Contacts of the helix formed by residues 400 - 421 (chain A) in PDB entry 1A8H
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 PHE 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TYR* 5.3 1.8 - - - -
28A VAL* 3.3 37.0 - - + -
31A PHE* 3.5 31.9 - + + -
32A LEU* 3.9 25.8 - - + -
325A LEU* 3.6 28.0 - - + +
328A ILE 5.5 2.9 - - - +
330A TYR* 3.9 29.6 - + + -
395A VAL* 3.7 24.7 - - + -
398A LEU* 3.5 18.7 + - + -
399A LYS* 1.3 71.2 - - - +
401A HIS* 1.3 65.2 + - - +
403A ALA* 3.6 6.9 - - - +
404A LEU* 3.1 29.7 + - + +
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Residues in contact with HIS 401 (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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325A LEU 3.3 13.3 + - - +
326A ARG* 3.2 33.0 + - - +
327A GLU 5.2 0.4 - - - -
328A ILE 5.0 0.6 + - - +
329A PRO* 3.6 48.1 - - + +
330A TYR 4.8 1.0 + - - -
332A GLN* 5.4 3.3 + - - -
398A LEU 4.6 3.1 + - - -
399A LYS* 3.7 36.3 - - + +
400A PHE* 1.3 75.7 + - - +
402A VAL* 1.3 71.0 + - + +
405A GLU* 3.1 28.2 + - - +
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Residues in contact with VAL 402 (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 LEU* 3.8 26.2 - - + -
399A LYS* 3.7 17.0 - - + +
400A PHE 3.2 0.4 - - - -
401A HIS* 1.3 104.1 + - + +
403A ALA* 1.3 61.4 + - - +
405A GLU* 3.4 16.8 + - - +
406A GLU* 2.9 39.4 + - - +
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Residues in contact with ALA 403 (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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31A PHE* 5.5 2.7 - - + -
391A LEU* 3.5 37.8 - - + +
394A LEU* 4.1 6.9 - - + +
395A VAL* 4.2 21.3 - - + -
399A LYS 3.2 10.7 + - - +
400A PHE* 3.3 10.0 + - - +
402A VAL* 1.3 79.1 - - - +
404A LEU* 1.3 65.0 + - + +
406A GLU* 3.1 7.3 + - - +
407A ALA* 3.1 17.0 + - - +
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Residues in contact with LEU 404 (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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31A PHE* 4.6 15.7 - - + -
322A TYR* 4.4 12.8 - - + -
325A LEU* 3.6 33.2 - - + -
326A ARG* 3.8 28.3 - - + +
391A LEU* 6.1 1.8 - - + -
400A PHE* 3.1 14.0 + - + +
401A HIS 4.3 0.2 - - - +
403A ALA* 1.3 77.5 - - + +
405A GLU* 1.3 60.0 + - - +
407A ALA* 3.8 5.7 - - + +
408A MET* 2.9 35.0 + - - +
451A LEU 4.8 8.3 - - - +
452A LEU* 3.8 23.6 - - + -
455A ALA* 4.2 20.9 - - + -
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Residues in contact with GLU 405 (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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326A ARG* 3.6 34.4 + - - +
401A HIS 3.1 20.2 + - - +
402A VAL* 3.6 22.9 - - - +
403A ALA 3.2 0.2 - - - -
404A LEU* 1.3 76.9 - - - +
406A GLU* 1.3 61.8 + - - +
408A MET* 3.7 2.5 + - - +
409A ALA* 3.0 28.1 + - + +
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Residues in contact with GLU 406 (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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387A LEU* 4.2 9.6 - - + +
390A ARG* 3.3 38.2 + - - +
391A LEU* 4.0 15.7 - - + -
394A LEU* 4.1 10.2 - - + +
402A VAL* 2.9 30.8 - - + +
403A ALA 3.1 7.2 + - - +
404A LEU 3.1 0.6 - - - -
405A GLU* 1.3 82.1 - - - +
407A ALA* 1.3 64.5 + - - +
409A ALA* 3.1 18.4 + - - +
410A TYR* 3.2 12.5 + - - +
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Residues in contact with ALA 407 (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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387A LEU* 4.4 11.7 - - - -
