Contacts of the strand formed by residues 368 - 376 (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 LYS 368 (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* 4.2 2.2 + - - -
278B PRO* 3.6 10.6 - - - +
289B GLU* 3.1 24.4 + - - +
290B LEU 2.9 27.9 + - - -
291B GLY* 4.4 0.6 - - - -
292B ILE* 3.7 15.7 - - - +
295B MET* 3.5 20.3 - - + +
323B TYR* 3.4 20.0 - - + +
324B ARG* 3.4 11.4 - - - +
325B GLY* 4.2 0.2 - - - -
326B ILE* 3.4 19.3 - - + +
328B GLU* 3.0 35.8 + - - +
366B HIS* 3.5 11.6 - - - +
367B ARG* 1.3 79.3 - - + +
369B SER* 1.3 64.4 + - - +
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Residues in contact with SER 369 (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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276B PHE* 3.6 25.1 - - - -
277B ALA 3.3 12.3 - - - -
278B PRO* 3.9 4.3 - - - -
295B MET* 4.4 2.2 - - - -
322B LEU 4.1 0.2 - - - +
323B TYR* 4.2 1.0 - - - -
324B ARG* 3.1 53.9 + - - +
363B GLY* 5.1 3.8 + - - -
366B HIS* 4.1 10.7 + - - +
368B LYS* 1.3 76.2 - - - +
370B MET* 1.3 67.7 + - - +
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Residues in contact with MET 370 (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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276B PHE* 3.4 8.2 - - - -
277B ALA* 2.7 35.3 + - + +
292B ILE* 4.7 1.1 - - + +
295B MET* 3.1 44.6 - - + +
296B ILE* 3.5 37.5 - - + +
299B LEU* 4.0 21.3 - - + +
321B VAL* 4.4 15.5 - - + -
322B LEU 3.4 7.9 - - - +
323B TYR* 3.4 34.8 - - + -
337B LEU* 5.8 0.7 - - - -
369B SER* 1.3 79.4 - - - +
371B VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 371 (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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236B ALA* 3.8 21.8 - - + +
239B GLY* 4.0 18.4 - - - -
240B ILE* 3.8 27.8 - - + -
274B CYS* 4.4 6.1 - - + -
275B ALA 3.4 9.0 - - - +
276B PHE* 3.7 21.3 - - + -
299B LEU* 4.3 2.5 - - - -
320B ALA 3.7 1.2 - - - +
321B VAL* 3.6 3.3 - - - +
322B LEU* 2.8 43.8 + - + +
370B MET* 1.3 77.8 - - - +
372B LEU* 1.3 69.5 + - - +
373B LEU* 4.0 4.7 + - + -
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Residues in contact with LEU 372 (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 CYS* 2.9 9.5 - - - +
275B ALA* 2.8 39.6 + - + +
299B LEU* 3.5 47.5 - - + +
300B PHE* 4.0 23.8 - - + -
305B VAL* 6.1 2.7 - - + -
311B PRO* 6.4 2.2 - - + -
316B PHE* 5.1 6.5 - - + -
319B THR* 3.6 24.0 - - + -
320B ALA 3.5 4.9 - - - +
321B VAL* 4.5 0.4 - - + -
371B VAL* 1.3 72.7 - - - +
373B LEU* 1.3 78.2 + - - +
374B ALA* 4.3 11.0 - - + -
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Residues in contact with LEU 373 (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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204B LEU* 3.9 17.9 - - + -
240B ILE* 3.8 28.5 - - + -
259B LEU* 4.3 13.9 - - + -
263B LEU* 3.7 31.9 - - + +
272B LEU* 5.1 6.7 - - + -
273B MET 3.4 3.6 - - - +
274B CYS* 3.7 21.8 - - + -
319B THR* 3.4 2.1 - - - -
320B ALA* 2.9 37.4 + - + +
322B LEU* 4.0 23.3 - - + -
371B VAL* 4.0 4.0 - - + -
372B LEU* 1.3 76.2 - - - +
374B ALA* 1.3 60.2 + - - +
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Residues in contact with ALA 374 (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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263B LEU* 4.9 0.9 - - - -
272B LEU* 3.4 8.8 - - - -
273B MET* 2.9 39.6 + - + +
311B PRO* 6.1 0.2 - - + -
316B PHE* 3.8 28.9 - - + -
318B SER 3.5 10.3 - - - +
319B THR* 4.4 0.9 - - - +
372B LEU* 4.1 12.3 - - + -
373B LEU* 1.3 76.9 - - - +
375B ASN* 1.3 62.2 + - - +
376B ASN* 3.6 7.6 + - + -
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Residues in contact with ASN 375 (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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263B LEU* 3.1 28.1 + - - +
265B PRO* 3.7 4.9 - - - +
269B LEU 2.8 28.7 + - - -
270B HIS* 4.2 0.8 - - - +
271B PHE 3.2 10.4 - - - +
272B LEU* 3.8 11.5 - - + +
316B PHE* 3.6 1.6 - - - -
317B LEU* 2.6 49.0 + - + +
318B SER* 3.0 14.9 + - - +
374B ALA* 1.3 70.8 - - - +
376B ASN* 1.3 54.3 + - - +
427B TYR* 2.8 34.3 + - - -
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Residues in contact with ASN 376 (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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271B PHE 4.8 1.4 + - - +
273B MET* 3.6 19.1 - - + +
311B PRO* 3.0 32.2 + - - +
315B ARG 3.3 16.4 + - - -
316B PHE* 3.4 33.5 - - + -
317B LEU* 4.5 2.2 - - - -
374B ALA* 3.6 6.2 + - + -
375B ASN* 1.3 77.2 + - - +
377B THR* 1.3 66.9 + - - +
378B GLU* 2.9 38.4 + - - +
379B ILE* 3.5 22.0 + - - +
427B TYR* 3.9 3.8 - - - -
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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