Contacts of the helix formed by residues 378 - 395 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A CYS* 3.6 37.1 - - - +
310A SER* 3.1 45.4 + - - +
313A GLU* 4.0 10.1 - - - +
314A GLY* 3.5 18.5 + - - +
376A ASN* 2.8 26.0 - - - +
377A THR* 1.3 67.0 + - - +
379A ILE* 1.3 60.0 + - - +
380A ALA 2.9 6.1 - - - -
381A ARG* 3.0 32.5 + - - +
382A VAL 3.7 1.0 + - - -
431A GLU* 4.8 5.2 - - - +
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Residues in contact with ILE 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ILE* 4.0 24.0 - - + -
271A PHE* 4.3 13.7 - - + +
272A LEU 3.8 15.7 - - - +
273A MET* 3.4 38.0 - - + -
376A ASN 3.2 18.3 + - - +
377A THR 3.1 0.6 - - - -
378A GLU* 1.3 76.5 - - - +
380A ALA* 1.3 60.8 + - - +
382A VAL* 3.1 10.7 + - + +
383A LEU* 2.9 41.9 + - + +
427A TYR* 3.7 38.4 - - + -
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A THR 3.1 16.6 + - - +
379A ILE* 1.3 81.8 - - - +
381A ARG* 1.3 55.6 + - - +
383A LEU* 4.0 10.9 - - - +
384A ASP* 2.8 33.3 + - - +
424A VAL* 4.3 20.7 - - + +
427A TYR* 4.2 14.8 - - + -
428A GLN* 4.8 13.0 - - + +
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Residues in contact with ARG 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA 4.3 15.5 + - - +
309A CYS* 4.7 5.3 - - + +
310A SER* 5.1 8.3 + - - -
313A GLU* 5.7 2.9 + - - -
378A GLU* 3.0 33.1 + - - +
380A ALA* 1.3 74.6 - - - +
382A VAL* 1.3 65.0 + - - +
384A ASP* 4.0 4.7 - - - +
385A ARG* 3.1 23.0 + - + +
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Residues in contact with VAL 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 3.7 30.3 - - + -
205A ILE* 5.0 4.9 - - + -
207A ASP* 3.8 15.3 - - + +
307A ALA* 4.1 9.9 - - + -
308A ALA 3.7 35.7 - - - +
309A CYS* 4.0 12.6 - - + -
378A GLU 3.7 0.6 + - - +
379A ILE* 3.1 14.2 + - + +
381A ARG* 1.3 78.3 - - - +
383A LEU* 1.3 64.3 + - + +
385A ARG* 3.3 23.7 + - - +
386A ILE* 3.3 14.0 + - + +
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 3.7 38.2 - - + +
205A ILE* 4.4 16.2 - - + -
271A PHE* 4.6 2.7 - - + -
379A ILE* 2.9 42.1 + - + +
380A ALA* 4.0 5.6 - - - +
382A VAL* 1.3 77.2 - - + +
384A ASP* 1.3 58.2 + - - +
386A ILE* 3.1 13.0 + - + +
387A CYS* 2.9 30.2 + - - -
420A ALA* 6.6 0.2 - - + -
423A LEU* 3.9 27.8 - - + -
424A VAL* 3.8 26.0 - - + +
427A TYR* 4.9 1.6 - - + -
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Residues in contact with ASP 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ALA 2.8 22.9 + - - +
381A ARG* 4.2 4.9 - - - +
383A LEU* 1.3 70.2 - - - +
385A ARG* 1.3 60.6 + - - +
387A CYS* 4.2 7.4 - - - +
388A HIS* 3.0 31.0 + - - +
421A GLN* 4.3 16.5 + - - +
424A VAL* 4.2 19.5 - - + +
428A GLN* 5.2 6.2 + - - +
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Residues in contact with ARG 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 5.0 2.0 - - - +
175A PRO 3.4 20.2 + - - -
177A PRO* 4.0 22.9 - - + +
207A ASP* 2.7 44.4 + - - -
209A GLU* 3.6 23.9 + - - -
308A ALA* 3.7 8.7 + - - +
381A ARG* 3.1 16.1 + - + +
382A VAL* 3.4 23.9 + - - +
383A LEU 3.2 0.4 - - - -
384A ASP* 1.3 78.4 - - - +
386A ILE* 1.3 70.9 - - - +
388A HIS* 3.6 3.5 + - - +
389A ASN* 3.1 34.9 + - - +
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Residues in contact with ILE 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 4.0 29.6 - - + -
175A PRO* 5.1 6.5 - - + +
186A PRO* 4.5 7.4 - - + +
189A THR* 3.8 35.0 - - + -
190A VAL* 3.7 22.7 - - + -
193A LEU* 4.7 10.1 - - + -
382A VAL* 3.3 16.5 + - + +
383A LEU* 3.1 14.9 + - + +
385A ARG* 1.3 87.2 - - - +
387A CYS* 1.3 66.6 + - - +
389A ASN* 3.2 8.0 + - - +