391A LEU* 4.7 5.3 - - + +
403A ALA 3.1 11.6 + - - +
404A LEU* 3.3 9.8 + - + +
406A GLU* 1.3 76.3 - - - +
408A MET* 1.3 61.5 + - - +
410A TYR* 3.1 16.1 + - - +
411A VAL* 3.2 15.2 + - - +
448A ALA* 4.9 3.3 - - - +
451A LEU* 4.2 27.1 - - + -
452A LEU* 4.2 20.4 - - + -
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Residues in contact with MET 408 (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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322A TYR* 3.2 35.2 - - + +
326A ARG* 5.3 2.0 - - - +
348A ASP* 3.5 43.5 - - + +
349A LEU* 5.2 0.7 - - - -
352A ASP* 4.1 15.3 - - + +
353A LEU* 4.6 9.6 - - + -
404A LEU 2.9 19.1 + - - +
405A GLU* 4.1 4.7 - - - +
407A ALA* 1.3 74.9 - - - +
409A ALA* 1.3 61.3 + - - +
411A VAL* 3.2 21.1 + - + +
412A LYS* 3.0 34.5 + - + +
452A LEU* 4.5 16.2 - - + -
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Residues in contact with ALA 409 (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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405A GLU* 3.0 22.5 + - + +
406A GLU* 3.1 15.5 + - - +
408A MET* 1.3 76.9 - - - +
410A TYR* 1.3 56.1 + - - +
412A LYS* 3.4 12.6 + - - +
413A ALA* 3.1 23.6 + - - +
416A ARG* 5.1 2.1 + - - -
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Residues in contact with TYR 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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381A LEU* 2.8 43.1 + - + +
383A GLU* 5.1 9.0 - - + -
384A GLY* 3.7 22.4 - - - -
387A LEU* 3.8 27.1 - - + -
406A GLU 3.2 4.0 + - - +
407A ALA 3.1 9.6 + - - +
409A ALA* 1.3 76.6 - - - +
411A VAL* 1.3 59.5 + - - +
413A ALA* 3.0 12.6 + - + +
414A LEU* 2.9 42.3 + - + +
444A GLY* 3.3 31.6 - - - -
447A ILE* 4.4 15.1 - - + +
448A ALA* 4.4 10.8 - - + -
451A LEU* 5.7 0.2 - - + -
481A TRP* 3.5 16.8 - - - -
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Residues in contact with VAL 411 (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 ASP* 3.4 30.7 - - + +
353A LEU* 4.0 22.2 - - + -
356A LEU* 4.7 5.8 - - + -
407A ALA 3.5 13.7 - - - +
408A MET* 3.2 27.8 + - + +
410A TYR* 1.3 79.2 - - - +
412A LYS* 1.3 58.9 + - - +
414A LEU* 3.2 11.8 + - + +
415A ASN* 3.0 29.0 + - - +
445A LEU* 5.2 0.7 - - + -
448A ALA* 3.8 24.2 - - + -
452A LEU* 4.6 3.4 - - + -
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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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347A ALA* 6.3 0.8 - - - +
348A ASP* 5.5 2.1 + - - -
352A ASP* 3.0 34.6 + - - +
408A MET* 3.0 18.9 + - + +
409A ALA* 3.6 13.9 - - - +
410A TYR 3.2 0.2 - - - -
411A VAL* 1.3 73.3 - - - +
413A ALA* 1.3 66.6 + - - +
415A ASN* 3.2 9.2 + - + +
416A ARG* 3.0 34.9 + - - +
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Residues in contact with ALA 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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381A LEU* 4.6 10.2 - - + +
409A ALA 3.1 13.1 + - - +
410A TYR* 3.0 21.7 + - + +
412A LYS* 1.3 77.6 - - - +
414A LEU* 1.3 57.1 + - - +
416A ARG* 3.5 25.2 + - - +
417A TYR* 2.9 29.0 + - - +
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Residues in contact with LEU 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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356A LEU* 3.9 12.3 - - + -
381A LEU* 3.7 34.5 - - + -
410A TYR* 2.9 30.0 + - + +
411A VAL* 3.3 16.8 - - - +
