Contacts of the helix formed by residues 378 - 392 (chain A) in PDB entry 5ID6
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 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A VAL* 3.3 24.2 + - + +
377A VAL* 1.3 78.0 - - - +
379A GLU* 1.3 65.3 + - - +
380A LYS* 3.4 7.9 + - - +
381A TYR* 3.2 24.0 + - + +
382A GLU* 3.1 25.2 + - - +
1056A ASP* 4.2 19.7 - - - +
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Residues in contact with GLU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A THR* 1.3 74.6 - - - +
380A LYS* 1.3 60.0 + - + +
382A GLU* 3.1 12.2 + - + +
383A ASP* 2.8 33.8 + - - +
386A ARG* 5.2 0.3 + - - -
999A TRP* 3.7 22.0 - - - -
1056A ASP* 5.1 1.4 + - - +
1057A ALA* 5.6 0.3 - - - +
1214A SER* 3.4 17.8 - - - -
1215A ASN* 2.8 45.9 + - + +
1216A LYS* 3.8 6.2 + - + +
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Residues in contact with LYS 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A THR* 3.3 7.4 + - - +
379A GLU* 1.3 78.1 - - + +
381A TYR* 1.3 57.2 + - - +
383A ASP* 2.9 9.6 + - + +
384A ASP* 2.6 47.8 + - - +
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Residues in contact with TYR 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A TYR* 3.8 22.5 + + - -
367A ASP* 2.5 45.3 + - - -
370A HIS* 4.1 22.4 - - + -
371A LEU* 3.8 15.1 + - + +
376A VAL 5.7 0.2 - - - +
377A VAL* 3.5 34.3 - - + -
378A THR* 3.2 24.0 + - + +
380A LYS* 1.3 79.0 - - - +
382A GLU* 1.3 59.6 + - + +
384A ASP* 4.0 5.0 - - - +
385A ARG* 3.0 40.4 + - - +
1054A ARG* 5.6 0.2 - - - -
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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
----------------------------------------------------------
359A ARG* 5.4 0.2 + - - -
377A VAL* 3.4 21.9 - - + +
378A THR 3.1 8.8 + - - +
379A GLU* 3.7 11.5 - - + +
381A TYR* 1.3 79.5 - - + +
383A ASP* 1.3 64.7 + - - +
385A ARG* 3.9 21.2 + - - +
386A ARG* 3.1 45.1 + - - +
1054A ARG* 3.0 41.4 + - - +
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Residues in contact with ASP 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A GLU* 2.8 20.0 + - - +
380A LYS* 2.9 11.6 + - + +
382A GLU* 1.3 76.0 - - - +
384A ASP* 1.3 62.1 + - - +
386A ARG* 2.6 34.6 + - - +
387A LYS* 2.8 48.2 + - - +
999A TRP* 5.9 5.7 - - - -
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Residues in contact with ASP 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A TYR* 4.2 7.4 - - - +
380A LYS* 2.6 29.8 + - - +
381A TYR* 4.0 5.2 - - - +
383A ASP* 1.3 72.5 - - - +
385A ARG* 1.3 62.9 + - - +
387A LYS* 3.1 29.3 + - - +
388A SER* 2.8 27.6 + - - -
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Residues in contact with ARG 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ARG* 4.4 2.7 - - - +
362A TRP* 3.7 4.5 - - + -
363A ASN* 3.3 52.0 + - - +
366A TYR* 3.3 50.6 + - + -
367A ASP* 3.2 19.3 + - - -
381A TYR* 3.0 24.0 + - + +
382A GLU* 3.9 19.9 + - - +
384A ASP* 1.3 75.8 - - - +
386A ARG* 1.3 63.6 + - - +
388A SER* 3.3 4.4 + - - -
389A PHE* 3.0 18.9 + - - +
1054A ARG* 3.1 45.6 - - - +
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Residues in contact with ARG 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ARG* 3.5 28.4 - - - +
382A GLU* 3.1 51.5 + - - +
383A ASP* 2.6 38.9 + - - +
385A ARG* 1.3 75.8 - - - +
387A LYS* 1.3 64.2 + - + +
389A PHE* 3.2 3.1 + - - +
390A LYS* 3.1 25.8 + - + +
931A PHE* 6.0 9.6 - - - -
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Residues in contact with LYS 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 ASP* 2.8 35.4 + - - +
384A ASP* 3.4 30.5 + - - +
386A ARG* 1.3 75.7 - - - +
388A SER* 1.3 61.3 + - - +
390A LYS* 4.0 6.2 - - - +
391A LYS* 3.2 26.2 + - - +
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A TRP* 3.7 15.3 - - - -
366A TYR* 3.6 19.8 + - - -
384A ASP 2.8 15.8 + - - -
385A ARG 3.3 7.4 - - - -
386A ARG 3.2 0.4 - - - -
387A LYS* 1.3 74.7 - - - +
389A PHE* 1.3 66.1 + - - +
391A LYS* 3.1 28.9 + - - +
392A ILE* 3.1 17.7 + - - +
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Residues in contact with PHE 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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340A ASN* 2.9 42.1 + - - -
341A GLY* 6.5 0.2 - - - -
344A ILE* 4.5 12.8 - - + -
358A ILE* 5.0 1.3 - - + -
359A ARG* 3.3 59.0 - - + +
362A TRP* 3.4 46.6 - + + -
385A ARG 3.0 6.9 + - - -
386A ARG 3.6 7.4 - - - +
388A SER* 1.3 77.2 - - - +
390A LYS* 1.3 68.8 + - + +
391A LYS 3.1 0.9 + - - -
392A ILE* 3.2 9.3 + - + +
395A PHE* 3.8 21.5 - + - -
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Residues in contact with LYS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASN* 3.8 5.4 + - - +
386A ARG* 3.1 14.9 + - + +
387A LYS* 4.0 6.7 - - - +
389A PHE* 1.3 87.0 - - + +
391A LYS* 1.3 63.2 + - - +
392A ILE 3.4 7.4 - - - +
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Residues in contact with LYS 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 LYS 3.2 18.3 + - - +
388A SER* 3.1 20.6 + - - +
389A PHE 3.1 1.0 - - - -
390A LYS* 1.3 76.1 - - - +
392A ILE* 1.3 67.0 + - - +
393A GLY* 3.3 4.9 + - - -
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Residues in contact with ILE 392 (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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340A ASN* 2.9 25.8 + - - +
362A TRP* 3.9 28.9 - - + +
388A SER 3.1 15.9 + - - +
389A PHE* 3.3 10.5 - - - +
390A LYS 3.4 3.6 - - - +
391A LYS* 1.3 76.1 - - - +
393A GLY* 1.3 62.8 + - - +
394A SER 3.6 22.0 - - - +
395A PHE* 3.9 23.1 - - + -
399A GLN* 6.0 0.2 - - - +
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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