Contacts of the helix formed by residues 382 - 398 (chain A) in PDB entry 5LUQ
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 ASP 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A ASP* 4.9 6.2 - - - +
381A VAL* 1.3 73.4 + - - +
383A PHE* 1.4 69.4 + - - +
384A MSE 2.7 15.1 - - - +
385A TYR* 5.2 3.6 - - - -
386A VAL* 2.6 51.1 - - + +
426A THR* 6.0 6.1 - - + -
431A TYR* 4.7 8.1 + - + +
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Residues in contact with PHE 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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343A GLU* 5.6 3.4 - - - -
346A TYR* 3.2 30.7 - + + +
379A LYS* 5.0 15.3 - - + -
380A ASP* 2.9 34.1 - - + -
381A VAL* 2.9 13.1 - - + -
382A ASP* 1.4 94.5 - - - +
384A MSE 1.3 57.7 + - + +
386A VAL* 3.9 1.5 - - - +
387A GLU* 2.9 27.9 + - - +
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Residues in contact with MSE 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A MSE 4.0 17.5 - - + -
346A TYR* 3.9 10.0 - - + -
368A LEU* 3.1 30.3 - - + -
372A PRO* 3.6 39.5 - - + +
376A ILE* 3.8 20.6 - - + -
381A VAL* 2.6 73.5 - - + +
382A ASP 2.7 12.1 - - - +
383A PHE* 1.3 80.6 - - + +
385A TYR* 1.3 69.5 + - + +
386A VAL 2.8 3.8 + - - -
387A GLU* 4.7 0.9 - - - +
420A VAL* 5.0 5.6 - - + +
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Residues in contact with TYR 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 3.8 11.7 - - - +
381A VAL 4.3 1.8 - - - +
382A ASP* 5.0 3.6 - - - -
384A MSE 1.3 90.9 - - + +
386A VAL* 1.3 71.8 + - + -
387A GLU 3.3 0.4 - - - -
388A LEU* 3.7 13.1 - - - +
389A ILE* 2.8 60.5 + - + +
420A VAL* 3.1 44.0 - - + +
421A LEU* 3.0 40.0 - - + +
423A TYR 4.5 2.0 - - - -
424A LEU* 3.0 37.7 - - + +
431A TYR* 4.8 7.9 - + - +
435A LEU* 5.2 3.5 - - - +
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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
----------------------------------------------------------
382A ASP* 2.6 35.6 + - + +
383A PHE 3.9 1.3 - - - +
384A MSE 2.8 10.7 + - - -
385A TYR* 1.3 79.3 - - + +
387A GLU* 1.3 56.5 + - - +
389A ILE* 3.5 9.1 - - + +
390A GLN* 3.0 29.4 + - + +
431A TYR* 3.0 46.7 - - + +
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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
----------------------------------------------------------
346A TYR* 5.4 7.6 - - + +
349A ILE* 3.6 27.2 - - + +
350A ARG* 2.5 40.1 + - + +
368A LEU* 5.3 1.1 - - + -
383A PHE 2.9 19.6 + - - +
384A MSE 4.9 2.7 - - - -
386A VAL* 1.3 75.6 - - - +
388A LEU* 1.3 66.9 + - - +
390A GLN* 3.1 20.2 + - - +
391A ARG* 2.9 55.4 + - - +
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Residues in contact with LEU 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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349A ILE* 4.9 5.8 - - + -
364A ARG* 4.7 9.2 - - - +
365A GLY* 3.6 31.2 - - - +
368A LEU* 4.3 15.8 - - + +
385A TYR* 3.7 22.3 + - - +
386A VAL 3.5 0.2 - - - -
387A GLU* 1.3 78.5 - - - +
389A ILE* 1.3 55.4 + - - +
391A ARG* 2.8 30.2 + - + +
392A CYS* 2.8 19.9 + - - -
413A PHE 4.9 1.8 - - - +
416A SER* 5.5 1.1 - - - +
417A VAL* 3.5 33.7 - - + +
420A VAL* 4.0 21.8 - - + -
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Residues in contact with ILE 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A TYR* 2.8 70.2 + - + +
386A VAL* 3.5 10.3 - - + +
388A LEU* 1.3 74.2 - - + +
390A GLN* 1.3 67.4 - - + +
391A ARG 3.0 0.3 + - - -
392A CYS* 3.0 7.7 + - - +
393A LYS* 3.0 21.3 + - - +
417A VAL* 5.9 4.0 - - + -
420A VAL* 5.3 2.5 - - + -
421A LEU* 4.6 6.3 - - + -
431A TYR* 5.2 13.9 - - + -
434A VAL* 3.8 36.4 - - + +
435A LEU* 5.3 7.2 - - + +
438A LEU* 5.4 6.1 - - + +
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Residues in contact with GLN 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ARG* 5.0 1.6 + - - -
