Contacts of the helix formed by residues 413 - 426 (chain A) in PDB entry 5BTL
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 THR 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408A ILE 5.1 0.2 - - - +
411A SER* 3.0 27.1 - - - +
412A GLU* 1.3 85.7 - - + +
414A VAL* 1.3 63.1 + - - +
415A ASP* 2.9 27.1 + - - +
416A ILE* 3.0 29.2 - - + +
417A ALA* 3.8 0.7 + - - +
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Residues in contact with VAL 414 (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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408A ILE* 6.5 0.9 - - + -
413A THR* 1.3 77.1 - - - +
415A ASP* 1.3 75.5 + - - +
416A ILE 3.4 0.4 - - - -
417A ALA* 3.3 7.8 + - - +
418A ARG* 2.8 36.2 + - - +
433A GLN* 6.1 0.9 - - - +
436A LEU* 4.1 16.7 - - + +
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Residues in contact with ASP 415 (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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413A THR* 2.9 13.6 + - - +
414A VAL* 1.3 85.1 - - - +
416A ILE* 1.3 63.9 + - + +
418A ARG* 3.2 35.5 + - - +
419A ALA* 2.8 32.7 + - - +
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Residues in contact with ILE 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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407A LEU* 5.1 2.9 - - + +
410A ALA 5.3 1.1 - - - +
411A SER* 3.5 29.3 + - - +
412A GLU* 4.5 7.9 - - + +
413A THR* 3.0 37.6 + - + +
415A ASP* 1.3 80.5 - - + +
417A ALA* 1.3 62.0 + - - +
419A ALA* 3.6 6.3 + - - +
420A GLY* 3.1 19.6 + - - -
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Residues in contact with ALA 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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407A LEU* 3.7 6.2 - - - +
408A ILE* 3.8 32.5 - - + +
411A SER* 3.0 29.4 + - - +
413A THR 4.0 3.4 - - - +
414A VAL* 3.3 12.7 + - - +
415A ASP 3.2 0.2 - - - -
416A ILE* 1.3 78.0 - - - +
418A ARG* 1.3 61.4 + - - +
420A GLY* 3.3 3.1 + - - -
421A LEU* 3.0 27.0 + - - +
436A LEU* 4.5 4.9 - - + -
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Residues in contact with ARG 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 VAL* 2.8 20.7 + - - +
415A ASP* 3.2 41.2 + - - +
417A ALA* 1.3 70.6 - - - +
419A ALA* 1.3 58.0 - - - +
421A LEU* 2.7 31.5 + - - +
422A ILE* 3.0 20.3 + - + +
429A GLU* 3.8 46.6 + - - +
432A ALA* 3.4 22.4 - - + -
433A GLN* 4.0 23.6 + - - +
436A LEU* 3.8 20.0 - - + +
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Residues in contact with ALA 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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415A ASP 2.8 22.6 + - - +
416A ILE* 3.8 6.7 - - - +
418A ARG* 1.3 73.4 - - - +
420A GLY* 1.3 60.3 + - - +
422A ILE* 3.5 12.6 + - - +
423A GLU* 3.3 30.5 + - - +
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Residues in contact with GLY 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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407A LEU* 3.3 22.1 - - - +
416A ILE 3.1 13.5 + - - -
417A ALA 3.7 3.8 - - - -
418A ARG 3.0 1.0 - - - -
419A ALA* 1.3 75.0 - - - +
421A LEU* 1.3 52.9 + - - +
423A GLU* 2.9 16.2 + - - +
424A LEU* 2.7 36.4 + - - +
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Residues in contact with LEU 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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404A VAL* 3.9 37.5 - - + +
407A LEU* 3.3 14.3 - - + +
408A ILE* 4.6 6.5 - - + -
417A ALA 3.0 20.0 + - - +
418A ARG* 2.7 21.7 + - - +
420A GLY* 1.3 70.5 - - - +
422A ILE* 1.3 61.9 + - - +
424A LEU* 3.8 6.6 - - + +
425A LEU* 3.1 30.2 + - + +
427A ILE* 3.9 9.0 - - + +
432A ALA* 4.2 23.3 - - + +
435A ILE* 4.5 17.7 - - + -
436A LEU* 4.1 21.5 - - + -
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Residues in contact with ILE 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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418A ARG* 3.0 42.8 + - + +
419A ALA* 3.6 11.7 - - - +
421A LEU* 1.3 75.1 - - - +
423A GLU* 1.3 62.7 + - + +
426A ASP* 2.8 32.7 + - - +
427A ILE* 3.1 31.2 - - - +
428A ASP 3.7 9.9 - - - +
429A GLU* 4.7 5.2 - - + +
432A ALA* 3.7 18.6 - - + -
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Residues in contact with GLU 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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419A ALA* 3.3 17.6 - - - +
420A GLY* 2.9 14.5 + - - +
422A ILE* 1.3 82.5 - - + +
424A LEU* 1.3 64.3 + - - +
426A ASP 4.2 2.6 + - - -
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Residues in contact with LEU 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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400A ALA 4.9 0.4 - - - +
403A GLU* 3.4 47.8 - - + +
404A VAL* 4.1 22.9 - - + +
407A LEU* 4.5 12.1 - - + -
420A GLY 2.7 19.3 + - - +
421A LEU* 3.3 7.8 + - + +
423A GLU* 1.3 76.5 - - - +
425A LEU* 1.3 81.3 + - + +
426A ASP 4.1 0.2 + - - -
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Residues in contact with LEU 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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396A LYS* 3.4 51.5 + - + +
397A ALA* 3.6 21.5 - - + +
400A ALA* 3.8 15.7 - - + -
404A VAL* 4.2 11.7 - - + -
421A LEU* 3.1 6.4 + - + +
424A LEU* 1.3 101.0 - - + +
426A ASP* 1.3 75.8 + - - +
427A ILE* 3.4 29.2 - - + -
435A ILE* 4.7 1.6 - - + -
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Residues in contact with ASP 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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396A LYS* 3.3 18.9 + - - +
422A ILE* 2.8 17.0 + - - +
423A GLU 4.2 2.3 + - - -
424A LEU 3.6 1.4 - - - -
425A LEU* 1.3 84.0 - - - +
427A ILE* 1.3 57.8 + - - +
431A GLN* 5.5 0.2 - - - +
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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