Contacts of the helix formed by residues 424 - 432 (chain A) in PDB entry 3KHU
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 424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A TYR* 2.8 21.6 + - + +
422A GLU 3.7 0.6 + - - -
423A LEU* 1.3 68.4 - - - +
425A TYR* 1.3 60.3 + - - +
426A GLU* 3.5 10.4 + - - +
427A ARG* 3.3 36.8 + - + +
428A ILE* 3.1 28.8 + - - +
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Residues in contact with TYR 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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334A LEU* 5.0 0.5 - - - +
411A VAL* 5.3 9.6 - - + -
413A ILE* 3.9 9.2 - - - +
420A PHE 2.6 30.5 + - - -
421A LYS 4.4 5.8 - - - -
423A LEU* 3.1 43.1 + - + +
424A ASP* 1.3 69.7 + - - +
426A GLU* 1.3 59.7 + - - +
427A ARG 3.3 0.2 - - - -
428A ILE* 3.8 21.3 - - + -
429A HIS* 2.9 23.6 + - - +
438A ILE* 4.0 27.4 - - + -
445A LEU* 3.7 27.8 - - + +
448A LEU* 5.2 4.9 - - + -
452A LEU* 3.6 25.4 - - + -
455A ILE* 4.3 6.5 - - + -
457A PHE* 3.4 19.1 - + + -
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Residues in contact with GLU 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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424A ASP* 3.5 9.6 + - - +
425A TYR* 1.3 76.1 - - - +
427A ARG* 1.3 63.4 + - - +
429A HIS* 3.3 4.0 + - - +
430A LYS* 3.3 43.2 + - - +
451A GLU* 5.4 2.8 - - - +
455A ILE* 4.0 34.9 - - + +
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Residues in contact with ARG 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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400A ASP* 5.3 0.2 + - - -
402A TYR* 3.5 58.1 - - + +
424A ASP* 3.3 28.9 + - - +
426A GLU* 1.3 79.5 - - - +
428A ILE* 1.3 65.3 + - - +
430A LYS* 3.3 24.8 + - - +
431A LYS* 3.7 13.8 + - + +
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Residues in contact with ILE 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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334A LEU* 6.0 0.2 - - + -
401A PRO 5.6 0.7 - - - +
402A TYR* 3.9 21.3 - - + -
405A CYS* 3.7 35.0 - - + +
411A VAL* 4.5 3.8 - - + -
423A LEU* 4.2 22.2 - - + -
424A ASP 3.1 16.6 + - - +
425A TYR* 3.7 31.9 - - + +
426A GLU 3.3 0.2 - - - -
427A ARG* 1.3 76.0 - - - +
429A HIS* 1.3 65.4 + - - +
431A LYS* 3.2 5.5 + - - +
432A MET* 3.2 38.6 + - - +
457A PHE* 4.2 7.2 - - + -
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Residues in contact with HIS 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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425A TYR 2.9 18.1 + - - +
426A GLU 3.5 3.8 - - - +
427A ARG 3.2 0.2 - - - -
428A ILE* 1.3 76.9 - - - +
430A LYS* 1.3 64.6 + - - +
432A MET* 3.1 10.5 + - - +
434A LYS* 2.9 43.1 + - + +
436A ALA* 4.7 5.1 - - + +
455A ILE* 2.7 51.3 + - + -
456A GLY* 3.3 23.3 - - - -
457A PHE* 3.6 19.0 - + + -
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Residues in contact with LYS 430 (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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426A GLU* 3.3 35.8 + - - +
427A ARG* 3.3 14.4 + - - +
429A HIS* 1.3 79.6 + - - +
431A LYS* 1.3 64.0 + - + +
432A MET 4.2 0.2 - - - +
434A LYS* 3.4 15.3 + - - +
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Residues in contact with LYS 431 (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 CYS 4.6 0.2 - - - -
406A ASP* 3.6 36.6 + - - +
407A GLY* 2.8 29.0 + - - +
427A ARG* 3.7 11.6 + - + +
428A ILE* 3.2 7.7 + - - +
429A HIS 3.2 0.6 - - - -
430A LYS* 1.3 81.8 - - + +
432A MET* 1.3 62.2 + - - +
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Residues in contact with MET 432 (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 CYS 3.5 15.5 - - - +
408A ALA* 3.3 26.2 - - + +
409A HIS 3.3 25.6 - - - +
410A ALA* 3.5 15.7 - - - +
411A VAL* 3.8 8.1 - - + -
428A ILE* 3.4 24.5 - - + +
429A HIS 3.1 10.3 + - - +
430A LYS 4.2 0.2 - - - +
431A LYS* 1.3 79.3 - - - +
433A LEU* 1.3 65.2 + - - +
434A LYS* 2.6 29.1 + - - +
436A ALA* 4.0 11.9 - - + -
437A PHE 3.8 9.0 - - - +
457A PHE* 3.6 27.1 - - - -
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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