413A ALA* 1.3 75.6 - - - +
415A ASN* 1.3 65.7 + - - +
417A TYR* 3.2 5.7 + - - +
418A ILE* 3.1 24.6 + - - +
440A ARG 4.5 1.8 - - - +
441A VAL* 4.5 12.2 - - + +
444A GLY* 3.6 40.6 - - - +
445A LEU* 3.8 20.4 - - + +
448A ALA* 4.8 1.6 - - + -
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Residues in contact with ASN 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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351A ASP 4.7 0.7 - - - +
352A ASP* 2.8 41.3 + - - +
356A LEU* 3.6 19.8 - - - +
359A ARG* 2.8 28.7 + - - +
411A VAL 3.0 26.5 + - - -
412A LYS* 3.2 11.0 + - + +
414A LEU* 1.3 77.5 - - - +
416A ARG* 1.3 63.9 + - + +
417A TYR 3.2 0.3 + - - -
418A ILE* 3.3 2.4 - - - +
419A ASN* 3.0 34.6 + - - +
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Residues in contact with ARG 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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409A ALA 5.1 2.4 + - - -
412A LYS* 3.0 21.4 + - - +
413A ALA* 3.8 28.1 + - - +
415A ASN* 1.3 77.2 - - + +
417A TYR* 1.3 64.0 + - - +
419A ASN* 3.4 8.8 + - - +
420A GLU* 2.9 26.8 + - - +
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Residues in contact with TYR 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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379A GLU* 5.2 1.3 - - + +
380A GLU* 3.7 30.6 + - - -
381A LEU* 3.9 31.4 - - + -
413A ALA 2.9 15.8 + - - +
414A LEU* 3.3 12.8 - - - +
415A ASN 3.1 0.2 - - - -
416A ARG* 1.3 76.1 - - - +
418A ILE* 1.3 61.1 + - - +
420A GLU* 3.1 10.6 + - - +
421A LYS* 2.9 58.9 + - + +
437A VAL* 3.4 35.8 - - + +
440A ARG* 3.0 39.3 + - + -
441A VAL* 4.3 7.9 - - + -
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Residues in contact with ILE 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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356A LEU* 4.2 6.7 - - + -
359A ARG* 3.7 16.2 - - - +
360A THR* 4.6 12.1 - - - +
363A MET* 3.2 37.9 - - + -
414A LEU 3.1 9.8 + - - +
415A ASN 3.3 10.8 - - - +
417A TYR* 1.3 84.9 - - - +
419A ASN* 1.3 70.6 + - - +
420A GLU 3.2 0.2 - - - -
422A LYS* 3.1 21.2 + - - -
423A PRO* 3.3 26.2 - - + +
424A TRP* 3.9 4.1 - - + -
437A VAL* 4.5 4.3 - - + -
438A LEU* 4.4 8.1 - - + -
441A VAL* 4.1 20.0 - - + -
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Residues in contact with ASN 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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359A ARG* 3.6 24.9 + - - +
415A ASN* 3.0 28.6 + - - +
416A ARG* 3.8 8.2 - - - +
418A ILE* 1.3 81.6 - - - +
420A GLU* 1.3 58.7 + - - +
422A LYS* 3.1 26.5 + - - +
424A TRP* 4.7 11.0 - - - -
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Residues in contact with GLU 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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380A GLU* 5.0 4.0 - - - +
416A ARG 2.9 18.9 + - - +
417A TYR* 3.6 11.7 - - - +
419A ASN* 1.3 76.0 - - - +
421A LYS* 1.3 80.1 + - + +
422A LYS* 3.1 24.0 + - - +
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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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379A GLU* 5.7 3.4 + - - -
380A GLU* 4.7 11.1 + - - -
417A TYR* 2.9 58.1 + - + +
418A ILE 4.7 0.4 - - - +
420A GLU* 1.3 89.4 - - + +
422A LYS* 1.3 70.3 + - - +
425A GLU* 5.5 0.2 - - - +
426A LEU* 3.2 26.3 - - + +
437A VAL* 3.8 28.0 - - + -
440A ARG* 6.0 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