Contacts of the helix formed by residues 381 - 391 (chain A) in PDB entry 1GUX
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 THR 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A ASN* 1.3 69.4 + - - +
382A ILE* 1.3 60.4 + - - +
384A GLN* 3.6 18.3 + - - +
385A LEU* 3.0 21.5 + - - +
540A GLY 5.2 2.4 + - - +
541A ASN* 3.1 44.6 + - - +
542A LEU 3.6 12.5 + - - -
543A THR* 3.6 10.8 - - - +
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Residues in contact with ILE 382 (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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380A ASN* 2.9 11.0 + - - +
381A THR* 1.3 74.4 + - - +
383A GLN* 1.3 67.5 + - + +
385A LEU* 3.1 13.6 + - + +
386A MET* 2.9 31.7 + - + +
493A VAL* 4.0 26.5 - - + -
497A THR* 3.6 31.4 - - + +
541A ASN 3.9 8.3 - - - +
542A LEU* 4.2 8.1 - - + -
543A THR* 3.6 31.4 - - + +
546A MET* 4.1 14.6 - - + -
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Residues in contact with GLN 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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380A ASN* 2.9 46.8 + - - +
382A ILE* 1.3 76.1 - - + +
384A GLN* 1.3 67.1 + - + +
386A MET* 3.3 9.4 + - - +
387A MET* 3.1 32.0 + - - +
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Residues in contact with GLN 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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380A ASN 3.0 31.0 + - - +
381A THR* 3.7 20.6 - - - +
383A GLN* 1.3 77.3 - - + +
385A LEU* 1.3 59.2 + - - +
387A MET* 3.3 11.7 + - - +
388A ILE* 2.9 30.3 + - + +
541A ASN* 4.4 7.9 - - - +
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Residues in contact with LEU 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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381A THR 3.0 18.3 + - - +
382A ILE* 3.1 17.4 + - + +
384A GLN* 1.3 74.5 - - - +
386A MET* 1.3 78.1 + - + +
388A ILE* 3.1 9.5 + - + +
389A LEU* 2.8 45.0 + - + +
452A LEU* 4.3 20.4 - - + -
455A ARG* 3.6 44.4 - - - +
493A VAL* 5.0 1.3 - - + -
539A GLU* 4.0 11.4 - - + +
541A ASN* 3.9 17.9 + - + +
542A LEU* 5.2 0.2 - - + -
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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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382A ILE* 2.9 20.6 + - + +
383A GLN* 3.3 10.1 + - - +
385A LEU* 1.3 97.1 - - + +
387A MET* 1.3 51.3 + - - +
389A LEU* 3.7 19.2 - - + +
390A ASN* 2.8 36.5 + - - +
448A LEU* 4.3 11.2 - - + +
452A LEU* 5.0 0.2 - - + -
493A VAL* 4.1 17.5 - - + -
494A VAL* 4.4 15.7 - - + -
497A THR* 3.8 27.1 - - + +
498A TYR* 3.0 42.2 - - + +
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Residues in contact with MET 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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383A GLN* 3.1 20.5 + - - +
384A GLN* 3.3 13.5 - - - +
385A LEU 3.1 0.2 - - - -
386A MET* 1.3 77.7 - - - +
388A ILE* 1.3 63.2 + - + +
390A ASN* 3.3 15.7 + - - +
391A SER* 3.3 13.9 + - - -
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Residues in contact with ILE 388 (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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384A GLN* 2.9 22.0 - - + +
385A LEU* 3.1 11.9 + - + +
387A MET* 1.3 78.2 - - + +
389A LEU* 1.3 72.9 + - + +
391A SER* 2.9 23.2 + - - +
392A ALA* 3.0 15.8 + - + +
455A ARG* 4.1 31.2 - - + +
541A ASN* 5.9 1.3 - - - +
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Residues in contact with LEU 389 (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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385A LEU* 2.8 36.5 + - + +
386A MET* 3.7 26.2 - - + +
388A ILE* 1.3 85.8 - - + +
390A ASN* 1.3 59.7 + - - +
392A ALA* 2.9 22.0 + - + -
448A LEU* 3.6 28.3 - - + +
451A ARG* 3.0 32.2 - - + +
452A LEU* 3.7 42.8 - - + +
455A ARG* 4.7 6.5 - - + -
494A VAL* 5.0 0.4 - - + -
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Residues in contact with ASN 390 (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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386A MET 2.8 19.0 + - - +
387A MET* 3.4 10.1 - - + +
388A ILE 3.2 0.2 - - - -
389A LEU* 1.3 77.3 - - - +
391A SER* 1.3 56.6 + - - +
444A GLN* 3.0 30.9 - - - +
448A LEU* 3.8 4.8 - - + +
451A ARG* 3.4 16.2 + - - +
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Residues in contact with SER 391 (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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387A MET 3.3 7.6 + - - -
388A ILE* 2.9 20.3 + - - +
389A LEU 3.0 0.6 - - - -
390A ASN* 1.3 77.7 - - - +
392A ALA* 1.3 62.2 + - - +
393A SER 3.9 0.9 + - - -
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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