Contacts of the helix formed by residues 414 - 426 (chain A) in PDB entry 5FLZ
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 ASP 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A PHE 3.1 2.8 + - - -
410A PHE 3.4 10.2 + - - +
411A GLN* 3.8 7.6 - - - +
412A GLY* 3.6 16.0 + - - -
413A TYR* 1.4 85.9 + - - +
415A LEU* 1.4 62.4 + - - +
416A ILE* 3.2 4.3 + - + +
417A ASN* 3.6 29.3 + - + +
418A VAL* 3.8 13.9 + - - +
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Residues in contact with LEU 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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406A LEU* 5.2 3.1 - - + -
409A PHE* 2.8 54.7 + - + +
410A PHE* 3.5 8.6 + - + +
413A TYR 3.5 1.3 - - - -
414A ASP* 1.4 68.7 - - - +
416A ILE* 1.3 67.6 + - - +
418A VAL* 3.1 20.1 - - + +
419A LEU* 3.0 34.7 + - + +
570A LEU* 5.6 3.4 - - + -
573A ILE* 4.8 11.2 - - + -
672A ILE* 4.0 28.5 - - + -
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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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410A PHE* 3.9 42.0 + - + +
414A ASP* 4.8 2.2 - - + +
415A LEU* 1.3 82.4 - - - +
417A ASN* 1.3 77.5 + - - +
419A LEU* 3.3 12.7 + - + +
420A LYS* 3.2 42.2 + - + +
663A TYR* 4.9 23.6 - - + +
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Residues in contact with ASN 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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414A ASP* 3.8 26.3 - - + +
415A LEU 3.2 0.4 - - - -
416A ILE* 1.3 82.3 - - - +
418A VAL* 1.3 66.2 - - + +
420A LYS* 3.2 33.8 - - - +
421A HIS* 3.2 39.4 + - + +
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Residues in contact with VAL 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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413A TYR 5.5 2.9 - - - +
414A ASP 3.8 7.8 + - - +
415A LEU* 3.1 43.5 - - + +
417A ASN* 1.3 74.6 - - + +
419A LEU* 1.4 62.9 + - - +
421A HIS* 3.1 14.5 + - + +
422A LEU* 3.0 33.2 + - + +
477A LEU* 3.9 27.1 - - + -
570A LEU* 4.8 21.5 - - + -
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Residues in contact with LEU 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 LEU* 3.0 26.3 + - + +
416A ILE* 3.3 16.8 + - + +
418A VAL* 1.4 74.1 - - - +
420A LYS* 1.4 62.2 + - + +
422A LEU* 3.1 23.6 + - + +
423A GLN* 3.0 37.1 + - + +
659A LEU* 5.4 9.6 - - + -
663A TYR* 4.8 31.4 - - + -
672A ILE* 5.8 11.9 - - + -
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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 ILE* 3.3 41.9 + - + +
417A ASN* 3.2 42.1 + - - +
419A LEU* 1.4 75.0 - - + +
421A HIS* 1.3 62.1 + - + +
423A GLN* 3.2 23.5 + - - +
424A GLN* 3.0 28.0 + - - +
663A TYR* 6.0 2.7 - - + +
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Residues in contact with HIS 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 ASN* 3.2 31.0 + - + +
418A VAL* 3.2 27.7 - - + +
420A LYS* 1.3 78.8 - - + +
422A LEU* 1.3 57.9 + - + +
424A GLN* 3.1 21.0 + - - +
425A ILE 2.9 24.8 + - - -
470A GLN* 5.1 9.8 + - - -
472A GLU* 6.5 0.7 - - + -
473A ASN* 6.0 0.6 + - - -
477A LEU* 4.3 11.9 - - + -
478A MET* 3.5 26.6 - - + +
45C GLU* 6.2 3.4 - - + -
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Residues in contact with LEU 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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415A LEU* 6.3 1.3 - - + -
418A VAL* 3.0 27.9 + - + +
419A LEU* 3.3 26.5 - - + +
421A HIS* 1.3 77.7 - - + +
423A GLN* 1.4 56.4 + - + +
425A ILE* 4.2 7.6 - - + -
426A PHE* 2.8 71.2 + - + +
427A LEU* 5.1 0.2 - - - -
478A MET* 5.7 4.7 - - + -
482A LEU* 6.2 2.5 - - + -
564A ILE* 6.1 0.9 - - + -
574A ILE* 5.9 7.6 - - + -
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Residues in contact with GLN 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 LEU* 3.0 23.2 + - + +
420A LYS* 3.3 35.5 - - - +
422A LEU* 1.4 73.0 - - + +
424A GLN* 1.3 62.9 + - - +
427A LEU* 3.2 46.4 - - + +
428A GLY 3.4 1.7 + - - -
429A TYR* 4.0 4.4 + - - +
430A GLN* 4.0 7.1 - - - +
656A VAL* 5.2 7.5 - - + +
659A LEU* 3.5 30.5 - - + +
660A GLU* 4.6 9.5 - - - +
663A TYR* 5.4 6.5 - - - -
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Residues in contact with GLN 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 LYS 3.0 12.5 + - - +
421A HIS* 3.1 31.0 + - - +
422A LEU 3.2 0.2 - - - -
423A GLN* 1.3 75.8 - - - +
425A ILE* 1.4 73.6 + - - +
428A GLY* 3.1 23.6 - - - -
429A TYR 3.4 3.5 + - - -
430A GLN* 3.4 39.2 + - + +
431A SER* 3.5 13.7 + - - -
469A ARG* 3.1 25.3 + - - +
478A MET* 3.1 23.7 - - - +
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Residues in contact with ILE 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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421A HIS 2.9 15.2 + - - +
422A LEU* 3.9 9.4 - - + +
424A GLN* 1.4 84.0 - - - +
426A PHE* 1.3 84.7 + - + +
428A GLY* 3.0 13.5 + - - -
431A SER* 4.2 7.0 + - - +
469A ARG* 5.1 8.1 - - - +
478A MET* 3.5 35.4 - - + +
479A ARG* 6.1 2.0 - - - +
482A LEU* 3.2 48.9 - - + -
562A PHE* 4.1 15.2 - - + -
586A LEU* 3.5 10.2 - - - +
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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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422A LEU* 2.8 49.1 + - + +
425A ILE* 1.3 77.2 - - + +
427A LEU* 1.3 67.7 + - + +
482A LEU* 3.6 24.9 - - + -
562A PHE* 4.3 12.1 - + - -
564A ILE* 3.6 35.4 - - + -
574A ILE* 5.5 8.3 - - + -
579A MET* 4.8 10.5 - - + -
582A TYR* 3.2 64.3 - + + +
585A ILE* 4.3 2.4 - - - +
586A LEU* 3.3 23.1 - - + +
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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