Contacts of the helix formed by residues 291 - 300 (chain B) in PDB entry 2BTO
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 291 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A ASP* 4.1 17.1 + - - +
289B GLU 4.0 1.0 + - - -
290B LEU* 1.3 76.7 - - - +
292B ILE* 1.3 66.5 + - - -
293B GLU* 3.2 3.5 + - - -
294B GLU* 3.6 7.7 + - - +
295B MET* 3.1 20.7 + - - +
328B GLU* 5.1 1.6 - - - -
368B LYS* 4.4 3.4 - - - -
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Residues in contact with ILE 292 (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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291B GLY* 1.3 72.5 - - - -
293B GLU* 1.3 57.3 + - - +
295B MET* 3.5 4.1 - - - +
296B ILE* 2.9 55.4 + - + +
323B TYR* 3.9 21.5 - - + +
327B MET* 5.0 2.7 - - - -
328B GLU* 3.2 42.6 - - + +
329B ASP* 4.7 13.2 - - + +
332B LEU* 4.5 20.2 - - + -
333B ALA* 4.1 18.2 - - + -
368B LYS* 3.7 9.9 - - - +
370B MET* 5.2 1.3 - - + -
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Residues in contact with GLU 293 (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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291B GLY* 3.2 1.3 - - - -
292B ILE* 1.3 79.1 - - - +
294B GLU* 1.3 65.2 + - - +
296B ILE* 3.9 3.2 - - - +
297B LYS* 2.9 60.3 + - + +
332B LEU* 4.9 19.0 - - + +
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Residues in contact with GLU 294 (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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290B LEU* 4.1 26.2 - - + -
291B GLY 3.6 9.9 + - - +
293B GLU* 1.3 79.5 - - - +
295B MET* 1.3 54.4 + - - +
297B LYS* 3.4 23.2 - - - +
298B SER* 2.5 46.6 + - - +
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Residues in contact with MET 295 (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 ALA* 3.6 23.5 - - + +
278B PRO* 4.0 15.0 - - + -
289B GLU* 5.6 0.9 - - - +
290B LEU* 3.9 24.4 - - + +
291B GLY 3.1 18.9 + - - +
292B ILE* 3.5 5.6 - - - +
293B GLU 3.1 0.2 - - - -
294B GLU* 1.3 76.9 - - - +
296B ILE* 1.3 58.4 + - - +
298B SER* 3.2 4.5 + - - -
299B LEU* 2.9 27.9 + - - +
323B TYR* 5.0 2.5 - - - -
368B LYS* 3.5 59.0 - - + +
369B SER* 4.4 1.6 - - - -
370B MET* 3.1 33.4 - - + -
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Residues in contact with ILE 296 (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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292B ILE* 2.9 37.7 + - + +
293B GLU* 4.0 2.7 - - - +
295B MET* 1.3 68.4 - - - +
297B LYS* 1.3 69.8 + - - +
299B LEU* 3.2 13.6 + - - +
300B PHE* 3.2 21.8 + - + +
323B TYR* 5.8 1.3 - - + -
333B ALA* 4.1 16.6 - - + +
336B ALA* 3.8 32.5 - - + -
337B LEU* 4.3 23.8 - - + -
340B MET* 4.7 10.5 - - + +
370B MET* 3.5 27.8 - - + -
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Residues in contact with LYS 297 (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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293B GLU* 2.9 50.9 + - + +
294B GLU* 3.4 24.9 - - - +
296B ILE* 1.3 78.6 - - - +
298B SER* 1.3 64.3 - - - +
300B PHE* 3.3 3.6 + - - +
301B ASP* 3.3 18.1 + - - +
340B MET* 5.0 11.6 - - + +
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Residues in contact with SER 298 (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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218B LYS* 5.8 4.9 + - - -
277B ALA* 4.6 8.5 - - - -
278B PRO* 6.2 0.2 - - - -
279B LEU* 6.3 1.1 - - - -
290B LEU* 4.4 8.3 - - - +
294B GLU* 2.5 36.9 + - - +
295B MET* 3.2 6.7 + - - -
297B LYS* 1.3 71.4 - - - +
299B LEU* 1.3 66.9 + - - +
301B ASP* 2.9 18.7 + - - +
304B SER* 2.9 26.1 + - - -
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Residues in contact with LEU 299 (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 ALA* 3.5 44.5 - - + +
276B PHE 3.9 11.9 - - - +
277B ALA* 4.1 5.8 - - + +
295B MET 2.9 13.0 + - - +
296B ILE* 3.4 12.8 - - - +
298B SER* 1.3 77.5 - - - +
300B PHE* 1.3 80.6 + - + +
301B ASP 3.5 1.7 + - - +
304B SER* 4.2 4.0 - - - -
321B VAL* 4.2 20.4 - - + -
337B LEU* 5.9 0.2 - - + -
370B MET* 4.0 24.9 - - + +
372B LEU* 3.5 43.5 - - + +
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Residues in contact with PHE 300 (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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296B ILE* 3.2 19.1 + - + +
297B LYS 3.3 2.2 + - - +
298B SER 3.1 0.8 - - - -
299B LEU* 1.3 94.1 - - + +
301B ASP* 1.3 61.4 - - - +
302B ASN* 3.8 1.4 + - - +
311B PRO* 6.2 0.3 - - - +
312B MET* 3.4 26.9 - - + +
316B PHE* 5.2 4.3 - + - -
319B THR* 4.6 2.5 - - + -
321B VAL* 3.6 23.1 - - + -
337B LEU* 4.1 19.7 - - + -
340B MET* 3.8 40.2 - - + -
344B LEU* 4.1 33.7 - - + -
354B PHE* 4.2 12.1 - + - -
372B LEU* 4.0 27.1 - - + -
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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