Contacts of the helix formed by residues 378 - 395 (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 GLU 378 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B MET* 5.3 0.2 - - + -
309B CYS* 3.6 24.9 - - - +
310B SER 3.2 33.5 + - - +
311B PRO* 4.3 0.2 - - + -
313B GLU* 3.5 17.5 - - - +
314B GLY* 3.4 19.8 + - - +
376B ASN* 2.9 10.9 + - - +
377B THR* 1.3 74.0 - - - +
379B ILE* 1.3 60.1 + - - +
380B ALA* 3.0 2.2 - - - -
381B ARG* 2.9 72.6 + - - +
382B VAL 3.8 0.3 + - - -
431B GLU* 3.7 9.9 - - - +
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Residues in contact with ILE 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 4.1 26.7 - - + -
271B PHE* 3.3 45.3 - - + +
272B LEU 4.3 10.1 - - - +
273B MET* 4.0 18.8 - - + -
376B ASN 3.5 18.4 + - - +
377B THR 3.0 0.8 - - - -
378B GLU* 1.3 78.8 - - - +
380B ALA* 1.3 66.2 + - - +
381B ARG 3.2 0.5 + - - -
382B VAL* 3.2 6.0 + - + +
383B LEU* 3.0 34.8 + - + +
427B TYR* 3.9 31.0 - - + -
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B THR 3.2 16.1 + - - +
378B GLU* 4.9 0.2 - - - -
379B ILE* 1.3 83.1 - - - +
381B ARG* 1.3 55.6 + - - +
383B LEU* 3.4 10.4 + - - +
384B ASP* 2.8 33.6 + - - +
424B VAL* 4.3 11.0 - - + +
427B TYR* 4.3 14.8 - - + -
428B GLN* 4.4 22.7 - - + +
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Residues in contact with ARG 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ALA 4.9 3.1 - - - +
309B CYS* 4.1 13.9 - - + +
310B SER* 5.8 0.4 - - - +
313B GLU* 4.6 18.4 + - - +
378B GLU* 2.9 48.2 + - - +
380B ALA* 1.3 75.7 - - - +
382B VAL* 1.3 67.2 + - - +
384B ASP* 3.2 7.4 + - + +
385B ARG* 2.9 23.9 + - - +
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Residues in contact with VAL 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 3.6 31.6 - - + -
205B ILE* 4.2 9.9 - - + -
207B ASP* 3.7 22.9 - - - +
307B ALA* 4.1 20.0 - - + -
308B ALA 3.8 18.6 - - - +
309B CYS* 4.2 9.9 - - + -
378B GLU 4.4 0.4 - - - +
379B ILE* 3.5 10.8 - - + +
381B ARG* 1.3 76.9 - - - +
383B LEU* 1.3 65.7 + - + +
385B ARG* 3.2 24.6 + - - +
386B ILE* 3.2 13.8 + - + +
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 5.2 13.0 - - + -
189B THR* 6.3 0.4 - - + -
193B LEU* 3.9 39.2 - - + +
205B ILE* 5.8 1.3 - - + -
271B PHE* 5.1 4.7 - - + -
379B ILE* 3.0 45.9 + - + +
380B ALA* 3.8 6.1 - - - +
382B VAL* 1.3 77.1 - - + +
384B ASP* 1.3 56.0 + - - +
386B ILE* 3.3 10.6 + - + +
387B CYS* 3.1 33.5 + - - -
423B LEU* 3.5 28.0 - - + -
424B VAL* 3.8 21.3 - - + -
427B TYR* 5.2 2.0 - - + -
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Residues in contact with ASP 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ALA* 2.8 23.3 + - - +
381B ARG* 3.4 10.4 - - + +
383B LEU* 1.3 71.1 - - - +
385B ARG* 1.3 66.2 + - - +
387B CYS* 3.2 8.2 + - - +
388B HIS* 2.9 27.1 + - - +
421B GLN* 5.8 1.4 + - - -
424B VAL* 4.1 11.0 - - - +
428B GLN* 3.8 21.7 + - - -
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Residues in contact with ARG 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 4.7 2.2 - - - +
175B PRO 3.0 22.2 + - - -
177B PRO* 3.6 21.4 - - + +
207B ASP* 2.8 42.2 + - - -
209B GLU* 3.0 27.6 + - - -
308B ALA* 3.7 9.1 + - - +
381B ARG 2.9 12.3 + - - +
382B VAL* 3.3 23.8 - - - +
384B ASP* 1.3 76.0 - - - +
386B ILE* 1.3 81.5 + - - +
388B HIS* 3.6 6.6 + - - +
389B ASN* 3.3 32.3 + - - +
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Residues in contact with ILE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 5.0 6.3 - - + -
175B PRO* 4.3 22.7 - - + +
186B PRO* 4.1 9.9 - - + +
189B THR* 3.7 34.1 - - + -
190B VAL* 4.0 16.4 - - + -
193B LEU* 5.1 3.4 - - + -
382B VAL* 3.2 18.6 + - + +
383B LEU* 3.4 13.2 - - + +