390A PHE* 3.0 20.6 + - - +
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Residues in contact with CYS 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A VAL* 4.7 4.0 - - - -
193A LEU* 5.9 1.3 - - - -
383A LEU* 2.9 20.1 + - - +
384A ASP* 3.8 11.0 - - - +
386A ILE* 1.3 76.9 - - - +
388A HIS* 1.3 58.1 + - - +
390A PHE* 3.2 10.5 - - - +
391A ASP* 3.0 32.1 + - - +
417A ARG* 3.1 37.2 + - - +
420A ALA* 3.7 28.7 - - - -
421A GLN* 4.2 3.8 - - - +
424A VAL* 4.4 8.5 - - - -
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Residues in contact with HIS 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP* 3.0 22.4 + - - +
385A ARG* 4.0 4.9 - - - +
387A CYS* 1.3 75.4 - - - +
389A ASN* 1.3 71.9 + - - +
391A ASP* 3.3 12.9 + - + +
392A LYS* 3.1 42.6 + - - +
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Residues in contact with ASN 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PRO* 4.3 24.9 - - - +
186A PRO* 4.0 18.5 - - + +
385A ARG* 3.1 24.4 + - - +
386A ILE* 3.2 6.6 + - - +
388A HIS* 1.3 81.6 + - - +
390A PHE* 1.3 62.2 + - - +
392A LYS* 3.1 43.6 - - - +
393A LEU* 3.4 14.6 + - - +
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Residues in contact with PHE 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PRO* 3.8 11.8 - - + +
187A TYR* 3.5 34.5 - + - -
190A VAL* 3.7 28.7 - - + -
191A PHE* 4.1 16.8 - + - -
386A ILE 3.0 11.8 + - - +
387A CYS* 3.2 9.9 - - - +
389A ASN* 1.3 74.0 - - - +
391A ASP* 1.3 66.5 + - - +
393A LEU* 2.9 9.3 + - - +
394A TRP* 2.7 54.9 + + + +
413A ILE* 3.6 24.9 - - + -
417A ARG* 3.4 33.7 - - + -
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Residues in contact with ASP 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A CYS 3.0 14.5 + - - +
388A HIS* 3.3 16.0 + - + +
390A PHE* 1.3 91.6 - - - +
392A LYS* 1.3 62.1 + - - +
394A TRP* 4.3 5.4 - - - +
395A GLN* 3.0 29.2 + - - +
417A ARG* 2.6 38.3 + - - +
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Residues in contact with LYS 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A HIS* 3.1 30.1 + - + +
389A ASN* 3.1 41.4 - - - +
391A ASP* 1.3 77.1 - - - +
393A LEU* 1.3 64.4 + - + +
395A GLN* 3.1 35.9 + - - +
396A ARG* 4.1 9.4 + - - +
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A VAL* 3.5 31.2 - - + -
183A VAL 3.4 21.5 - - - +
186A PRO* 3.7 28.5 - - + -
187A TYR* 3.3 31.0 - - + +
389A ASN 3.4 7.6 + - - +
390A PHE* 2.9 7.5 + - - +
392A LYS* 1.3 81.9 - - + +
394A TRP* 1.3 61.5 + - - +
396A ARG* 3.4 5.1 + - - +
397A LYS 3.4 1.7 + - - -
398A ALA* 2.9 42.2 + - + +
399A PHE* 4.4 4.5 - - + -
50T TRP* 4.9 1.6 - - + -
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Residues in contact with TRP 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A TYR* 3.7 22.9 - + + -
390A PHE* 2.7 43.8 + + + +
391A ASP* 4.5 4.5 - - - +
393A LEU* 1.3 68.8 - - - +
395A GLN* 1.3 64.8 + - - +
396A ARG 3.1 2.2 - - - -
397A LYS* 3.0 74.0 + - + +
400A ALA* 4.1 21.3 - - + -
404A LEU* 5.3 2.7 - - + -
410A GLU* 3.9 23.1 - - + -
413A ILE* 3.6 40.5 - - + +
414A ASN* 2.8 29.7 + - - +
417A ARG* 5.5 3.6 - - + -
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Residues in contact with GLN 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A ASP 3.0 14.7 + - - +
392A LYS* 3.1 38.4 + - - +
394A TRP* 1.3 77.1 - - - +
396A ARG* 1.3 78.7 + - + +
397A LYS* 5.1 4.1 + - - +
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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
------------------------------------------------------------
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