Contacts of the helix formed by residues 404 - 421 (chain A) in PDB entry 4OE4
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 HIS 404 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A PHE* 5.6 1.0 - + - -
238A THR* 4.0 28.3 - - + -
402A VAL* 3.5 1.1 + - - +
403A ILE* 1.3 96.9 - - + +
405A GLU* 1.3 62.1 + - - +
406A GLN* 3.4 24.7 + - + +
407A SER* 3.0 46.0 + - - -
408A PHE* 2.9 25.6 + - - +
438A TRP* 3.5 18.8 - - + +
1000A NAD 5.3 5.5 + - - -
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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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404A HIS* 1.3 75.8 - - - +
406A GLN* 1.3 69.1 + - - +
408A PHE* 3.4 0.6 - - - +
409A ASP* 2.7 47.9 + - - +
434A LYS* 3.0 24.5 + - - +
438A TRP* 3.5 46.3 - - + -
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Residues in contact with GLN 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A HIS* 3.2 27.5 + - + +
405A GLU* 1.3 96.1 + - - +
407A SER* 1.3 61.5 + - - +
409A ASP* 3.6 6.8 + - - +
410A LYS* 3.1 23.2 + - - +
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Residues in contact with SER 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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349A GLN* 4.5 1.7 + - - -
402A VAL* 3.8 10.4 - - - +
403A ILE* 4.3 11.9 - - - -
404A HIS* 3.0 30.3 + - - -
406A GLN* 1.3 73.9 - - - +
408A PHE* 1.3 66.4 + - - +
410A LYS* 3.3 6.5 + - - +
411A LEU* 3.1 39.7 + - - +
459A PHE 5.3 0.7 + - - -
460A PHE 4.2 9.2 + - - -
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Residues in contact with PHE 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL* 4.0 7.2 - - - +
404A HIS 2.9 13.5 + - - +
405A GLU* 3.2 12.3 + - - +
407A SER* 1.3 77.7 + - - +
409A ASP* 1.3 61.7 + - - +
411A LEU* 3.3 5.3 + - - +
412A VAL* 3.0 39.3 + - + +
432A TYR* 3.7 21.1 - + + -
433A ASP 3.7 18.6 - - - -
434A LYS* 3.4 46.2 - - + -
438A TRP* 3.8 26.5 - + + -
439A PHE 3.3 27.8 - - - -
440A VAL* 3.6 13.4 - - + +
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Residues in contact with ASP 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLU* 2.7 36.3 + - - +
406A GLN* 4.0 6.4 + - - +
408A PHE* 1.3 75.9 - - - +
410A LYS* 1.3 65.0 + - - +
412A VAL* 3.3 7.6 + - - +
413A LYS* 3.1 21.8 + - - +
434A LYS* 3.0 31.2 + - - -
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Residues in contact with LYS 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLN 3.1 17.9 + - - +
407A SER* 3.3 7.1 + - - +
409A ASP* 1.3 75.2 - - - +
411A LEU* 1.3 60.1 + - + +
413A LYS* 3.2 10.0 + - - +
414A VAL* 3.0 33.0 + - + +
459A PHE 5.9 1.8 - - - +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL* 3.6 30.5 - - + -
407A SER* 3.1 25.0 + - - +
408A PHE 3.6 3.8 - - - +
410A LYS* 1.3 76.1 - - + +
412A VAL* 1.3 64.7 + - - +
414A VAL* 3.3 7.3 + - + +
415A ILE* 3.0 29.8 + - - +
440A VAL* 4.1 22.4 - - + -
459A PHE* 3.7 28.3 - - + +
460A PHE 4.5 0.2 - - - +
461A GLY* 4.0 17.7 - - - -
462A PRO* 4.2 2.7 - - + -
463A ILE* 3.6 23.5 - - + +
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Residues in contact with VAL 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PHE* 3.0 34.9 + - + +
409A ASP* 3.6 11.7 - - - +
410A LYS 3.3 0.2 - - - -
411A LEU* 1.3 75.9 - - + +
413A LYS* 1.3 57.8 + - - +
415A ILE* 3.2 5.6 + - - +
416A GLU* 2.8 37.5 + - + +
432A TYR* 3.5 53.2 - - + +
440A VAL* 5.5 0.7 - - + -
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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