386A VAL* 3.0 18.4 + - - +
387A GLU* 3.6 21.7 - - - +
389A ILE* 1.3 78.2 - - + +
391A ARG* 1.3 59.8 + - - +
393A LYS* 2.9 53.6 + - - +
394A GLN* 3.0 7.3 + - + +
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Residues in contact with ARG 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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349A ILE* 3.6 20.2 + - + +
350A ARG* 4.9 2.8 - - - +
352A VAL* 4.9 6.0 - - - +
353A ASP* 3.2 30.2 + - - -
364A ARG* 4.3 29.0 - - - +
387A GLU* 2.9 35.9 + - - +
388A LEU* 2.8 21.0 + - + +
390A GLN* 1.3 78.6 - - - +
392A CYS* 1.3 56.0 + - - +
394A GLN* 2.8 51.7 + - - +
395A MSE 2.8 26.2 + - + +
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Residues in contact with CYS 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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388A LEU* 2.8 19.0 + - - +
389A ILE* 3.0 6.0 + - - +
391A ARG* 1.3 72.9 - - - +
393A LYS* 1.3 58.2 + - - +
395A MSE 3.9 6.8 - - - +
396A PHE* 3.0 32.4 + - - +
410A MSE 5.7 5.2 - - - +
413A PHE* 3.9 27.1 - - - -
414A LEU* 5.4 0.7 - - - -
417A VAL* 3.3 30.7 - - + -
438A LEU* 3.6 27.0 - - + +
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Residues in contact with LYS 393 (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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389A ILE 3.0 11.2 + - - +
390A GLN* 2.9 47.4 + - - +
392A CYS* 1.3 73.9 - - - +
394A GLN* 1.3 72.2 + - - +
396A PHE* 3.2 11.8 - - + -
397A LEU* 3.0 35.3 + - + +
434A VAL* 3.9 17.0 - - + +
437A HIS* 3.7 23.8 - - + +
438A LEU* 4.8 0.8 - - - +
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Residues in contact with GLN 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLN* 3.0 12.0 + - - +
391A ARG* 2.8 47.9 + - - +
393A LYS* 1.3 82.9 - - - +
395A MSE 1.3 56.0 + - + +
396A PHE 3.0 0.3 + - - -
398A THR* 2.5 57.3 + - + +
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Residues in contact with MSE 395 (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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361A ILE* 3.5 18.6 - - + -
364A ARG* 5.3 1.6 - - - +
391A ARG* 2.8 32.5 + - + +
392A CYS* 4.2 7.6 - - - +
394A GLN* 1.3 73.9 - - + +
396A PHE* 1.3 59.2 + - - +
398A THR* 3.5 11.2 + - - -
399A GLN* 4.1 10.7 + - - +
405A ASP* 3.5 35.4 - - + +
409A GLN* 5.6 1.1 - - + -
410A MSE 5.7 4.6 - - + +
413A PHE* 3.1 47.1 - - + -
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Residues in contact with PHE 396 (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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392A CYS 3.0 25.9 + - - +
393A LYS* 3.2 17.5 - - + -
395A MSE 1.3 77.1 - - - +
397A LEU* 1.3 96.2 + - + +
398A THR 3.2 1.8 - - - -
399A GLN* 2.8 28.5 + - - +
410A MSE 4.8 11.0 - - + +
437A HIS* 2.9 50.5 - + + -
438A LEU* 3.8 13.7 - - + -
441A MSE 3.2 45.6 - - + +
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Residues in contact with LEU 397 (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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393A LYS* 3.0 22.9 + - + +
394A GLN* 4.4 0.7 - - - +
396A PHE* 1.3 112.6 - - + +
398A THR* 1.3 58.2 + - + +
400A THR* 3.0 26.3 + - - +
437A HIS* 5.1 6.1 - - + +
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Residues in contact with THR 398 (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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394A GLN* 2.5 47.1 + - + +
395A MSE 3.5 10.0 + - - -
397A LEU* 1.3 73.4 - - + +
399A GLN* 1.3 49.6 + - - +
400A THR* 2.7 13.4 - - - +
401A ASP* 2.3 53.7 + - - +
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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
------------------------------------------------------------
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