Contacts of the helix formed by residues 276 - 286 (chain A) in PDB entry 3K1L
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 ASN 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ASP 5.2 1.0 + - - -
199A ASN* 3.2 23.2 + - - +
202A ASP* 3.4 38.4 + - - +
243A ILE* 5.4 2.5 - - - -
271A TRP* 4.7 0.9 - - - -
275A MET* 1.3 77.8 - - - +
277A ILE* 1.3 61.5 + - - +
278A HIS* 3.6 4.8 - - - +
279A LYS* 2.8 37.6 + - - +
280A ASN* 3.0 19.8 + - - +
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Residues in contact with ILE 277 (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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199A ASN* 3.0 23.5 + - + +
203A ILE* 4.1 5.6 - - + -
234A LEU* 4.0 26.0 - - + -
236A ILE* 4.3 21.1 - - + -
242A CYS 4.9 1.3 - - - +
243A ILE* 4.4 12.8 - - + -
246A MET* 3.7 30.3 - - + -
271A TRP* 3.9 22.7 - - + -
276A ASN* 1.3 74.3 - - - +
278A HIS* 1.3 61.1 + - - +
280A ASN* 3.2 2.1 + - - +
281A LEU* 2.8 50.1 + - + +
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Residues in contact with HIS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASN* 4.7 1.2 + - - +
202A ASP* 3.6 29.2 + - + -
203A ILE* 4.3 15.4 - - + +
206A LEU* 3.6 43.3 - - + +
207A CYS* 3.8 16.4 - - - -
276A ASN* 3.2 5.1 + - - +
277A ILE* 1.3 78.5 - - - +
279A LYS* 1.3 74.4 + - + +
281A LEU* 2.9 22.6 + - - +
282A LEU* 3.0 32.5 + - + +
289A TYR* 5.9 0.4 - - - -
290A PHE* 3.6 29.7 - + + -
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Residues in contact with LYS 279 (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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202A ASP* 3.6 21.5 + - - -
206A LEU* 6.2 0.4 - - - -
275A MET* 3.1 31.6 - - + +
276A ASN* 2.8 27.9 + - - +
278A HIS* 1.3 85.1 - - + +
280A ASN* 1.3 58.0 + - - +
282A LEU* 3.3 12.0 + - + +
283A ARG* 3.0 22.7 + - - +
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Residues in contact with ASN 280 (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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267A GLY 5.1 0.5 - - - +
271A TRP* 3.1 42.2 - - + +
272A ASP* 2.7 46.2 + - - +
275A MET* 3.1 28.2 + - - +
276A ASN 3.0 13.4 + - - +
277A ILE 3.5 0.9 - - - +
278A HIS 3.1 0.6 - - - -
279A LYS* 1.3 79.5 - - - +
281A LEU* 1.3 57.4 + - - +
283A ARG* 3.2 14.5 + - - +
284A MET* 2.9 28.2 + - - +
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Residues in contact with LEU 281 (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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203A ILE* 4.6 7.2 - - + -
224A PHE* 3.7 29.6 - - + -
232A LEU* 4.3 4.5 - - + -
234A LEU* 5.2 1.1 - - + -
248A LEU* 3.6 28.7 - - + -
271A TRP* 4.5 2.5 - - + -
277A ILE* 2.8 38.0 + - + +
278A HIS* 2.9 8.0 + - - +
280A ASN* 1.3 75.4 - - - +
282A LEU* 1.3 64.2 + - - +
284A MET* 3.1 26.1 + - + -
285A PHE* 3.0 38.1 + - + +
290A PHE* 3.7 18.7 - - + -
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Residues in contact with LEU 282 (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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278A HIS* 3.0 39.4 + - + +
279A LYS* 3.5 13.0 - - + +
281A LEU* 1.3 73.1 - - - +
283A ARG* 1.3 67.5 + - - +
285A PHE 3.8 0.2 - - - -
286A ASP* 3.0 19.8 + - - -
287A LEU* 3.0 38.2 + - + +
288A CYS 3.6 19.3 - - - +
289A TYR* 3.8 15.0 - - - -
290A PHE* 3.4 28.5 - - + +
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Residues in contact with ARG 283 (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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267A GLY* 4.7 4.2 + - - -
270A ASN* 2.6 48.0 + - - +
272A ASP* 4.4 11.8 + - - +
275A MET* 4.1 25.1 - - + -
279A LYS 3.0 12.7 + - - +
280A ASN* 3.2 21.9 + - - +
282A LEU* 1.3 78.3 - - - +
284A MET* 1.3 66.0 + - - +
285A PHE 3.3 0.3 + - - -
286A ASP* 3.3 9.1 + - - +
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Residues in contact with MET 284 (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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248A LEU* 3.8 5.8 - - + -
263A VAL* 3.2 24.6 - - + +
264A LEU* 3.3 43.3 - - + +
267A GLY* 3.9 22.6 - - - +
268A LEU* 4.8 0.7 - - + -
271A TRP* 3.6 26.2 - - + -
280A ASN 2.9 14.0 + - - +
281A LEU* 3.1 33.3 + - + +
283A ARG* 1.3 79.4 - - - +
285A PHE* 1.3 79.1 + - + +
286A ASP* 3.4 1.1 + - - +
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Residues in contact with PHE 285 (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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226A LEU* 3.8 41.3 - - + -
232A LEU* 3.6 31.9 - - + -
250A ILE* 4.4 24.0 - - + -
260A LEU* 4.2 11.2 - - + -
263A VAL* 4.1 19.7 - - + -
264A LEU* 4.8 5.6 - - + -
281A LEU* 3.0 34.6 + - + +
284A MET* 1.3 102.7 - - + +
286A ASP* 1.3 73.9 + - - +
287A LEU* 3.5 12.6 - - + +
290A PHE* 4.7 1.3 - + - -
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Residues in contact with ASP 286 (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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282A LEU 3.0 6.5 + - - -
283A ARG 3.3 9.4 + - - +
284A MET 3.4 1.5 - - - +
285A PHE* 1.3 82.6 - - - +
287A LEU* 1.3 65.8 + - - +
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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