Contacts of the helix formed by residues 380 - 391 (chain A) in PDB entry 3I5G
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 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A ALA* 4.2 15.4 - - - +
378A ASP 3.7 3.6 - - - +
379A GLY* 1.3 74.8 + - - +
381A ALA* 1.3 58.2 + - - +
382A GLU* 3.5 4.9 + - - -
383A ALA* 3.9 13.3 - - + +
384A GLU* 2.9 37.5 + - + +
394A ALA* 5.8 4.3 - - + -
398A LEU* 4.6 15.9 - - + +
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Residues in contact with ALA 381 (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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379A GLY* 2.4 26.2 + - - +
380A THR* 1.3 67.2 - - - +
382A GLU* 1.3 71.1 + - + +
384A GLU* 2.7 31.4 - - - +
385A LYS* 3.1 24.0 + - - +
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Residues in contact with GLU 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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362A HIS* 4.2 8.7 - - + +
365A GLU* 3.8 15.1 - - + +
366A MET* 3.5 36.3 - - + +
367A LYS* 2.7 43.4 + - - +
378A ASP 5.0 0.2 - - - -
379A GLY* 3.6 2.6 - - - -
380A THR 3.6 9.2 + - - -
381A ALA* 1.3 83.4 + - + +
383A ALA* 1.3 51.7 + - - +
385A LYS* 2.6 36.9 + - + +
386A VAL* 2.8 19.9 + - - +
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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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366A MET* 3.9 10.6 - - + +
380A THR* 3.9 13.6 - - + +
382A GLU* 1.3 79.6 + - - +
384A GLU* 1.3 58.1 + - - +
386A VAL* 2.9 13.3 - - - +
387A ALA* 2.7 30.1 + - - +
394A ALA* 3.9 6.1 - - + +
397A LEU* 4.2 3.8 - - + +
398A LEU* 3.7 39.7 - - + -
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Residues in contact with GLU 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 THR* 2.9 27.4 - - - +
381A ALA* 2.7 31.4 - - - +
383A ALA* 1.3 78.3 - - - +
385A LYS* 1.3 61.4 - - + +
387A ALA* 3.7 8.0 - - - +
388A PHE* 2.8 30.5 + - - +
394A ALA* 4.0 11.4 - - + +
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Residues in contact with LYS 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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306A LEU* 3.8 45.0 + - + +
362A HIS* 4.1 29.1 + - + +
381A ALA* 3.1 26.2 + - - +
382A GLU* 2.6 23.3 + - + +
384A GLU* 1.3 75.0 - - + +
386A VAL* 1.3 54.1 + - - +
388A PHE* 3.8 1.3 - - - +
389A LEU* 2.9 36.9 + - - +
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Residues in contact with VAL 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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359A CYS* 3.9 17.7 - - - +
362A HIS* 3.8 11.4 - - + -
363A LEU* 3.7 46.0 - - + +
366A MET* 4.2 9.6 - - - -
382A GLU 2.8 10.1 + - - +
383A ALA* 2.9 38.4 - - - +
385A LYS* 1.3 74.8 - - - +
387A ALA* 1.3 67.5 + - - +
389A LEU* 4.4 0.9 - - - -
390A LEU* 3.0 33.4 + - + +
397A LEU* 3.8 17.0 - - + -
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Residues in contact with ALA 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 ALA 2.7 25.5 + - - +
384A GLU* 3.8 4.3 - - - +
385A LYS 3.4 0.2 - - - -
386A VAL* 1.3 75.8 - - - +
388A PHE* 1.3 56.4 + - - +
390A LEU* 3.4 2.9 + - - +
391A GLY 2.9 21.3 + - - -
392A VAL* 2.9 23.5 + - - +
393A ASN 4.2 0.4 - - - -
394A ALA* 3.4 38.1 - - + +
397A LEU* 4.5 9.4 - - + -
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Residues in contact with PHE 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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304A LYS 5.7 1.8 - - - -
306A LEU* 4.7 20.6 - - + -
355A LYS* 5.3 11.0 - - - -
384A GLU 2.8 19.8 + - - +
385A LYS* 3.8 2.9 - - - +
387A ALA* 1.3 72.9 - - - +
389A LEU* 1.3 65.9 + - + +
390A LEU 2.9 4.5 - - - -
391A GLY* 2.5 27.1 + - - +
392A VAL 4.7 1.8 - - - -
616A LYS* 3.7 28.6 + - - -
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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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304A LYS 3.9 22.2 - - - +
305A ILE* 3.6 11.7 - - - +
306A LEU* 4.4 8.5 - - + -
355A LYS* 3.9 42.0 - - + +
356A CYS* 5.6 2.4 - - - -
359A CYS* 3.5 40.2 - - + +
362A HIS* 3.5 22.2 - - + -
385A LYS 2.9 29.1 + - - +
386A VAL 3.9 3.6 - - - +
388A PHE* 1.3 80.9 - - + +
390A LEU* 1.3 63.4 + - - +
616A LYS* 4.5 9.7 + - - +
619A ILE* 4.2 3.8 - - - +
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Residues in contact with LEU 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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356A CYS* 4.8 7.0 - - - -
359A CYS* 3.6 31.0 - - + -
363A LEU* 5.9 0.9 - - + -
386A VAL* 3.0 22.4 + - + +
387A ALA* 3.9 3.8 - - - +
388A PHE 2.9 0.6 - - - -
389A LEU* 1.3 79.9 - - - +
391A GLY* 1.3 66.8 + - - +
392A VAL* 3.6 12.6 - - + +
397A LEU* 6.0 4.7 - - + -
429A LEU* 5.0 15.5 - - + -
433A LEU* 4.6 16.4 - - + -
612A LEU* 3.6 26.9 - - + -
614A ASN 4.1 3.5 - - - +
616A LYS* 3.6 8.2 - - - +
619A ILE* 3.0 37.1 - - + +
623A LEU* 5.8 1.1 - - + -
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Residues in contact with GLY 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 ALA 2.9 3.2 + - - -
388A PHE* 2.5 25.4 + - - -
390A LEU* 1.3 72.3 - - - +
392A VAL* 1.3 64.0 + - - +
614A ASN* 3.3 1.9 - - - +
615A SER* 2.6 33.5 - - - -
616A LYS* 3.6 19.5 - - - +
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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