Contacts of the helix formed by residues 382 - 387 (chain A) in PDB entry 3IXK
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 GLY 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A ASP 3.2 12.1 - - - -
279A THR 3.1 12.6 - - - -
281A ASN 3.0 24.2 + - - -
380A VAL* 3.2 4.6 + - - -
381A MET* 1.3 77.8 - - - +
383A ALA* 1.3 64.7 + - - -
384A VAL 3.1 3.1 - - - -
385A ILE* 3.0 13.2 + - - +
386A MET* 3.2 10.8 + - - +
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Residues in contact with ALA 383 (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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62A TYR* 4.4 0.7 - - + -
202A LEU* 4.4 13.9 - - + -
276A ASP 4.0 2.8 + - - -
277A SER 4.8 1.1 - - - +
279A THR 2.9 9.4 + - - +
280A THR 3.4 4.5 + - - +
355A ARG* 4.5 2.0 - - - +
382A GLY* 1.3 67.0 - - - -
384A VAL* 1.3 66.1 + - - +
386A MET* 3.6 11.0 - - - +
387A GLU* 2.9 48.5 + - - +
500A 929 3.7 30.1 - - + -
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Residues in contact with VAL 384 (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 THR 3.1 20.4 + - - +
281A ASN* 4.0 0.7 - - - -
282A LEU* 4.0 22.7 - - + +
348A ILE* 3.9 22.8 - - + +
352A GLN* 3.1 51.0 - - - +
353A TYR* 4.0 9.9 - - + -
355A ARG* 4.1 7.4 - - - +
371A ALA* 3.7 30.7 - - + +
383A ALA* 1.3 78.6 - - - +
385A ILE* 1.3 60.4 + - - +
387A GLU* 4.3 4.0 + - - +
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Residues in contact with ILE 385 (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* 4.0 23.6 - - + -
331A ILE* 6.6 0.2 - - + -
333A LEU* 3.8 19.7 - - + -
346A ILE* 3.9 14.6 - - + -
348A ILE* 3.8 33.0 - - + -
352A GLN* 3.8 0.3 - - - +
381A MET* 3.7 51.8 - - + +
382A GLY 3.0 7.9 + - - +
384A VAL* 1.3 77.7 - - + +
386A MET* 1.3 56.3 + - + +
387A GLU 3.6 0.5 + - - -
388A GLY 3.7 2.1 + - - -
389A PHE* 2.8 37.4 - - + -
402A PHE* 4.9 3.8 - - + -
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Residues in contact with MET 386 (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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200A LEU* 3.7 40.8 - - + +
202A LEU* 3.9 21.3 + - + +
275A VAL* 3.9 22.2 - - + -
276A ASP 3.9 3.8 - - - +
277A SER* 3.6 33.7 - - - -
381A MET 4.3 2.7 - - - +
382A GLY 3.2 13.6 + - - +
383A ALA* 3.3 1.9 + - - -
385A ILE* 1.3 79.0 - - + +
387A GLU* 1.3 61.1 + - - +
388A GLY 3.3 2.2 - - - -
389A PHE* 2.9 33.0 + - - +
391A VAL* 4.2 20.0 - - + +
393A PHE* 4.0 17.5 - - + -
402A PHE* 5.5 1.3 - - + -
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Residues in contact with GLU 387 (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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62A TYR* 2.7 30.9 + - - +
202A LEU* 3.2 29.6 - - + +
203A CYS* 5.0 0.9 - - - -
204A GLY* 4.0 19.0 - - - +
205A ALA 5.2 0.3 + - - -
218A VAL* 4.9 0.2 - - - +
352A GLN* 5.0 10.9 - - + +
355A ARG* 2.8 34.2 + - - -
383A ALA* 2.9 26.4 + - + +
384A VAL* 4.7 4.7 - - - +
385A ILE 3.5 0.2 - - - -
386A MET* 1.3 76.5 - - - +
388A GLY* 1.3 61.7 + - - +
389A PHE 3.3 0.9 + - - -
405A SER* 3.9 6.8 + - - -
407A CYS 4.5 8.5 - - - +
409A VAL* 4.9 10.0 - - + +
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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