ARG* 3.1 49.9 + - + +
251B PHE* 3.2 27.5 - - - -
282B ARG* 3.1 18.8 + - + +
283B GLY* 1.3 78.7 - - - +
285B ARG* 1.3 59.7 + - + +
286B TYR 3.0 4.2 + - - -
287B LEU* 3.6 21.6 + - - +
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Residues in contact with ARG 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 5.6 0.7 - - - -
251A PHE* 5.5 2.8 - - - -
284A ASP* 3.2 29.8 + - - +
287A LEU* 4.8 13.0 - - + -
37B ALA 3.1 22.4 + - - -
38B GLY* 3.1 25.3 + - - -
39B SER* 3.7 6.1 + - - -
71B ASN* 2.7 29.2 + - - -
74B ILE* 3.4 22.2 - - - +
99B ARG* 6.2 0.5 - - - +
100B ARG* 3.3 39.3 + - - +
102B ALA* 4.6 13.1 - - - +
281B ASP* 4.8 4.2 + - - +
282B ARG 4.3 5.0 + - - +
283B GLY 3.3 0.8 - - - -
284B ASP* 1.3 76.7 - - + +
286B TYR* 1.3 65.7 + - + +
287B LEU 3.6 0.4 - - - -
288B SER* 4.8 6.1 + - - -
289B THR* 4.4 6.2 - - - +
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Residues in contact with TYR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ASN* 4.4 3.1 + - - -
100B ARG* 4.5 14.1 + - - -
207B PRO* 3.9 31.2 + - + +
253B GLY* 3.3 27.0 - - - -
254B VAL* 4.2 16.0 + - + -
281B ASP* 2.7 32.4 + - - -
282B ARG 3.8 4.0 - - - -
283B GLY* 3.0 20.3 + - - +
285B ARG* 1.3 89.8 - - + +
287B LEU* 1.3 62.5 - - - +
288B SER 3.2 2.5 - - - -
289B THR* 2.5 40.1 + - + +
291B VAL* 3.6 18.2 - - + +
292B PHE* 3.9 5.4 - - + -
320B PLP 3.7 15.9 - - - +
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Residues in contact with LEU 287 (chain B).
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 39.0 - - + +
101A ALA* 3.6 34.9 - - + +
102A ALA* 3.7 9.9 - - + +
285A ARG* 4.9 0.4 - - + -
251B PHE* 3.5 26.9 - - + -
283B GLY 3.5 7.4 + - - +
284B ASP* 3.6 35.6 + - - +
285B ARG 3.6 0.6 - - - -
286B TYR* 1.3 77.4 - - - +
288B SER* 1.3 57.2 + - - +
290B GLY* 2.8 23.0 + - - -
292B PHE* 4.0 15.8 + - + +
100C ARG* 5.0 0.3 + - - -
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Residues in contact with SER 288 (chain B).
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* 4.7 14.7 + - - -
288A SER* 4.9 15.3 - - - -
99B ARG* 5.3 9.3 + - - +
285B ARG 4.8 5.6 + - - -
286B TYR 3.2 0.8 - - - -
287B LEU* 1.3 77.6 - - - +
289B THR* 1.3 55.5 + - - +
290B GLY 3.1 0.4 + - - -
100C ARG* 2.6 34.1 + - - +
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Residues in contact with THR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ARG* 4.9 19.3 - - + +
285B ARG 4.4 5.2 - - - +
286B TYR* 2.5 40.4 + - + +
288B SER* 1.3 82.1 + - - +
290B GLY* 1.3 57.0 + - - +
291B VAL* 2.8 25.5 + - + +
93C ASP* 3.8 26.5 - - - +
100C ARG* 3.5 11.2 + - - +
112C LEU* 3.6 13.7 - - - +
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Residues in contact with GLY 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B LEU 2.8 16.5 + - - -
288B SER 3.1 0.8 - - - -
289B THR* 1.3 78.7 + - - +
291B VAL* 1.3 61.0 + - - +
292B PHE 3.1 6.3 - - - -
293B GLY* 3.1 18.3 + - - +
295B GLU* 4.3 6.6 - - - +
100C ARG* 3.5 17.0 - - - -
112C LEU* 4.5 9.5 - - - +
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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