Contacts of the helix formed by residues 415 - 430 (chain A) in PDB entry 5Z66
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 ALA 415 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376A GLU* 2.9 20.2 + - - +
387A TYR* 3.7 1.8 + - - -
414A ALA* 1.3 74.3 - - - +
416A GLN* 1.3 67.5 + - - +
417A ASP* 3.3 18.4 - - - +
418A ARG* 3.1 11.8 + - + +
419A ALA* 2.9 19.9 + - - +
467A TYR* 4.3 0.4 - - - -
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Residues in contact with GLN 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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414A ALA 3.8 1.2 + - - -
415A ALA* 1.3 72.9 - - - +
417A ASP* 1.3 58.0 + - - +
419A ALA* 3.1 3.1 + - - +
420A ASP* 2.9 63.9 + - - +
467A TYR* 3.1 50.8 + - + +
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Residues in contact with ASP 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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415A ALA* 3.4 18.0 - - - +
416A GLN* 1.3 78.4 - - - +
418A ARG* 1.3 78.2 + - - +
420A ASP* 3.4 11.7 + - - +
421A LYS* 3.2 39.0 + - - +
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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
----------------------------------------------------------
376A GLU* 2.8 73.5 + - - +
380A TRP* 3.3 62.3 - - + +
382A ASP* 5.1 1.6 + - - -
387A TYR* 3.5 15.9 - - - +
415A ALA* 3.1 8.3 + - + +
417A ASP* 1.3 91.4 + - - +
419A ALA* 1.3 59.3 + - - +
421A LYS* 3.2 4.5 + - - +
422A VAL* 2.9 32.7 + - - +
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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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409A LEU* 3.7 30.6 - - + +
414A ALA* 4.4 2.5 - - + +
415A ALA 2.9 9.8 + - - +
416A GLN 3.5 4.9 - - - +
418A ARG* 1.3 76.7 - - - +
420A ASP* 1.3 58.8 + - - +
422A VAL* 3.3 2.4 + - - +
423A ALA* 2.9 27.9 + - - +
467A TYR* 3.4 44.4 - - + -
469A GLN* 4.8 1.2 - - - +
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Residues in contact with ASP 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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416A GLN* 2.9 46.2 + - - +
417A ASP* 3.6 11.4 - - - +
418A ARG 3.2 0.2 - - - -
419A ALA* 1.3 78.6 - - - +
421A LYS* 1.3 62.9 + - + +
423A ALA* 3.3 4.2 + - - +
424A ALA* 3.0 21.1 + - - +
469A GLN* 2.8 29.2 + - - +
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Residues in contact with LYS 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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380A TRP* 3.9 19.8 - - + -
382A ASP* 4.2 20.4 + - - -
385A GLY* 3.5 23.6 - - - +
417A ASP* 3.2 25.8 + - - +
418A ARG* 3.2 7.6 + - - +
420A ASP* 1.3 74.4 - - + +
422A VAL* 1.3 60.4 + - - +
424A ALA* 3.2 8.5 + - - +
425A ALA* 2.9 27.2 + - - +
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Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A TRP* 4.1 0.4 - - + -
385A GLY 4.3 1.8 - - - -
386A TRP* 4.0 20.9 - - + -
387A TYR* 3.8 28.9 - - + +
401A LEU* 6.3 0.7 - - + -
405A ALA* 4.0 14.6 - - + +
406A LEU* 4.1 18.2 - - + -
409A LEU* 4.0 19.5 - - + -
418A ARG 2.9 19.8 + - - +
419A ALA 3.7 4.5 - - - +
421A LYS* 1.3 71.9 - - - +
423A ALA* 1.3 60.6 + - - +
425A ALA* 3.2 6.6 + - + +
426A THR* 2.8 42.2 + - - +
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Residues in contact with ALA 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 2.9 12.4 + - - +
420A ASP 3.5 9.2 - - - +
421A LYS 3.3 0.2 - - - -
422A VAL* 1.3 78.7 - - - +
424A ALA* 1.3 56.8 + - - +
426A THR* 3.3 2.6 + - - -
427A SER* 2.9 30.5 + - - -
464A LEU* 3.8 20.2 - - + +
469A GLN* 3.6 37.2 - - + +
472A VAL* 4.5 7.7 - - + +
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Residues in contact with ALA 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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420A ASP 3.0 12.5 + - - +
421A LYS* 3.2 12.1 + - - +
423A ALA* 1.3 75.3 - - - +
425A ALA* 1.3 59.8 + - - +
427A SER* 3.9 4.5 - - - +
428A SER* 2.8 34.0 + - - -
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Residues in contact with ALA 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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385A GLY 4.6 0.4 - - - +
386A TRP* 3.6 36.3 - - + -
401A LEU* 4.2 12.7 - - + +
421A LYS 2.9 13.6 + - - +
422A VAL* 3.2 10.7 + - + +
424A ALA* 1.3 76.7 - - - +
426A THR* 1.3 56.7 + - - +
428A SER* 3.7 6.1 - - - -
429A ARG* 2.9 35.7 + - - +
430A LEU* 3.6 0.9 + - - -
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Residues in contact with THR 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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406A LEU* 3.6 24.3 - - + +
422A VAL* 2.8 28.0 + - - +
423A ALA* 3.5 8.5 - - - -
425A ALA* 1.3 73.0 - - - +
427A SER* 1.3 61.4 + - - +
430A LEU* 3.0 15.1 + - - +
431A LEU* 2.8 31.6 + - + +
436A ILE* 3.8 29.2 - - + -
464A LEU* 4.4 9.2 - - + -
472A VAL* 4.1 16.2 - - + -
476A VAL* 4.8 4.9 - - + -
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Residues in contact with SER 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ALA 2.9 16.7 + - - -
424A ALA* 4.1 4.9 - - - -
426A THR* 1.3 78.9 - - - +
428A SER* 1.3 61.0 + - - +
431A LEU* 4.0 30.0 + - - +
472A VAL* 4.3 20.0 - - - +
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Residues in contact with SER 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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424A ALA 2.8 22.0 + - - -
425A ALA* 3.6 7.1 + - - -
427A SER* 1.3 80.1 - - - +
429A ARG* 1.3 73.5 + - - +
431A LEU 6.0 0.4 - - - -
432A LYS* 5.7 0.7 + - - -
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Residues in contact with ARG 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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384A GLU* 4.9 5.7 + - - -
386A TRP* 3.4 31.1 - - - -
401A LEU* 3.6 27.8 - - + -
425A ALA* 2.9 12.6 + - - +
428A SER* 1.3 94.7 + - - +
430A LEU* 1.3 60.7 + - - +
431A LEU 3.8 1.3 - - - -
432A LYS* 3.5 24.0 + - - +
437A ALA* 5.2 0.2 - - - +
440A THR* 3.9 20.2 - - + +
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Residues in contact with LEU 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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401A LEU* 3.9 44.4 - - + +
402A THR 4.2 14.1 - - - +
403A ALA* 4.3 4.0 - - - -
406A LEU* 4.5 3.4 - - + -
425A ALA 3.6 2.2 + - - +
426A THR* 3.0 21.0 + - - +
429A ARG* 1.3 82.4 - - - +
431A LEU* 1.3 64.3 + - - +
432A LYS* 3.3 2.4 + - - +
436A ILE* 3.5 29.1 - - + -
437A ALA* 2.7 47.6 + - + +
438A THR 5.0 1.1 - - - +
439A THR* 4.7 7.9 - - - -
440A THR* 4.0 15.0 - - + -
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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
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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