Contacts of the helix formed by residues 276 - 287 (chain A) in PDB entry 1K9I
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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275A ARG* 1.3 74.5 - - - +
277A TRP* 1.3 60.9 + - - +
278A HIS* 2.9 10.9 + - - +
279A ASP* 2.7 54.6 + - - +
280A SER* 2.7 25.6 + - - -
315A TRP* 3.6 0.2 - - - -
369A CYS 3.4 12.8 - - - +
370A ASN* 3.4 21.0 + - - +
371A LEU 3.0 10.8 - - - -
372A ALA* 3.8 3.2 - - - +
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Residues in contact with TRP 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ASN* 1.3 70.3 - - - +
278A HIS* 1.3 79.9 + + - +
280A SER* 3.3 5.5 - - - -
281A ILE* 3.2 43.1 + - + +
291A LEU* 3.7 7.4 - - + +
315A TRP* 3.4 44.2 - + + +
316A MET 2.7 20.7 + - - -
317A GLY* 3.9 0.4 - - - -
318A LEU 3.6 23.0 + - - -
319A SER* 3.5 21.8 - - - -
321A LEU* 3.9 17.7 - - + -
328A GLN 5.8 0.4 - - - -
330A VAL* 3.6 26.5 - - + -
356A CYS* 3.3 28.7 - - + +
369A CYS* 3.0 23.4 + - + +
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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
----------------------------------------------------------
276A ASN* 2.9 8.2 + - - +
277A TRP* 1.3 85.7 - + - +
279A ASP* 1.3 68.7 + - - +
280A SER 3.0 4.7 + - - -
281A ILE* 3.1 13.8 + - + +
282A THR* 3.1 28.8 + - + +
321A LEU* 3.9 30.1 - - + +
369A CYS* 4.5 14.8 + - + +
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Residues in contact with ASP 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ARG* 3.9 28.9 + - + +
276A ASN* 2.7 38.4 + - - +
278A HIS* 1.3 77.6 - - - +
280A SER* 1.3 56.2 + - - +
282A THR* 2.6 22.3 + - - +
283A ALA* 2.9 18.2 + - - +
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ARG* 3.6 18.2 + - - +
276A ASN 2.7 18.5 + - - -
277A TRP* 3.3 10.8 - - - -
278A HIS 3.0 0.2 - - - -
279A ASP* 1.3 76.1 - - - +
281A ILE* 1.3 64.3 + - - +
283A ALA* 3.1 8.5 + - - +
284A CYS* 3.0 26.7 + - - -
291A LEU* 4.2 11.0 - - - -
315A TRP* 3.7 5.9 - - - -
375A TRP* 3.7 29.7 - - - -
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TRP* 3.4 45.8 - - + +
278A HIS* 3.1 13.2 + - + +
280A SER* 1.3 75.8 - - - +
282A THR* 1.3 65.6 + - + +
284A CYS* 3.0 8.0 + - - +
285A LYS* 3.0 48.9 + - + +
290A GLN* 6.1 3.1 - - + -
291A LEU* 3.3 31.2 - - + +
330A VAL* 3.9 15.5 - - + -
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Residues in contact with THR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A HIS* 3.4 12.6 - - + +
279A ASP* 2.6 32.8 + - - +
281A ILE* 1.3 77.0 - - + +
283A ALA* 1.3 61.0 + - - +
285A LYS* 3.2 14.6 + - + +
286A GLU* 3.0 26.2 + - - +
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ARG* 4.4 6.7 - - - +
279A ASP 2.9 20.3 + - - +
280A SER* 3.2 10.8 - - - +
282A THR* 1.3 76.5 + - - +
284A CYS* 1.3 62.7 + - - +
286A GLU* 2.9 37.1 + - - +
287A VAL 3.8 0.9 + - - -
375A TRP* 4.2 23.8 - - + +
258B TRP* 3.5 16.0 + - + +
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Residues in contact with CYS 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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280A SER 3.0 17.8 + - - -
281A ILE 3.0 7.2 + - - +
283A ALA* 1.3 75.3 - - - +
285A LYS* 1.3 55.5 + - - +
287A VAL* 3.3 9.6 + - - +
289A ALA* 2.6 49.6 + - - +
290A GLN* 3.7 4.5 - - - +
291A LEU* 3.8 17.7 - - - +
375A TRP* 4.0 7.9 - - - -
377A CYS* 2.0 55.9 - - - -
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Residues in contact with LYS 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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281A ILE* 3.0 39.1 + - + +
282A THR* 3.6 14.6 - - + +
283A ALA 3.1 0.2 - - - -
284A CYS* 1.3 72.6 - - - +
286A GLU* 1.3 67.4 + - - +
287A VAL 3.0 2.5 - - - -
288A GLY* 2.7 15.4 + - - +
289A ALA 3.7 15.0 - - - +
290A GLN* 5.8 2.9 - - - +
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Residues in contact with GLU 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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275A ARG* 5.9 2.3 + - - -
282A THR 3.0 17.2 + - - +
283A ALA* 2.9 26.2 + - - +
285A LYS* 1.3 77.6 - - - +
287A VAL* 1.3 59.3 + - - +
288A GLY 3.7 0.9 + - - -
258B TRP* 3.6 26.5 + - + +
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A TRP* 4.6 10.7 - - + -
284A CYS* 3.3 12.1 - - - +
286A GLU* 1.3 80.6 - - - +
288A GLY* 1.3 66.3 + - - +
289A ALA* 4.0 10.9 - - + +
377A CYS* 5.3 0.2 - - - -
379A LYS* 5.3 5.5 - - - +
258B TRP* 3.5 64.4 - - + -
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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