Contacts of the helix formed by residues 276 - 283 (chain A) in PDB entry 3KMU
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 SER 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A GLY* 1.3 75.2 - - - +
277A LEU* 1.3 65.1 + - - +
278A TYR* 3.4 7.4 + - - +
279A ASN* 3.0 35.5 + - - +
280A VAL* 3.0 22.2 + - - +
322A SER 3.5 9.0 - - - -
323A ARG* 3.9 10.1 + - - +
325A VAL 3.2 13.7 - - - -
326A MSE 3.9 18.4 - - - -
327A ILE* 4.0 1.8 - - - -
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Residues in contact with LEU 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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276A SER* 1.3 71.4 - - - +
278A TYR* 1.3 57.5 + - - +
280A VAL* 3.2 1.8 + - + -
281A LEU* 2.8 54.0 + - + +
297A PHE* 3.5 39.5 - - + -
301A MSE 4.0 25.4 - - + -
322A SER* 3.5 12.8 - - - +
325A VAL* 2.8 18.7 + - + +
327A ILE* 3.9 18.8 - - + +
381A LEU* 3.9 28.3 - - + -
385A LEU* 4.4 4.3 - - + -
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Residues in contact with TYR 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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276A SER* 3.1 6.0 - - - +
277A LEU* 1.3 76.1 - - - +
279A ASN* 1.3 63.6 + - - +
282A HIS* 3.0 38.2 + - + +
283A GLU* 3.6 28.7 + - - -
322A SER* 2.9 42.7 + - - +
323A ARG* 3.4 50.9 + - + -
355A TRP* 4.7 8.1 - + - -
384A GLU* 4.3 1.1 - - - -
390A VAL* 3.6 39.5 - - + +
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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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274A TYR 4.0 8.3 - - - +
275A GLY* 3.6 7.4 - - - -
276A SER* 3.0 42.0 + - - +
278A TYR* 1.3 79.4 - - - +
280A VAL* 1.3 59.4 + - - +
283A GLU* 2.8 64.0 + - + +
284A GLY* 3.9 0.7 - - - -
323A ARG* 4.7 6.3 - - - +
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Residues in contact with VAL 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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274A TYR* 3.4 38.4 - - + +
276A SER 3.0 12.5 + - - +
277A LEU* 3.2 4.2 + - - +
279A ASN* 1.3 83.1 - - - +
281A LEU* 1.3 60.7 + - + +
284A GLY* 4.1 13.4 - - - -
287A PHE* 5.2 8.0 - - + +
288A VAL* 6.0 0.3 - - - -
289A VAL* 3.7 34.0 + - + +
297A PHE* 4.2 18.4 - - + -
327A ILE* 3.8 19.5 - - + -
331A MSE 4.8 3.6 - - + -
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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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277A LEU* 2.8 49.1 + - + +
280A VAL* 1.3 73.3 - - - +
282A HIS* 1.3 80.8 + - + +
284A GLY 5.0 1.0 + - - -
289A VAL* 4.0 25.4 - - + -
297A PHE* 4.6 1.8 - - + -
381A LEU* 6.1 0.2 - - + -
384A GLU* 4.1 31.4 - - + +
385A LEU* 3.7 31.0 - - + -
388A ARG* 4.1 28.0 + - - +
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Residues in contact with HIS 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 TYR* 3.0 38.5 + + + +
281A LEU* 1.3 94.6 - - + +
283A GLU* 1.3 65.8 + - + +
284A GLY 3.6 1.3 - - - -
384A GLU* 2.6 39.8 + - + +
388A ARG 4.1 10.9 - - - -
389A GLU* 3.4 23.5 + - - -
390A VAL* 3.6 34.1 - - + +
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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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278A TYR* 3.6 26.5 + - + -
279A ASN* 2.8 42.5 + - + +
282A HIS* 1.3 84.5 - - + +
284A GLY* 1.3 60.9 + - - +
285A THR* 3.5 14.4 + - - +
323A ARG* 4.9 4.6 + - - -
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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