Contacts of the helix formed by residues 419 - 429 (chain A) in PDB entry 4FGU
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 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417A PRO* 3.1 19.5 - - + +
418A LEU* 1.3 81.1 + - + +
420A ARG* 1.3 91.1 + - + +
421A ILE 3.2 1.8 - - - -
422A LYS* 3.4 14.8 + - + +
423A LEU* 3.2 28.0 + - + +
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Residues in contact with ARG 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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356A LEU* 3.9 15.5 - - + +
416A TYR* 5.9 1.6 - - - -
417A PRO* 3.2 38.2 + - + +
419A HIS* 1.3 105.3 - - + +
421A ILE* 1.3 59.8 + - - +
423A LEU* 3.4 21.4 - - + +
424A SER* 2.8 29.1 + - - -
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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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352A ILE* 5.4 2.1 - - + +
356A LEU* 4.2 18.8 - - + -
383A LEU* 3.9 20.6 - - + -
408A LEU* 5.4 3.1 - - + +
411A LEU* 4.1 24.0 - - + +
412A CYS* 3.7 25.4 - - - -
416A TYR* 3.7 26.0 - - + +
417A PRO* 3.2 18.4 + - + +
419A HIS 3.2 0.6 - - - -
420A ARG* 1.3 76.8 - - - +
422A LYS* 1.3 61.4 + - - +
423A LEU 3.2 0.2 - - - -
424A SER* 4.1 5.6 - - - +
425A MET* 3.3 45.0 + - + +
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Residues in contact with LYS 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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382A ALA* 4.6 14.8 + - + +
383A LEU* 3.4 23.1 - - + -
386A PHE* 3.4 48.5 - - + -
418A LEU 3.5 12.6 - - - +
419A HIS* 3.4 13.2 + - + +
421A ILE* 1.3 75.8 - - - +
423A LEU* 1.3 58.1 + - - +
425A MET* 3.7 2.0 + - - +
426A ASP* 2.9 36.1 + - - +
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Residues in contact with LEU 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 HIS* 3.2 19.2 + - + +
420A ARG* 3.4 27.6 - - + +
422A LYS* 1.3 75.8 - - - +
424A SER* 1.3 64.6 + - - +
425A MET 3.2 0.2 - - - -
426A ASP* 3.1 12.8 + - + +
427A HIS* 3.1 22.3 + - - +
433A TYR* 5.0 20.8 - - + -
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Residues in contact with SER 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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352A ILE* 3.4 34.9 + - - +
355A LEU* 3.6 19.6 - - - +
356A LEU* 3.9 16.9 - - - +
420A ARG 2.8 18.7 + - - -
421A ILE* 3.6 6.0 + - - -
422A LYS 3.5 0.2 - - - -
423A LEU* 1.3 75.9 - - - +
425A MET* 1.3 60.7 + - - +
427A HIS* 3.6 4.1 + - - +
428A VAL* 3.4 25.1 + - - +
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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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352A ILE* 3.6 25.1 - - + -
383A LEU* 4.4 11.9 - - + +
386A PHE* 4.3 27.6 - - + +
387A ARG* 3.7 22.9 - - - +
390A CYS* 4.0 17.7 - - - -
408A LEU* 3.5 31.6 - - + -
421A ILE* 3.3 31.1 + - + +
422A LYS* 3.8 5.2 - - - +
423A LEU 3.2 0.4 - - - -
424A SER* 1.3 76.6 - - - +
426A ASP* 1.3 60.2 + - - +
428A VAL 2.9 3.1 + - - -
429A CYS* 2.7 35.8 + - - +
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Residues in contact with ASP 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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386A PHE* 3.2 30.1 - - - -
422A LYS* 2.9 21.5 + - - +
423A LEU* 3.1 16.0 + - + +
425A MET* 1.3 78.1 - - - +
427A HIS* 1.3 50.9 + - - +
430A LEU* 3.7 14.9 + - - +
431A GLY 3.1 9.0 + - - -
432A HIS* 2.6 57.5 + - + +
433A TYR* 5.3 6.3 - - + -
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Residues in contact with HIS 427 (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 LEU* 3.6 33.1 - - + +
423A LEU 3.1 14.2 + - - +
424A SER* 4.0 7.6 - - - +
425A MET 3.1 0.2 - - - -
426A ASP* 1.3 76.6 - - - +
428A VAL* 1.3 61.1 + - + +
431A GLY* 3.3 13.9 - - - -
432A HIS 3.7 5.2 - - - +
433A TYR* 3.9 12.1 - - + +
434A GLY* 3.0 44.5 - - - -
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Residues in contact with VAL 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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348A SER* 3.7 36.8 - - - +
351A LYS* 4.0 31.4 - - + +
352A ILE* 3.8 14.8 - - + -
355A LEU* 4.7 8.3 - - + -
424A SER 3.4 17.9 + - - +
425A MET 2.9 4.0 + - - -
427A HIS* 1.3 84.5 - - + +
429A CYS* 1.3 64.6 + - - +
430A LEU 3.5 0.4 + - - -
431A GLY* 3.8 5.1 + - - -
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Residues in contact with CYS 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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348A SER* 5.7 3.1 - - - -
352A ILE* 4.9 4.5 - - - -
387A ARG* 4.3 4.7 - - - -
390A CYS* 2.0 59.9 - - + +
391A PHE* 4.9 11.0 - - + -
425A MET* 2.7 22.7 + - - +
428A VAL* 1.3 83.6 - - - +
430A LEU* 1.3 67.7 + - + +
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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