Contacts of the helix formed by residues 411 - 426 (chain A) in PDB entry 4AB1
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 VAL 411 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A GLY 4.1 15.8 - - - +
372A GLN* 4.1 4.2 - - + +
409A ASP* 2.7 22.5 + - - +
410A THR* 1.3 71.7 + - - +
412A LYS* 1.3 57.4 + - + +
414A LYS* 3.1 19.4 + - - +
415A ASP* 3.1 17.5 + - - +
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Residues in contact with LYS 412 (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 THR* 4.0 22.9 - - + +
409A ASP* 3.1 32.3 + - + +
411A VAL* 1.3 72.0 - - + +
413A LYS* 1.3 53.4 + - - +
414A LYS 2.9 1.6 - - - -
415A ASP* 2.6 37.2 + - - +
416A LEU* 2.7 25.7 + - + +
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Residues in contact with LYS 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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373A LEU* 3.4 26.7 - - - +
374A ASP* 5.3 0.2 - - - +
375A GLN* 2.8 39.5 + - + +
404A LEU* 2.9 36.4 + - + +
405A GLY* 4.7 1.2 - - - -
407A THR* 2.7 38.3 + - + +
408A ASP* 3.9 13.7 - - - +
409A ASP 2.9 19.0 + - - +
410A THR* 3.9 5.6 - - - +
412A LYS* 1.3 72.4 - - - +
414A LYS* 1.3 56.5 + - - +
416A LEU* 4.2 6.5 - - - -
417A PHE* 2.9 30.1 + - - +
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Residues in contact with LYS 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 4.5 21.1 - - + -
371A GLY* 3.9 33.2 - - - +
372A GLN* 4.1 6.3 - - - +
373A LEU* 4.2 11.4 - - + +
410A THR 3.3 12.7 + - - +
411A VAL 3.1 11.8 + - - +
412A LYS 2.9 1.2 - - - -
413A LYS* 1.3 79.8 - - - +
415A ASP* 1.3 66.1 + - - +
417A PHE* 3.5 4.8 + - + +
418A LEU* 3.1 44.1 + - + +
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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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411A VAL 3.1 16.4 + - - +
412A LYS* 2.6 23.2 + - - +
414A LYS* 1.3 79.5 - - - +
416A LEU* 1.3 53.9 + - + +
418A LEU* 2.9 16.2 + - - +
419A ASP* 2.8 37.2 + - - +
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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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403A TYR* 3.3 38.6 - - + +
404A LEU* 3.6 10.8 - - + -
406A GLY* 5.8 2.0 - - - +
407A THR* 3.7 30.3 - - + -
412A LYS* 2.7 22.3 + - + +
413A LYS* 3.9 1.3 - - - +
415A ASP* 1.3 72.5 - - + +
417A PHE* 1.3 58.8 + - - +
419A ASP* 3.2 23.6 - - + +
420A LEU* 3.0 23.9 + - - +
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Residues in contact with PHE 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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366A TYR* 4.9 10.3 - + - -
368A LEU* 5.2 4.3 - - + -
373A LEU* 3.5 21.5 - - + -
378A ALA* 3.4 28.9 - - + -
381A LEU* 3.7 34.3 - - + -
382A LEU* 4.0 23.3 - - + -
385A SER* 4.6 2.9 - - - -
400A THR* 5.8 1.6 - - + -
404A LEU* 3.3 12.2 - - + +
413A LYS 2.9 19.7 + - - +
414A LYS* 3.5 6.7 - - + +
416A LEU* 1.3 74.1 - - - +
418A LEU* 1.3 77.0 + - + +
420A LEU* 3.3 18.5 + - + +
421A ILE* 3.4 35.1 + - + +
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Residues in contact with LEU 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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355A PHE* 3.5 49.3 - - + +
356A GLY* 4.2 16.8 - - - +
360A PRO* 4.9 3.1 - - + -
366A TYR* 6.0 0.2 - - + -
368A LEU* 4.5 20.4 - - + -
414A LYS* 3.1 39.0 + - + +
415A ASP* 2.9 16.7 + - - +
417A PHE* 1.3 87.2 - - + +
419A ASP* 1.3 62.3 + - - +
421A ILE* 3.4 4.5 + - - +
422A ALA* 3.0 24.8 + - - +
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Residues in contact with ASP 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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352A LYS 4.9 8.8 - - - +
353A GLN* 5.3 7.1 - - - +
403A TYR* 4.1 11.4 - - + -
415A ASP* 2.8 14.2 + - - +
416A LEU* 3.2 33.4 - - - +
418A LEU* 1.3 77.0 - - - +
420A LEU* 1.3 56.6 + - - +
422A ALA* 3.4 6.4 + - - +