384B ASP 3.2 0.4 - - - -
385B ARG* 1.3 105.0 - - - +
387B CYS* 1.3 59.4 + - - +
389B ASN* 3.0 24.4 + - - +
390B PHE* 3.0 11.6 + - - +
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Residues in contact with CYS 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B VAL* 4.3 14.6 - - - -
193B LEU* 5.6 2.5 - - - -
383B LEU* 3.1 20.8 + - - +
384B ASP* 3.2 9.1 + - - +
386B ILE* 1.3 77.3 - - - +
388B HIS* 1.3 56.8 + - - +
390B PHE* 3.4 7.6 + - - +
391B ASP* 2.8 38.5 + - - +
417B ARG* 3.7 39.5 - - - +
420B ALA* 4.5 12.3 - - - -
421B GLN* 5.6 0.4 - - - +
424B VAL* 4.7 11.0 - - - -
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Residues in contact with HIS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ASP* 2.9 19.1 + - - +
385B ARG* 3.8 7.4 - - - +
387B CYS* 1.3 75.6 - - - +
389B ASN* 1.3 60.6 + - - +
391B ASP* 3.7 8.0 + - + +
392B LYS* 3.1 54.2 + - + +
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Residues in contact with ASN 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PRO* 4.5 14.5 - - - +
186B PRO* 3.8 21.8 - - + -
385B ARG* 3.3 23.6 + - - +
386B ILE* 3.0 11.9 + - - +
388B HIS* 1.3 79.5 + - - +
390B PHE* 1.3 65.0 + - - +
392B LYS* 3.2 33.5 + - - +
393B LEU* 3.2 18.4 + - - +
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Residues in contact with PHE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PRO* 3.5 19.5 - - - +
187B TYR* 3.5 26.1 - + - -
190B VAL* 3.6 32.8 - - + -
191B PHE* 3.6 19.3 - + - -
386B ILE 3.0 11.7 + - - +
387B CYS* 3.5 8.1 - - - +
389B ASN* 1.3 75.4 - - - +
391B ASP* 1.3 69.1 + - - +
393B LEU* 3.1 8.3 + - - +
394B TRP* 2.8 48.2 + + + +
413B ILE* 3.5 24.5 - - + -
417B ARG* 3.6 31.9 - - + -
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Residues in contact with ASP 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B CYS 2.8 23.9 + - - +
388B HIS* 4.0 7.6 - - + +
390B PHE* 1.3 85.6 - - - +
392B LYS* 1.3 57.9 + - - +
394B TRP* 4.4 5.1 - - - +
395B GLN* 2.9 44.8 + - - +
417B ARG* 2.8 34.9 + - - +
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Residues in contact with LYS 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B HIS* 3.1 45.6 + - + +
389B ASN* 3.2 23.1 + - - +
391B ASP* 1.3 75.3 - - - +
393B LEU* 1.3 62.8 + - + +
395B GLN* 4.4 5.8 - - - +
396B ARG* 3.6 19.6 + - - +
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Residues in contact with LEU 393 (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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183B VAL 4.0 14.6 - - - +
186B PRO* 3.8 28.3 - - + -
187B TYR* 3.2 26.0 - - + +
389B ASN 3.2 14.8 + - - +
390B PHE* 3.1 4.8 + - - +
392B LYS* 1.3 80.4 - - + +
394B TRP* 1.3 59.3 + - - +
395B GLN 3.4 0.4 - - - -
396B ARG* 3.3 6.5 + - - +
397B LYS 2.8 21.1 + - - -
398B ALA* 2.9 31.9 + - + -
399B PHE* 4.6 11.2 - - + -
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Residues in contact with TRP 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 3.3 24.7 + + + +
390B PHE* 2.8 38.7 + + + +
391B ASP* 4.3 3.6 - - - +
393B LEU* 1.3 72.6 - - - +
395B GLN* 1.3 66.4 + - - +
396B ARG 3.1 2.0 - - - -
397B LYS* 3.2 53.0 + - + +
400B ALA* 3.9 24.5 - - + -
404B LEU* 4.6 9.0 - - + -
410B GLU* 3.8 30.1 - - + -
413B ILE* 3.4 39.9 - - + +
414B ASN* 3.0 22.6 + - - +
417B ARG* 5.7 2.5 - - + -
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Residues in contact with GLN 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ASP* 2.9 30.7 + - - +
392B LYS* 4.4 7.3 - - - +
394B TRP* 1.3 79.4 - - - +
396B ARG* 1.3 58.9 + - + +
397B LYS* 4.1 4.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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