Contacts of the helix formed by residues 443 - 450 (chain L) in PDB entry 1KYO
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 443 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249L ARG* 4.3 5.8 - - - +
442L LEU* 1.3 76.4 - - - +
444L TYR* 1.3 67.7 + - - +
445L MET* 3.4 2.8 + - - +
446L ARG* 2.8 44.6 + - - +
447L ILE* 3.2 9.1 + - - +
219N ILE* 5.3 4.0 - - + -
220N PRO* 3.1 34.1 - - + +
223N SER* 5.1 1.2 + - - +
224N TYR* 2.8 39.8 + - + +
295O ILE* 4.9 10.5 - - + -
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Residues in contact with TYR 444 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245L GLY* 3.4 11.9 - - - -
246L SER* 3.8 12.8 - - - -
247L GLU* 3.2 38.7 + - + +
249L ARG* 4.1 0.2 - - - +
429L ASP* 3.5 2.4 + - - -
430L ILE* 2.7 58.6 + - + -
432L ILE* 3.8 16.2 - - + -
443L ASP* 1.3 71.5 - - - +
445L MET* 1.3 63.0 + - + +
447L ILE* 3.1 4.7 + - - +
448L ARG* 2.7 45.2 + - + +
294O GLY* 6.2 4.5 - - - -
295O ILE* 6.2 0.2 - - - +
28S ALA* 5.7 4.5 - - + -
29S VAL 5.1 2.7 - - - -
30S SER* 3.2 40.0 - - - -
31S PRO* 4.3 9.2 - - + -
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Residues in contact with MET 445 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443L ASP* 3.3 10.1 + - - +
444L TYR* 1.3 81.9 - - + +
446L ARG* 1.3 53.0 + - - +
448L ARG* 3.9 19.3 - - - -
449L SER* 2.6 36.6 + - - +
223N SER* 4.7 12.2 + - - +
224N TYR* 3.7 12.9 + - + +
290O PHE* 3.8 30.7 - - + -
291O LYS* 4.1 30.1 - - + +
294O GLY* 5.7 2.7 - - - -
31S PRO* 3.9 35.7 - - + -
32S TYR* 4.0 13.2 - - + +
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Residues in contact with ARG 446 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340L ASP* 5.6 0.6 - - - +
442L LEU* 3.0 38.3 - - + +
443L ASP* 2.8 38.3 + - - +
445L MET* 1.3 70.6 - - - +
447L ILE* 1.3 66.8 + - + +
449L SER* 3.4 18.0 + - - -
450L ASP* 3.7 10.8 + - - +
4N ARG* 3.4 19.5 - - - +
18N ILE* 3.4 30.6 + - - +
19N ASP* 2.5 26.7 + - - +
220N PRO* 4.3 5.8 - - + +
222N HIS* 4.1 26.8 + - - +
223N SER* 5.5 3.6 - - - -
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Residues in contact with ILE 447 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262L LEU* 3.8 8.3 - - + -
343L ILE* 3.6 21.5 - - + -
347L LEU* 3.6 23.0 - - + +
430L ILE* 3.6 19.1 - - + -
432L ILE* 3.8 20.6 - - + -
441L LEU* 3.6 27.4 - - + -
442L LEU* 3.6 24.7 - - + +
443L ASP 3.2 8.3 + - - +
444L TYR 3.1 5.5 + - - +
446L ARG* 1.3 76.6 - - + +
448L ARG* 1.3 67.3 + - - +
450L ASP* 3.0 21.6 + - - +
451L MET* 3.9 0.7 + - - +
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Residues in contact with ARG 448 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427L ASP* 2.7 56.1 + - - +
428L GLN 3.0 22.8 + - - +
429L ASP* 2.8 39.8 + - - +
430L ILE* 3.9 12.0 - - + +
444L TYR* 2.7 40.4 + - + +
445L MET* 3.9 22.2 - - - +
447L ILE* 1.3 72.3 - - - +
449L SER* 1.3 64.1 + - - +
451L MET* 3.1 23.3 + - - +
53P ARG* 3.8 5.1 - - - +
32S TYR* 2.9 37.6 - - + -
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Residues in contact with SER 449 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427L ASP* 5.6 0.4 - - - +
445L MET* 2.6 26.1 + - - -
446L ARG* 3.5 9.9 - - - -
447L ILE 3.1 0.4 - - - -
448L ARG* 1.3 79.3 - - - +
450L ASP* 1.3 58.4 + - - +
451L MET 2.9 6.2 + - - -
452L SER* 3.4 20.3 + - - +
223N SER* 5.3 4.7 + - - -
291O LYS* 5.9 0.7 + - - -
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Residues in contact with ASP 450 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343L ILE* 5.1 2.1 - - - +
344L HIS* 3.3 37.1 + - - +
347L LEU* 3.9 21.9 - - + +
348L LYS* 3.2 24.2 + - - -
351L ASN* 3.2 20.1 + - - +
446L ARG 3.7 8.7 + - - +
447L ILE* 3.0 15.7 + - - +
449L SER* 1.3 73.0 - - - +
451L MET* 1.3 56.3 + - - +
452L SER 2.9 15.5 + - - +
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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