Contacts of the helix formed by residues 275 - 287 (chain A) in PDB entry 1K89
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 GLU 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A THR 4.1 0.6 + - - -
274A THR* 1.3 71.3 - - - +
276A GLU* 1.3 64.7 + - - +
278A ILE* 4.7 4.5 - - - -
279A ASN* 2.7 51.8 + - - +
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Residues in contact with GLU 276 (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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274A THR* 3.0 9.1 - - - +
275A GLU* 1.3 81.9 - - - +
277A LYS* 1.3 63.2 + - - +
279A ASN* 4.1 2.9 - - - +
280A TYR* 3.0 25.8 + - - +
299A PHE* 3.8 28.6 - - + -
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Residues in contact with LYS 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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268A ASP* 2.6 32.1 + - - -
270A GLU* 3.3 20.2 + - - +
271A GLY 3.0 26.9 + - - +
272A ILE* 3.5 9.6 - - - -
273A THR 3.8 1.3 - - - +
274A THR* 2.6 38.7 + - + +
276A GLU* 1.3 71.2 - - - +
278A ILE* 1.3 66.9 + - - +
280A TYR* 3.2 11.8 + - - +
281A MET* 3.6 11.8 + - - +
295A TYR* 2.9 24.9 - - + +
299A PHE* 4.2 31.6 - - + -
301A VAL* 5.5 0.4 - - - -
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Residues in contact with ILE 278 (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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243A TRP* 3.4 35.6 - - + +
246A ALA* 4.8 1.8 - - + -
247A LYS* 4.1 37.0 - - + +
250A ALA* 4.2 7.9 - - + -
272A ILE* 3.4 27.4 - - + +
273A THR* 3.8 15.0 - - - +
274A THR 2.4 34.9 + - - +
275A GLU* 4.2 4.0 - - - +
277A LYS* 1.3 65.8 - - - +
279A ASN* 1.3 66.8 + - - +
281A MET* 2.9 32.8 + - - +
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Residues in contact with ASN 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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243A TRP* 4.9 4.9 + - - -
247A LYS* 5.9 2.8 - - - +
275A GLU* 2.7 56.1 + - - +
276A GLU* 4.2 2.4 - - - +
278A ILE* 1.3 73.6 - - - +
280A TYR* 1.3 61.4 + - - +
282A LEU* 2.9 38.9 + - + +
283A GLU* 3.2 4.2 + - - +
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Residues in contact with TYR 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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276A GLU 3.0 20.0 + - - +
277A LYS 3.6 5.4 - - - +
278A ILE 3.0 0.6 + - - -
279A ASN* 1.3 76.5 - - - +
281A MET* 1.3 55.3 + - - +
283A GLU* 2.6 75.8 + - + +
284A MET* 2.8 51.8 + - + +
294A ASP* 3.7 29.4 + - - +
295A TYR* 4.4 5.2 - + - -
298A LYS* 2.8 47.9 + - + +
299A PHE* 4.3 13.2 - + + -
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Residues in contact with MET 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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238A PHE* 3.4 39.7 - - + +
242A ALA* 3.6 7.6 - - + -
243A TRP* 3.3 44.6 - - + +
246A ALA* 4.4 10.3 - - + -
259A LEU* 3.9 25.4 - - + -
272A ILE* 4.1 19.5 - - + -
277A LYS 3.9 7.9 - - - +
278A ILE* 2.9 17.5 + - - +
280A TYR* 1.3 79.0 - - - +
282A LEU* 1.3 62.4 + - - +
284A MET* 3.4 15.4 + - + +
285A ARG* 3.0 23.9 + - - +
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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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240A ASN* 6.3 1.1 - - - -
243A TRP* 4.0 51.8 - - + +
279A ASN* 2.9 26.3 + - + +
281A MET* 1.3 74.2 - - - +
283A GLU* 1.3 67.4 + - - +
285A ARG* 3.4 10.9 + - + +
286A ALA* 2.9 24.8 + - - +
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Residues in contact with GLU 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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279A ASN 3.2 3.3 + - - +
280A TYR* 2.6 60.6 + - + +
282A LEU* 1.3 72.3 - - - +
284A MET* 1.3 48.7 + - - +
286A ALA* 2.7 28.9 + - - +
287A SER* 2.8 22.7 + - - -
298A LYS* 4.1 11.8 + - - -
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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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238A PHE* 4.0 30.1 - - + -
259A LEU* 4.2 9.0 - - + -
280A TYR* 2.8 45.5 + - + +
281A MET* 3.7 18.8 - - + +
283A GLU* 1.3 72.5 - - - +
285A ARG* 1.3 61.9 + - - +
287A SER* 2.8 27.4 + - - -
288A GLY 3.8 0.9 + - - -
289A ARG 4.5 1.4 + - - -
290A ASN 4.6 3.8 + - - -
291A LYS 4.5 14.6 + - - +
292A VAL* 4.7 2.9 - - - +
294A ASP* 4.9 6.1 - - + +
295A TYR* 2.9 60.1 - - + -
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Residues in contact with ARG 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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238A PHE* 4.0 21.7 - - - +
239A GLY* 4.0 26.7 - - - -
240A ASN* 5.0 10.7 - - - +
281A MET 3.0 18.3 + - - +
282A LEU* 3.5 14.4 - - + +
284A MET* 1.3 78.4 - - - +
286A ALA* 1.3 65.9 + - - +
288A GLY* 3.3 9.2 + - - -
290A ASN* 5.9 0.8 + - - -
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Residues in contact with ALA 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 2.9 12.9 + - - +
283A GLU* 2.7 13.0 + - - +
285A ARG* 1.3 77.7 - - - +
287A SER* 1.3 54.6 + - - +
288A GLY* 2.5 19.2 + - - -
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Residues in contact with SER 287 (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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283A GLU* 2.8 19.3 + - - -
284A MET* 2.8 20.9 + - - -
286A ALA* 1.3 70.6 - - - +
288A GLY* 1.3 58.1 + - - +
289A ARG* 2.8 42.8 + - - +
294A ASP* 4.6 1.5 + - - -
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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