Contacts of the helix formed by residues 409 - 431 (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 SER 409 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A LEU* 3.5 5.8 - - - -
408A MET* 1.3 73.3 - - - +
410A GLU* 1.3 64.0 + - - +
411A GLU* 3.1 24.6 - - - +
412A GLN* 3.0 43.9 + - - +
413A ILE* 3.1 25.6 + - - +
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Residues in contact with GLU 410 (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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394A TRP* 3.9 9.9 - - + -
397A LYS* 4.0 29.5 - - - +
400A ALA* 6.1 0.3 - - - +
404A LEU* 3.4 24.8 - - + +
409A SER* 1.3 72.2 - - - +
411A GLU* 1.3 71.7 + - - +
413A ILE* 3.3 16.6 + - - +
414A ASN* 3.3 22.6 + - - +
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Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A SER* 3.1 30.5 - - - +
410A GLU* 1.3 84.6 + - + +
412A GLN* 1.3 56.9 + - + +
414A ASN* 3.2 14.3 + - - +
415A VAL* 3.0 34.0 + - + +
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Residues in contact with GLN 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 5.6 2.2 - - - +
407A GLY 3.8 7.7 + - - +
408A MET* 3.3 25.9 - - + +
409A SER* 3.0 46.4 + - - +
411A GLU* 1.3 75.9 - - + +
413A ILE* 1.3 64.2 + - - +
415A VAL* 3.4 9.1 + - + +
416A LEU* 3.2 30.7 + - + +
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Residues in contact with ILE 413 (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* 4.8 1.1 - - + -
191A PHE* 3.6 32.9 - - + -
390A PHE* 3.6 26.2 - - + -
394A TRP* 3.6 39.7 - - + -
403A TYR* 4.5 9.9 - - + -
404A LEU* 4.6 4.0 - - + -
408A MET* 3.8 27.1 - - + -
409A SER 3.1 18.0 + - - +
410A GLU* 3.6 4.9 - - - +
412A GLN* 1.3 75.5 - - - +
414A ASN* 1.3 62.2 + - - +
416A LEU* 3.2 5.7 + - - +
417A ARG* 2.9 20.1 + - - +
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Residues in contact with ASN 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TRP* 2.8 33.3 + - - +
397A LYS* 5.1 0.4 + - - +
410A GLU* 3.3 24.2 + - - +
411A GLU* 3.2 14.8 + - - +
413A ILE* 1.3 76.1 - - - +
415A VAL* 1.3 57.4 + - + +
417A ARG* 3.1 9.5 + - - +
418A ALA* 2.9 31.0 + - - +
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Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A GLU* 3.0 23.0 + - + +
412A GLN* 3.6 12.3 - - + +
413A ILE 3.3 0.2 - - - -
414A ASN* 1.3 74.4 - - + +
416A LEU* 1.3 66.0 + - + +
418A ALA* 3.3 8.0 + - - +
419A SER* 2.9 26.2 + - - -
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Residues in contact with LEU 416 (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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105A PHE* 5.3 3.1 - - + -
190A VAL* 3.7 11.4 - - + +
191A PHE* 3.4 41.7 - - + +
194A ASN* 3.2 40.8 - - + +
408A MET* 3.6 20.6 - - + -
412A GLN* 3.2 16.4 + - + +
413A ILE 3.2 6.3 + - - +
415A VAL* 1.3 80.8 - - + +
417A ARG* 1.3 65.2 + - - +
419A SER* 3.1 14.7 + - - -
420A ALA* 3.2 10.6 + - - +
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Residues in contact with ARG 417 (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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190A VAL* 4.0 9.5 - - - +
387A CYS* 3.1 33.7 + - - +
390A PHE* 3.4 34.8 - - + -
391A ASP* 2.6 44.7 + - - +
394A TRP* 5.5 2.7 - - + -
413A ILE 2.9 13.2 + - - +
414A ASN* 3.1 12.5 + - - +
416A LEU* 1.3 75.4 - - - +
418A ALA* 1.3 62.3 + - - +
420A ALA* 3.3 3.9 + - - +
421A GLN* 2.2 60.6 + - - +
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Residues in contact with ALA 418 (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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414A ASN 2.9 13.2 + - - +
415A VAL* 3.5 11.9 - - - +
417A ARG* 1.3 74.7 - - - +
419A SER* 1.3 62.9 + - - +
421A GLN* 3.2 10.0 + - - +
422A GLU* 3.0 25.8 + - - +
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Residues in contact with SER 419 (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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194A ASN* 2.7 35.3 + - - +
197A ARG* 3.0 35.4 + - - +
198A ARG* 4.7 0.2 - - - -
415A VAL* 2.9 15.1 + - - -
416A LEU* 3.1 10.3 + - - -
418A ALA* 1.3 76.5 - - - +
420A ALA* 1.3 61.6 + - - +
422A GLU* 3.2 9.9 + - - +
423A LEU* 3.1 16.3 + - - +
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Residues in contact with ALA 420 (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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190A VAL* 4.1 20.4 - - + +
193A LEU* 4.8 19.7 - - + -
194A ASN* 6.0 1.4 - - - +
387A CYS* 3.7 20.4 - - - -
416A LEU 3.2 5.6 + - - +
417A ARG 3.7 8.1 - - - +
418A ALA 3.3 0.2 - - - -
419A SER* 1.3 72.7 - - - +
421A GLN* 1.3 62.6 + - - +
423A LEU* 2.8 27.8 + - + +
424A VAL* 3.0 18.0 + - + +
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Residues in contact with GLN 421 (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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384A ASP* 4.3 14.6 + - - +
387A CYS* 4.2 3.1 - - - +