423A ASP* 3.0 37.1 + - - +
540A LYS* 6.3 1.1 - - - -
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Residues in contact with LEU 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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382A LEU* 4.0 33.7 - - + -
389A VAL* 5.7 0.4 - - + -
391A ILE* 4.4 0.9 - - + -
399A ALA 3.7 30.3 - - - +
400A THR* 4.2 5.2 - - - -
403A TYR* 3.5 36.1 - - + -
404A LEU* 5.1 1.3 - - + -
416A LEU 3.0 11.4 + - - +
417A PHE* 3.6 15.3 - - + +
418A LEU 3.3 0.4 - - - -
419A ASP* 1.3 72.2 - - - +
421A ILE* 1.3 69.0 + - + +
423A ASP* 3.3 3.1 + - - +
424A VAL* 3.0 26.1 + - + +
547A TRP* 3.4 27.5 - - + -
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Residues in contact with ILE 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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355A PHE* 3.6 44.4 - - + -
366A TYR* 4.8 2.0 - - + +
382A LEU* 3.8 28.7 - - + -
385A SER* 4.3 12.3 - - - +
388A LEU* 4.9 3.4 - - + -
389A VAL* 4.1 19.1 - - + -
417A PHE* 3.4 34.1 - - + +
418A LEU 3.4 4.9 + - - +
420A LEU* 1.3 75.7 - - - +
422A ALA* 1.3 58.7 + - - +
424A VAL* 3.2 1.9 + - - +
425A MET* 2.8 42.4 + - + +
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Residues in contact with ALA 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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352A LYS 5.8 1.3 - - - +
353A GLN* 5.1 1.1 - - - -
354A GLU* 3.9 15.9 - - + +
355A PHE* 3.9 23.8 - - - +
418A LEU 3.0 18.5 + - - +
419A ASP* 3.6 8.5 - - - +
420A LEU 3.3 0.2 - - - -
421A ILE* 1.3 77.2 - - - +
423A ASP* 1.3 57.5 + - - +
425A MET* 4.8 0.2 - - - -
426A PHE* 2.7 43.0 + - - +
427A GLY 3.1 5.7 + - - -
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Residues in contact with ASP 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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403A TYR* 2.6 39.8 + - - +
419A ASP* 3.0 21.9 + - - +
420A LEU 3.6 3.1 - - - +
421A ILE 3.3 0.2 - - - -
422A ALA* 1.3 75.1 - - - +
424A VAL* 1.3 65.4 + - - +
427A GLY* 3.3 9.3 + - - +
428A VAL* 2.9 37.5 + - + +
540A LYS* 2.8 34.2 + - - -
543A GLU* 3.3 15.5 - - - +
547A TRP* 4.4 4.3 - - - +
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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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252A THR* 5.0 1.4 + - - -
388A LEU 4.9 1.1 - - - +
389A VAL* 3.8 37.9 - - + +
391A ILE* 4.8 2.9 - - + -
420A LEU* 3.0 24.6 + - + +
421A ILE 3.2 3.6 + - - +
423A ASP* 1.3 82.0 - - - +
425A MET* 1.3 63.1 + - - +
428A VAL* 5.0 2.5 - - - -
429A PRO* 3.4 15.5 - - - +
547A TRP* 3.5 45.1 - - + -
551A PHE* 5.0 11.0 - - + -
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Residues in contact with MET 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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249A VAL* 5.9 1.6 + - - +
253A SER* 5.5 6.9 - - - -
254A VAL* 4.2 18.2 - - + -
355A PHE* 3.8 18.8 - - + -
359A ILE* 4.9 7.4 - - + -
388A LEU* 3.9 45.8 - - + +
389A VAL* 4.4 2.5 - - + -
421A ILE* 2.8 39.5 + - + +
424A VAL* 1.3 79.4 - - - +
426A PHE* 1.3 94.8 + - + +
429A PRO* 3.6 13.2 - - - +
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Residues in contact with PHE 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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221A SER* 4.5 4.5 - - - -
247A SER* 3.3 38.6 - - - -
248A GLY* 4.1 7.6 - - - -
249A VAL* 6.4 0.2 - - - -
350A ILE* 4.2 5.6 - - + -
354A GLU* 3.6 38.1 - - + +
355A PHE* 5.2 1.3 - + - -
359A ILE* 3.7 24.2 - - + -
422A ALA* 2.7 16.4 + - - +
425A MET* 1.3 109.8 - - + +
427A GLY* 1.3 62.9 + - - +
428A VAL 3.6 1.8 - - - -
429A PRO* 3.7 2.5 - - - +
430A SER* 2.7 33.3 + - - +
468A HIS* 3.6 18.6 - + - -
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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
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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