Contacts of the helix formed by residues 446 - 459 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370B ILE* 4.1 4.9 - - - -
444B ARG 4.0 0.8 + - - -
445B PRO* 1.3 76.0 - - - +
447B ILE* 1.3 65.1 + - + +
448B LYS* 3.6 24.2 + - - +
449B LYS* 3.3 18.6 + - - +
450B VAL* 3.2 19.2 + - - +
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Residues in contact with ILE 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B ALA* 3.6 16.6 - - + +
299B ILE* 3.6 29.6 - - + -
300B ASN* 3.6 41.5 - - + +
303B HIS* 3.5 27.7 + - + +
370B ILE* 3.6 22.5 - - + +
373B PHE* 4.9 4.3 - - + -
446B ASP* 1.3 75.8 - - + +
448B LYS* 1.3 60.3 + - + +
450B VAL* 3.2 18.3 + - + +
451B GLN* 2.9 27.8 + - - +
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Residues in contact with LYS 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ASN* 4.2 8.3 - - - +
304B GLU* 6.0 2.2 - - - +
446B ASP* 3.3 15.9 + - - +
447B ILE* 1.3 81.0 - - + +
449B LYS* 1.3 57.2 + - - +
451B GLN* 3.4 19.8 - - - +
452B GLN* 3.0 47.8 + - + +
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Residues in contact with LYS 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B GLN* 5.6 0.7 - - - +
445B PRO* 4.0 18.8 - - + -
446B ASP* 3.3 24.6 + - - +
447B ILE 3.2 0.4 - - - -
448B LYS* 1.3 76.8 - - - +
450B VAL* 1.3 59.1 + - - +
452B GLN* 3.2 28.6 + - - +
453B LEU* 2.9 64.6 + - + +
456B GLU* 5.3 3.2 + - - -
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Residues in contact with VAL 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ALA* 4.3 0.9 - - + -
370B ILE* 4.3 9.6 - - + -
373B PHE* 3.6 34.5 - - + -
432B VAL* 4.0 17.9 - - + +
436B CYS* 3.6 24.0 - - - -
445B PRO* 3.9 14.4 - - + -
446B ASP 3.2 14.6 + - - +
447B ILE* 3.5 17.3 - - + +
449B LYS* 1.3 76.5 - - - +
451B GLN* 1.3 56.6 + - - +
453B LEU* 3.4 4.8 + - - +
454B LEU* 3.0 38.8 + - + +
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Residues in contact with GLN 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B GLN* 5.3 0.4 - - - +
296B ALA* 4.4 15.2 - - + +
297B ASN* 3.0 44.3 + - - +
300B ASN* 3.3 36.5 + - - +
447B ILE 2.9 15.3 + - - +
448B LYS* 3.4 16.2 - - - +
450B VAL* 1.3 76.5 - - - +
452B GLN* 1.3 56.5 + - + +
454B LEU* 3.4 4.6 + - - +
455B GLN* 3.0 44.7 + - - +
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Residues in contact with GLN 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B LYS* 3.0 45.5 + - + +
449B LYS* 3.2 33.3 + - + +
451B GLN* 1.3 75.7 - - - +
453B LEU* 1.3 56.5 + - + +
455B GLN* 3.2 14.4 + - - +
456B GLU* 3.0 45.5 + - - +
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Residues in contact with LEU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B ALA* 5.9 0.2 - - - +
432B VAL* 3.6 26.4 - - + +
435B GLN* 3.8 33.4 - - - +
445B PRO* 5.6 3.1 - - + -
449B LYS* 2.9 49.2 + - + +
450B VAL* 3.8 3.8 - - - +
452B GLN* 1.3 76.5 - - - +
454B LEU* 1.4 58.1 + - - +
456B GLU* 3.5 23.8 + - - +
457B MET* 3.1 25.3 + - - +
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Residues in contact with LEU 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ALA* 3.7 33.0 - - + +
293B GLN* 3.0 29.7 + - + +
296B ALA* 3.8 18.8 - - + -
373B PHE* 4.0 15.3 - - + -
377B LEU* 4.5 2.2 - - + -
429B MET* 4.4 13.2 - - + -
432B VAL* 4.2 24.5 - - + -
450B VAL* 3.0 20.2 + - + +
451B GLN* 3.8 4.3 - - - +
452B GLN 3.3 0.2 - - - -
453B LEU* 1.4 72.6 - - - +
455B GLN* 1.3 63.9 + - - +
457B MET* 3.4 39.0 + - + +
458B THR 3.8 0.3 + - - -
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Residues in contact with GLN 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B GLN* 3.9 15.7 - - + +
297B ASN* 4.3 8.8 + - - +
451B GLN* 3.0 35.8 + - - +
452B GLN* 3.5 15.9 - - - +
454B LEU* 1.3 77.9 - - - +
456B GLU* 1.3 61.1 + - + +
458B THR* 3.1 18.0 + - - -
459B ALA* 3.5 6.2 + - - -
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Residues in contact with GLU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B LYS* 5.3 3.5 + - - -
452B GLN* 3.0 36.2 + - - +
453B LEU* 3.6 26.7 - - - +
454B LEU 3.4 0.2 - - - -
455B GLN* 1.3 76.1 - - + +
457B MET* 1.3 62.0 + - - +
459B ALA* 3.5 13.5 + - - +
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Residues in contact with MET 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B CYS* 3.8 34.8 - - + +
293B GLN* 4.5 2.5 - - - +
425B SER* 3.7 33.7 - - - +
428B ALA* 4.0 17.7 - - + -
429B MET* 3.7 47.8 - - + -
432B VAL* 6.3 0.4 - - + -
453B LEU 3.1 12.7 + - - +
454B LEU* 3.4 31.6 - - + +
455B GLN 3.2 0.2 - - - -
456B GLU* 1.3 77.2 - - - +
458B THR* 1.3 63.1 + - + +
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Residues in contact with THR 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B HIS* 6.3 0.4 - - - +
289B CYS* 4.0 26.5 - - + -
293B GLN* 3.0 32.2 + - - +
425B SER* 6.1 0.2 - - - -
454B LEU 3.8 0.4 + - - -
455B GLN* 3.1 10.1 + - - -
457B MET* 1.3 81.1 - - + +
459B ALA* 1.4 55.6 + - - +
166D HIS* 5.0 10.0 - - - -
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Residues in contact with ALA 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B GLN 3.5 6.5 + - - -
456B GLU* 3.5 15.7 + - - +
458B THR* 1.4 83.3 + - - +
166D HIS* 5.9 4.3 - - - -
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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