Contacts of the helix formed by residues 273 - 282 (chain B) in PDB entry 3BUW
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 THR 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A PTR 5.7 0.2 - - - -
78B LYS* 4.8 5.5 + - - -
81B PRO 4.7 1.3 - - - -
82B PRO* 3.5 22.2 - - + -
152B THR* 3.7 9.6 - - + +
156B LEU* 3.0 37.9 - - + -
272B LEU* 1.3 73.8 - - - +
274B TYR* 1.3 65.4 + - - +
275B ASP* 3.5 7.0 + - - +
276B GLU* 2.9 37.7 + - - +
277B VAL* 3.0 25.1 + - - +
294B ARG* 3.8 6.5 - - - +
297B CYS* 6.4 1.3 - - - -
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Residues in contact with TYR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ASN* 3.3 45.3 - - + +
322A PRO* 2.7 50.7 + - + +
323A PTR 3.6 17.5 + + - +
81B PRO 4.5 2.6 + - - +
273B THR* 1.3 73.9 - - - +
275B ASP* 1.3 77.9 + - - +
277B VAL* 3.3 2.3 + - - +
278B LYS* 3.2 29.9 + - + +
294B ARG* 3.3 32.3 - - - +
314B ILE 5.2 2.6 + - - -
315B LEU* 5.9 0.3 - - - -
316B GLN* 3.0 46.1 + - + +
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Residues in contact with ASP 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ASN* 4.5 0.5 - - - +
78B LYS* 3.1 40.9 + - - +
80B SER* 3.0 29.2 + - - -
273B THR* 3.3 3.6 + - - +
274B TYR* 1.3 91.0 - - - +
276B GLU* 1.3 63.5 + - + +
278B LYS* 3.3 7.9 + - - +
279B ALA* 3.0 22.6 + - - +
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Residues in contact with GLU 276 (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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149B ARG* 3.5 27.1 - - - -
152B THR* 3.5 26.7 + - + +
271B PHE 3.8 2.9 - - - +
272B LEU* 3.0 33.9 - - + +
273B THR* 2.9 38.7 + - - +
275B ASP* 1.3 76.7 - - + +
277B VAL* 1.3 57.3 + - - +
279B ALA* 3.3 7.4 + - - +
280B ARG* 2.8 30.9 + - - +
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B MET* 5.5 0.7 - - + -
272B LEU* 4.3 9.4 - - + -
273B THR 3.0 8.6 + - - +
274B TYR 3.6 8.3 - - - +
275B ASP 3.2 0.2 - - - -
276B GLU* 1.3 73.0 - - - +
278B LYS* 1.3 68.0 + - - +
280B ARG* 3.3 1.4 + - - +
281B LEU* 3.0 35.9 + - + +
292B ILE* 3.7 36.1 - - + +
294B ARG* 3.4 38.1 - - + +
304B ALA 5.9 0.4 - - - +
306B GLY* 4.2 7.6 - - - +
314B ILE* 5.1 0.4 - - + -
316B GLN* 3.8 20.2 - - + +
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Residues in contact with LYS 278 (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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274B TYR* 3.2 28.8 + - + +
275B ASP* 3.3 12.8 + - - +
277B VAL* 1.3 78.2 - - - +
279B ALA* 1.3 61.5 + - - +
282B GLN* 3.3 20.4 + - - +
314B ILE* 3.3 60.4 - - + +
316B GLN* 4.2 3.8 + - - +
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Residues in contact with ALA 279 (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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275B ASP 3.0 15.9 + - - +
276B GLU* 3.6 9.0 - - - +
278B LYS* 1.3 78.9 - - - +
280B ARG* 1.3 62.1 + - - +
282B GLN* 3.4 20.1 + - - +
283B LYS* 4.5 1.6 + - - -
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Residues in contact with ARG 280 (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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269B MET* 3.5 32.6 - - - +
272B LEU* 4.4 10.6 - - + +
276B GLU 2.8 17.4 + - - +
277B VAL* 3.3 3.8 + - - +
279B ALA* 1.3 77.5 - - - +
281B LEU* 1.3 61.2 + - - +
283B LYS* 2.8 46.4 + - - +
284B PHE* 4.1 2.6 - - - -
292B ILE* 3.9 15.5 - - + -
341B ASP* 2.9 40.3 + - - +
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Residues in contact with LEU 281 (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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277B VAL* 3.0 24.9 + - + +
279B ALA 3.3 0.2 - - - -
280B ARG* 1.3 74.4 - - - +
282B GLN* 1.3 65.6 + - - +
283B LYS 3.2 3.1 - - - -
284B PHE* 2.9 34.1 + - + +
285B ILE 3.4 6.8 + - - -
290B SER* 4.1 18.8 - - - +
291B TYR* 4.2 8.1 - - - +
292B ILE* 3.9 22.7 - - + -
306B GLY 3.6 31.6 - - - +
307B TYR* 3.7 10.8 - - - +
308B VAL* 4.0 6.9 - - + +
314B ILE* 3.8 30.0 - - + +
341B ASP* 5.3 1.1 - - - +
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Residues in contact with GLN 282 (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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278B LYS* 3.3 12.0 + - - +
279B ALA* 3.4 16.4 - - - +
280B ARG 3.3 1.2 - - - -
281B LEU* 1.3 76.5 - - - +
283B LYS* 1.3 63.3 + - - +
284B PHE 3.0 0.2 - - - -
285B ILE* 3.0 45.6 + - - +
314B ILE* 4.0 14.1 - - - +
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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