Contacts of the helix formed by residues 379 - 390 (chain A) in PDB entry 4DQM
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 MET 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A PRO 3.0 20.9 + - - +
376A LYS* 3.5 15.9 - - + +
377A MET 3.1 0.4 + - - -
378A LEU* 1.3 73.2 - - + +
380A LYS* 1.3 64.0 + - - +
381A ILE 3.2 0.4 - - - -
382A THR* 3.1 28.7 + - - +
383A ASP* 3.7 9.2 + - - +
332C ILE* 4.2 11.9 - - + +
333C CYS* 5.8 0.7 - - - -
336C CYS* 5.2 10.1 - - - -
352C GLN* 3.5 28.7 - - - +
356C LEU* 4.3 27.1 - - - -
378C LEU* 4.4 21.5 - - + +
381C ILE* 4.9 12.3 - - + -
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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
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312A PHE* 3.7 28.6 - - + -
315A GLN* 3.9 33.0 + - - +
316A LEU* 4.6 7.0 - - + -
319A LEU* 4.1 22.4 - - + -
321A MET* 6.0 0.2 - - - -
329A LEU* 4.3 12.3 - - + -
376A LYS* 3.5 17.4 - - - +
377A MET* 2.8 22.0 + - - +
379A MET* 1.3 76.4 - - - +
381A ILE* 1.3 65.1 + - - +
382A THR 3.1 0.4 - - - -
383A ASP* 3.0 23.4 + - - +
384A LEU* 3.1 14.1 + - + +
338C ASP* 2.9 37.6 + - - -
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Residues in contact with ILE 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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267A ASP* 5.0 0.2 - - - +
329A LEU* 3.6 39.0 - - + +
332A ILE* 4.1 22.7 - - + -
333A CYS* 4.1 33.0 - - + +
378A LEU* 3.0 19.9 + - + +
380A LYS* 1.3 77.7 - - - +
382A THR* 1.3 56.2 + - - +
384A LEU* 3.2 14.5 - - + +
385A ARG* 2.9 31.7 + - - +
379C MET* 4.4 12.6 - - + -
382C THR* 4.1 16.6 - - + +
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Residues in contact with THR 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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379A MET* 3.1 21.5 + - - +
380A LYS 3.1 0.8 - - - -
381A ILE* 1.3 78.2 - - - +
383A ASP* 1.3 58.6 + - - +
385A ARG* 3.4 2.1 + - - +
386A SER* 3.1 25.5 + - - -
378C LEU 5.2 0.9 + - - -
381C ILE* 4.0 20.6 - - + +
382C THR* 2.5 35.1 + - - -
385C ARG* 3.5 34.4 - - + +
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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
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312A PHE* 3.6 24.2 - - + -
315A GLN* 4.7 9.0 - - - +
379A MET 3.7 11.7 + - - +
380A LYS* 3.0 24.1 + - - +
382A THR* 1.3 74.3 - - - +
384A LEU* 1.3 64.6 + - - +
386A SER* 3.3 8.7 + - - -
387A ILE* 3.0 32.6 + - + +
336C CYS* 5.6 1.0 - - - -
338C ASP* 4.2 13.8 - - - +
339C ARG* 5.1 9.2 + - - -
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Residues in contact with LEU 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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267A ASP* 3.6 39.9 - - + +
270A ILE* 4.1 16.8 - - + +
271A LEU* 4.0 23.6 - - + +
312A PHE* 3.2 43.3 - - + -
329A LEU* 5.7 2.9 - - + -
333A CYS* 5.2 3.8 - - + -
380A LYS 3.1 6.5 + - - +
381A ILE* 3.2 29.4 - - + +
383A ASP* 1.3 73.8 - - - +
385A ARG* 1.3 52.9 + - - +
387A ILE* 3.3 6.7 + - + +
388A SER* 2.7 37.1 + - - -
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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
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263A ALA* 4.0 9.0 + - - +
267A ASP* 3.6 23.4 + - - -
333A CYS* 4.9 5.9 - - - -
339A ARG* 2.8 42.8 - - - +
381A ILE* 2.9 11.6 + - - +
382A THR 3.5 9.0 - - - +
383A ASP 3.2 0.2 - - - -
384A LEU* 1.3 73.9 - - - +
386A SER* 1.3 59.2 + - - +
388A SER* 3.6 10.5 + - - -
389A ALA* 2.8 41.1 + - - +
382C THR* 3.5 45.8 - - + +
383C ASP* 5.9 0.6 + - - -
385C ARG* 4.7 2.2 - - + -
386C SER* 3.7 27.4 + - - +
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Residues in contact with SER 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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308A LEU* 5.2 4.2 - - - +
382A THR 3.1 11.2 + - - -
383A ASP* 3.5 14.6 - - - -
385A ARG* 1.3 78.7 - - - +
387A ILE* 1.3 64.1 + - - +
389A ALA* 4.3 4.5 - - - +
390A LYS* 3.0 35.5 + - - +
385C ARG* 3.7 29.0 + - - +
389C ALA* 4.6 3.3 - - - +
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Residues in contact with ILE 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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270A ILE* 3.9 25.4 - - + -
305A LEU* 4.0 20.9 - - + +
308A LEU* 3.9 44.4 - - + +
309A VAL* 4.1 19.7 - - + +
312A PHE* 4.1 19.3 - - + -
383A ASP* 3.0 20.3 + - + +
384A LEU* 3.7 5.4 - - - +
386A SER* 1.3 78.5 - - - +
388A SER* 1.3 64.4 + - - +
390A LYS* 3.1 18.6 + - - +
391A GLY* 3.9 2.3 + - - -
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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
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266A LEU* 3.7 30.3 - - - +
267A ASP* 2.7 32.5 + - - -
270A ILE* 3.9 12.3 - - - -
384A LEU 2.7 17.7 + - - -
385A ARG* 3.4 9.9 + - - -
387A ILE* 1.3 73.0 - - - +
389A ALA* 1.3 54.6 + - - +
391A GLY* 2.7 29.0 + - - -
392A ALA 4.4 0.5 + - - -
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Residues in contact with ALA 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 ARG* 2.8 26.9 + - - +
386A SER 4.3 0.9 - - - +
388A SER* 1.3 69.1 + - - +
390A LYS* 1.3 57.9 + - - +
391A GLY* 2.8 10.1 + - - -
392A ALA* 4.1 6.9 + - - +
393A GLU* 4.3 4.6 - - - +
386C SER* 4.6 14.4 - - - +
389C ALA* 3.7 29.2 - - + -
390C LYS* 4.8 14.5 + - + +
393C GLU* 4.4 8.1 - - - +
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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
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305A LEU* 3.4 24.1 - - + +
308A LEU* 4.1 25.0 - - + +
386A SER* 3.0 27.6 + - - +
387A ILE 3.1 7.8 + - - +
389A ALA* 1.3 75.0 - - - +
391A GLY* 1.3 63.0 + - - +
392A ALA 3.6 0.9 - - - -
393A GLU* 3.5 27.4 - - - +
394A ARG* 3.4 18.5 + - - +
389C ALA* 4.3 19.6 - - + +
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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