Contacts of the helix formed by residues 273 - 280 (chain C) in PDB entry 1KXT
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 LYS 273 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C VAL* 3.1 16.3 - - - +
271C GLY 3.8 9.2 - - - +
272C GLU* 1.3 83.2 - - - +
274C MET* 1.3 65.9 + - - +
275C SER* 3.3 4.5 - - - +
276C TYR* 3.3 47.2 + - + +
277C LEU 4.3 0.3 + - - -
413C GLY 4.0 16.6 + - - +
414C SER* 3.4 22.5 + - - +
415C ASN* 3.2 15.5 - - - +
46D GLU* 5.9 1.8 - - - -
59D TYR 4.9 0.2 + - - -
60D ALA* 4.0 4.7 - - - +
61D ASP* 3.0 52.5 + - - +
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Residues in contact with MET 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C VAL* 3.8 13.0 - - + +
266C VAL* 5.0 13.0 - - + -
273C LYS* 1.3 67.7 - - - +
275C SER* 1.3 57.8 + - - +
276C TYR 2.9 5.2 - - - -
277C LEU* 2.8 45.4 + - + +
323C ILE* 4.8 7.9 - - - -
327C PHE* 5.6 5.8 - - + -
409C TRP* 4.0 0.7 - - - -
414C SER 3.6 0.2 + - - -
415C ASN* 2.9 27.9 + - - +
417C VAL* 3.5 33.3 - - + +
429C PHE* 3.3 44.6 - - + -
431C ASN* 4.2 22.7 - - + +
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Residues in contact with SER 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C LYS* 4.0 0.9 - - - +
274C MET* 1.3 77.8 - - - +
276C TYR* 1.3 76.4 + - - +
277C LEU 3.1 1.5 + - - -
278C LYS* 3.5 7.3 + - - +
409C TRP* 3.4 14.3 - - - -
411C ASP* 3.6 33.3 - - - +
413C GLY* 3.5 18.6 + - - -
414C SER 2.9 22.0 + - - -
417C VAL* 3.5 11.8 - - - +
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Residues in contact with TYR 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C GLY 3.8 13.4 + - - -
272C GLU* 3.4 10.1 - - - +
273C LYS* 3.3 43.4 - - + +
274C MET 2.9 0.6 + - - -
275C SER* 1.3 88.7 - - - +
277C LEU* 1.3 54.6 + - - +
278C LYS* 3.0 11.5 + - - +
279C ASN* 3.4 17.0 + - - -
284C TRP* 3.4 11.6 + - + -
413C GLY 5.2 1.8 - - - -
47D LEU* 3.8 16.4 + - + +
50D ARG* 3.3 27.8 - - - +
58D ASN* 3.7 38.7 + - + +
59D TYR 3.3 24.8 + - - -
60D ALA* 3.4 16.1 + - - +
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Residues in contact with LEU 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C LEU* 5.3 9.2 - - + -
265C VAL* 4.3 17.3 - - + -
266C VAL* 5.7 1.3 - - + -
274C MET* 2.8 37.8 + - + +
276C TYR* 1.3 76.2 - - - +
278C LYS* 1.3 64.8 + - - +
279C ASN 3.2 1.1 - - - -
280C TRP* 2.8 53.9 + - + +
284C TRP* 3.8 15.5 - - + +
327C PHE* 3.7 43.8 - - + -
331C HIS* 5.1 0.9 + - - -
409C TRP* 3.6 9.7 - - + -
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Residues in contact with LYS 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C SER 3.5 6.9 + - - +
276C TYR 3.0 3.8 - - - +
277C LEU* 1.3 78.1 - - - +
279C ASN* 1.3 59.4 + - + +
280C TRP 3.5 1.6 + - - +
331C HIS* 5.2 0.9 + - - -
406C PHE* 3.8 23.2 - - + -
409C TRP* 3.3 56.9 - - + +
411C ASP* 5.0 2.0 - - - +
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Residues in contact with ASN 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C TYR 3.4 8.7 + - - -
278C LYS* 1.3 75.5 - - + +
280C TRP* 1.3 65.5 + - - +
281C GLY 3.4 1.7 + - - -
283C GLY* 3.8 18.4 + - - +
284C TRP* 2.7 35.9 - - - +
52D PHE* 3.2 41.7 - - - +
54D ASP* 4.2 6.5 - - - +
56D SER* 4.0 7.4 + - - +
58D ASN* 5.6 0.2 - - - +
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Residues in contact with TRP 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C TYR* 2.7 55.8 + + - -
261C LYS* 3.8 2.2 - - + -
262C LEU* 3.7 30.7 - - + -
277C LEU* 2.8 43.3 + - + +
278C LYS 3.3 1.4 + - - -
279C ASN* 1.3 80.3 - - - +
281C GLY* 1.3 61.0 + - - +
282C GLU* 5.1 0.7 - - - +
284C TRP* 3.6 40.2 - + - -
286C PHE* 3.6 24.7 - + - -
327C PHE* 3.3 22.7 - + + -
331C HIS* 3.4 42.4 + + + +
333C TYR* 4.9 0.4 - - + -
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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