Contacts of the helix formed by residues 446 - 459 (chain A) in PDB entry 5KX8
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 446 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A ILE* 4.1 4.9 - - - -
444A ARG 4.0 0.6 + - - -
445A PRO* 1.3 77.7 - - - +
447A ILE* 1.3 64.5 + - + +
448A LYS* 3.6 23.6 + - - +
449A LYS* 3.3 18.8 + - - +
450A VAL* 3.2 18.4 + - - +
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Residues in contact with ILE 447 (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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296A ALA* 3.6 16.2 - - - +
299A ILE* 3.6 29.6 - - + -
300A ASN* 3.5 41.3 - - + +
303A HIS* 3.5 28.2 + - + +
370A ILE* 3.6 22.7 - - + +
373A PHE* 4.8 3.1 - - + -
446A ASP* 1.3 75.3 - - + +
448A LYS* 1.3 60.5 + - + +
450A VAL* 3.2 19.5 + - + +
451A GLN* 2.9 27.5 + - - +
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Residues in contact with LYS 448 (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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300A ASN* 3.5 22.8 - - - +
304A GLU* 3.1 25.0 + - + +
446A ASP* 3.3 15.8 + - - +
447A ILE* 1.3 80.8 - - + +
449A LYS* 1.3 56.9 + - - +
451A GLN* 3.4 18.3 + - - +
452A GLN* 3.1 42.7 + - + +
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Residues in contact with LYS 449 (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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435A GLN* 5.5 1.3 - - - +
445A PRO* 4.0 18.2 - - + -
446A ASP* 3.3 25.4 + - - +
447A ILE 3.2 0.4 - - - -
448A LYS* 1.3 77.0 - - - +
450A VAL* 1.3 58.2 + - - +
452A GLN* 3.2 28.0 + - - +
453A LEU* 2.9 63.8 + - + +
456A GLU* 5.3 3.4 + - - -
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Residues in contact with VAL 450 (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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296A ALA* 4.3 1.1 - - + -
370A ILE* 4.3 9.2 - - + -
373A PHE* 3.6 34.5 - - + -
432A VAL* 4.0 17.2 - - + +
436A CYS* 3.6 24.7 - - - -
445A PRO* 3.9 14.8 - - + +
446A ASP 3.2 13.4 + - - +
447A ILE* 3.2 17.5 + - + +
449A LYS* 1.3 75.1 - - - +
451A GLN* 1.3 57.2 + - - +
453A LEU* 3.4 5.2 + - - +
454A LEU* 3.0 35.3 + - + +
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Residues in contact with GLN 451 (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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296A ALA* 4.4 15.7 - - + +
297A ASN* 3.0 44.2 + - - +
300A ASN* 3.3 35.6 - - - +
447A ILE 2.9 14.5 + - - +
448A LYS* 3.4 26.0 - - - +
450A VAL* 1.3 75.2 - - - +
452A GLN* 1.3 56.5 + - + +
454A LEU* 3.4 4.5 + - - +
455A GLN* 3.0 45.7 + - - +
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Residues in contact with GLN 452 (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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448A LYS* 3.1 36.0 + - + +
449A LYS* 3.5 33.6 + - + +
451A GLN* 1.3 76.0 - - + +
453A LEU* 1.3 59.5 + - + +
455A GLN* 3.2 14.5 + - - +
456A GLU* 2.9 43.1 + - - +
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Residues in contact with LEU 453 (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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428A ALA* 5.8 0.7 - - - +
432A VAL* 3.6 26.1 - - + +
435A GLN* 3.8 33.7 - - - +
445A PRO* 5.6 2.9 - - + -
449A LYS* 2.9 49.7 + - + +
450A VAL* 3.8 4.3 - - - +
452A GLN* 1.3 76.6 - - - +
454A LEU* 1.4 56.9 + - - +
456A GLU* 3.5 23.1 + - - +
457A MET* 3.1 25.5 + - - +
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Residues in contact with LEU 454 (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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292A ALA* 3.7 33.2 - - + +
293A GLN* 3.0 30.9 + - + -
296A ALA* 3.8 19.3 - - + -
373A PHE* 4.0 15.3 - - + -
377A LEU* 4.5 2.5 - - + -
429A MET* 4.4 14.4 - - + -
432A VAL* 4.2 23.1 - - + -
450A VAL* 3.0 19.2 + - + +
451A GLN* 3.8 5.2 - - - +
453A LEU* 1.4 71.5 - - - +
455A GLN* 1.3 64.4 + - - +
457A MET* 3.4 39.5 + - + +
458A THR 3.8 0.2 + - - -
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Residues in contact with GLN 455 (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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293A GLN* 3.9 17.0 - - + +
297A ASN* 4.4 10.7 + - - +
451A GLN* 3.0 36.2 + - + +
452A GLN* 3.2 16.9 + - - +
454A LEU* 1.3 76.0 - - - +
456A GLU* 1.3 61.5 + - + +
458A THR* 3.1 18.8 + - - -
459A ALA* 3.5 6.1 + - - -
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Residues in contact with GLU 456 (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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449A LYS* 5.3 3.5 + - - -
452A GLN* 2.9 36.4 + - - +
453A LEU* 3.6 27.3 - - - +
455A GLN* 1.3 75.7 - - + +
457A MET* 1.3 63.2 + - - +
458A THR 3.4 0.2 - - - -
459A ALA* 3.5 13.3 + - - +
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Residues in contact with MET 457 (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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289A CYS* 3.8 28.9 - - + +
293A GLN* 4.5 2.0 - - - +
425A SER* 3.7 33.8 - - - +
428A ALA* 4.0 17.7 - - + -
429A MET* 3.7 52.5 - - + -
432A VAL* 6.3 0.2 - - + -
453A LEU 3.1 13.5 + - - +
454A LEU* 3.4 31.4 - - + +
456A GLU* 1.3 77.8 - - - +
458A THR* 1.3 63.3 + - + +
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Residues in contact with THR 458 (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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289A CYS* 4.0 26.9 - - + -
293A GLN* 3.0 32.6 + - - +
425A SER* 6.1 0.4 - - - -
454A LEU 3.8 0.6 + - - -
455A GLN* 3.1 9.4 + - - -
457A MET* 1.3 79.6 - - + +
459A ALA* 1.4 55.2 + - - +
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Residues in contact with ALA 459 (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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455A GLN 3.5 6.7 + - - -
456A GLU* 3.5 15.0 + - - +
458A THR* 1.4 82.8 + - - +
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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