417A ARG* 2.2 48.5 + - - +
418A ALA* 3.2 12.5 + - - +
420A ALA* 1.3 78.1 - - - +
422A GLU* 1.3 55.8 + - - +
424A VAL* 3.6 12.3 + - - +
425A GLN* 3.0 42.9 + - + +
428A GLN* 5.7 2.2 + - - +
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Residues in contact with GLU 422 (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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197A ARG* 2.8 38.2 + - - +
418A ALA 3.0 12.5 + - - +
419A SER* 3.3 12.2 - - - +
420A ALA 3.0 0.2 - - - -
421A GLN* 1.3 75.6 - - - +
423A LEU* 1.3 58.9 + - - +
425A GLN* 3.4 16.8 + - + +
426A SER* 3.0 30.3 + - - -
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Residues in contact with LEU 423 (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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193A LEU* 4.8 10.8 - - + +
197A ARG* 3.8 28.7 - - + +
268A SER 4.4 11.9 - - - +
271A PHE* 3.4 45.5 - - + -
383A LEU* 3.9 24.7 - - + -
419A SER 3.1 10.6 + - - +
420A ALA* 2.8 13.2 + - - +
422A GLU* 1.3 74.5 - - - +
424A VAL* 1.3 66.4 + - + +
426A SER* 3.1 19.9 + - - -
427A TYR* 3.4 24.6 + - + -
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Residues in contact with VAL 424 (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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380A ALA* 4.3 17.2 - - + +
383A LEU* 3.8 34.7 - - + +
384A ASP* 4.2 21.1 - - + +
387A CYS* 4.4 9.4 - - - -
420A ALA 3.0 14.9 + - - +
421A GLN* 3.6 15.5 - - - +
423A LEU* 1.3 76.5 - - + +
425A GLN* 1.3 62.9 + - - +
427A TYR* 3.1 6.0 + - - +
428A GLN* 2.9 47.3 + - - +
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Residues in contact with GLN 425 (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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421A GLN* 3.0 33.0 + - + +
422A GLU* 3.7 18.8 - - + +
423A LEU 3.2 0.4 - - - -
424A VAL* 1.3 77.5 - - + +
426A SER* 1.3 58.6 + - - +
428A GLN* 3.2 17.4 + - - +
429A VAL* 2.8 38.2 + - + +
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Residues in contact with SER 426 (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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197A ARG* 5.1 4.7 + - - -
268A SER* 3.9 22.9 + - - -
269A LEU* 3.9 19.6 - - - +
422A GLU 3.0 15.8 + - - -
423A LEU* 3.1 13.1 + - - -
425A GLN* 1.3 76.1 - - - +
427A TYR* 1.3 57.3 + - - +
429A VAL* 3.3 6.5 + - - +
430A ALA* 2.9 26.5 + - - +
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Residues in contact with TYR 427 (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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269A LEU* 3.2 34.7 - - + -
271A PHE* 2.8 34.8 + - + -
317A LEU* 4.5 7.4 - - + -
375A ASN* 3.0 24.3 + - - -
376A ASN 4.1 4.0 - - - -
377A THR* 3.6 41.6 - - + +
379A ILE* 3.7 30.1 - - + -
380A ALA* 4.2 7.6 - - + -
383A LEU* 4.9 2.2 - - + -
423A LEU* 3.4 33.8 + - + +
424A VAL 3.1 7.2 + - - +
426A SER* 1.3 76.6 - - - +
428A GLN* 1.3 65.7 + - - +
430A ALA* 3.4 5.3 + - + +
431A GLU* 3.2 18.0 + - - +
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Residues in contact with GLN 428 (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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380A ALA* 4.8 9.9 + - + +
384A ASP* 5.2 7.3 + - - +
421A GLN* 5.7 2.7 + - - +
424A VAL* 2.9 33.1 + - + +
425A GLN* 3.2 24.6 + - + +
427A TYR* 1.3 77.0 - - - +
429A VAL* 1.3 61.8 + - + +
431A GLU* 3.3 17.2 + - - +
432A GLU 3.5 12.0 - - - +
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Residues in contact with VAL 429 (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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425A GLN* 2.8 24.0 + - + +
426A SER* 3.6 5.8 - - - +
428A GLN* 1.3 71.9 - - + +
430A ALA* 1.3 62.3 + - - +
431A GLU 3.1 2.0 - - - -
432A GLU* 2.9 32.4 + - - +
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Residues in contact with ALA 430 (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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269A LEU* 4.1 22.9 - - + -
315A ARG* 5.0 0.3 - - - -
317A LEU* 4.6 7.0 - - + -
347A THR* 3.5 15.4 - - - +
350A ILE* 4.3 15.2 - - + +
377A THR* 4.1 12.3 - - + -
426A SER 2.9 14.6 + - - +
427A TYR* 3.4 12.5 + - - +
429A VAL* 1.3 76.7 - - - +
431A GLU* 1.3 57.3 + - - +
432A GLU* 2.9 18.9 - - - +
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Residues in contact with GLU 431 (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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313A GLU 4.4 8.3 - - - +
314A GLY* 4.2 10.6 - - - -
315A ARG* 3.8 30.5 + - + +
377A THR* 2.8 36.0 + - - +
378A GLU* 4.7 5.1 + - - +
427A TYR 3.2 11.9 + - - +
428A GLN* 3.6 12.5 - - - +
429A VAL 3.1 1.4 - - - -
430A ALA* 1.3 74.7 - - - +
432A GLU* 1.3 69.6 + - - +
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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
------------------------------------------------------------
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