----------------------------------------------------------
409A ASP 3.1 12.6 + - - +
410A LYS* 3.2 12.8 + - - +
412A VAL* 1.3 76.4 - - - +
414A VAL* 1.3 59.9 + - + +
416A GLU* 4.5 4.3 - - - +
417A ASP* 2.6 71.0 + - - +
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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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410A LYS* 3.0 23.7 + - + +
411A LEU* 3.5 9.6 - - + +
413A LYS* 1.3 76.3 - - + +
415A ILE* 1.3 63.7 + - - +
417A ASP* 4.7 1.1 - - - -
418A ALA* 3.1 8.1 + - - +
445A ILE* 4.6 1.1 - - + -
454A TYR* 2.5 47.7 + - + +
459A PHE* 3.5 41.5 - - + -
463A ILE* 3.6 24.7 - - + -
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Residues in contact with ILE 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 LEU 3.0 20.7 + - - +
412A VAL* 3.7 3.8 - - - +
414A VAL* 1.3 75.8 - - - +
416A GLU* 1.3 66.8 + - - +
418A ALA* 3.1 20.8 + - - +
419A LYS* 3.4 15.5 + - - +
426A ILE* 3.8 19.6 - - + +
430A GLY* 3.6 39.3 - - - +
432A TYR* 4.1 19.3 - - + -
440A VAL* 3.9 26.2 - - + -
443A THR* 4.0 11.7 - - + +
445A ILE* 5.0 2.2 - - + -
463A ILE* 4.1 14.1 - - + -
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Residues in contact with GLU 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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412A VAL* 2.8 30.9 + - + +
413A LYS* 4.1 4.0 - - - +
415A ILE* 1.3 73.4 - - - +
417A ASP* 1.3 63.7 + - - +
419A LYS* 2.7 52.7 + - - +
420A LYS* 3.7 14.5 + - + +
432A TYR* 2.6 33.2 + - + +
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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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413A LYS* 2.6 62.1 + - - +
414A VAL* 5.1 0.3 - - - -
416A GLU* 1.3 74.1 - - - +
418A ALA* 1.3 62.0 + - - +
420A LYS* 2.9 26.5 + - - +
421A ASP* 3.3 14.1 + - - +
424A LEU* 5.1 0.2 - - - -
454A TYR* 3.4 14.3 + - + +
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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 VAL 3.1 15.1 + - - +
415A ILE 3.1 11.6 + - - +
417A ASP* 1.3 75.8 - - - +
419A LYS* 1.3 61.2 + - - +
420A LYS 3.2 0.9 + - - -
421A ASP 3.4 16.3 + - - +
424A LEU* 3.7 27.4 - - + +
425A GLU* 5.2 0.3 - - - -
426A ILE* 4.1 13.3 + - + +
445A ILE* 3.8 28.0 - - + -
454A TYR* 3.5 5.3 + - + -
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Residues in contact with LYS 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 ILE* 3.4 16.7 + - - +
416A GLU* 2.7 47.6 + - - +
418A ALA* 1.3 76.9 - - - +
420A LYS* 1.3 62.6 + - + +
421A ASP 3.5 1.4 - - - +
426A ILE* 3.8 24.9 - - + -
430A GLY 4.9 3.5 + - - -
432A TYR* 4.7 3.2 + - - -
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Residues in contact with LYS 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 GLU* 3.8 16.2 - - + +
417A ASP* 2.9 17.7 + - - +
419A LYS* 1.3 82.5 - - + +
421A ASP* 1.3 59.9 + - - +
422A PRO* 3.6 8.5 - - - +
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Residues in contact with ASP 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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417A ASP 3.3 8.6 + - - +
418A ALA 3.4 3.6 + - - +
419A LYS 5.0 1.1 - - - +
420A LYS* 1.3 77.9 - - - +
422A PRO* 1.3 69.0 - - - +
423A GLU* 3.0 21.3 + - - +
424A LEU* 3.0 45.6 + - + +
452A HIS* 2.9 30.8 + - - -
454A TYR* 5.5 0.7 - - - -
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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