Contacts of the helix formed by residues 430 - 445 (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 VAL 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A PRO 3.6 11.2 - - - +
429A GLU* 1.3 74.9 - - + +
431A TYR* 1.3 71.4 + - + +
432A THR 3.4 0.7 - - - -
433A PRO* 3.6 20.1 - - - +
434A VAL* 3.0 19.6 - - + +
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Residues in contact with TYR 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ASP* 4.7 8.9 + - + +
385A TYR* 4.8 15.3 - + - +
386A VAL* 3.0 42.6 - - + +
389A ILE* 5.2 10.3 - - + -
424A LEU* 5.0 6.7 - - + -
426A THR* 4.0 12.1 - - + -
428A PRO* 3.4 39.1 - - + +
429A GLU 2.1 19.2 + - - +
430A VAL* 1.3 83.0 - - + +
432A THR* 1.3 67.5 + - - +
434A VAL* 3.1 9.7 - - + +
435A LEU* 2.9 37.3 + - + +
471A LYS* 5.2 5.2 - - - +
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Residues in contact with THR 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A VAL* 4.8 11.3 - - - +
428A PRO 5.6 0.2 - - - -
429A GLU* 2.6 25.8 + - - -
431A TYR* 1.3 73.9 - - - +
433A PRO* 1.3 73.0 - - + +
435A LEU* 3.4 11.4 - - - +
436A GLU* 3.0 26.9 + - - +
475A LEU* 3.3 31.0 - - + -
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Residues in contact with PRO 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLU* 4.0 1.6 - - + -
430A VAL* 3.6 27.4 - - - +
432A THR* 1.3 95.4 - - + +
434A VAL* 1.3 63.4 + - + +
436A GLU* 3.3 11.6 - - + +
437A HIS* 3.0 27.0 + - - +
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ILE* 3.8 33.9 - - + +
393A LYS* 3.9 21.5 - - + -
430A VAL* 3.0 23.1 - - + +
431A TYR* 3.1 14.8 - - + +
433A PRO* 1.3 77.9 - - + +
435A LEU* 1.3 76.7 + - + +
436A GLU 3.1 0.5 + - - -
437A HIS* 2.9 53.5 + - + +
438A LEU* 3.0 5.6 + - + +
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Residues in contact with LEU 435 (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 TYR* 5.2 2.0 - - - +
389A ILE* 5.3 6.5 - - + -
421A LEU* 4.8 17.0 - - + -
424A LEU* 5.0 6.3 - - + -
431A TYR* 2.9 38.7 + - + +
432A THR* 3.4 8.7 - - - +
434A VAL* 1.3 77.8 - - + +
436A GLU* 1.3 67.2 + - - +
438A LEU* 3.1 10.3 + - - +
439A VAL* 2.9 27.2 + - + +
468A LEU* 3.5 43.7 - - + -
471A LYS* 4.5 14.8 - - - +
475A LEU* 3.5 18.6 - - + -
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Residues in contact with GLU 436 (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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432A THR* 3.0 23.6 + - - +
433A PRO* 3.3 9.5 - - - +
435A LEU* 1.3 82.2 - - - +
437A HIS* 1.3 65.2 + - - +
439A VAL* 3.1 10.1 + - - +
440A VAL* 3.1 29.3 + - + +
475A LEU* 2.6 39.3 - - + +
478A CYS* 4.2 18.2 - - - +
479A ILE* 3.8 17.8 + - + +
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Residues in contact with HIS 437 (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* 3.7 10.1 - - + +
396A PHE* 2.9 47.2 - + + -
397A LEU* 5.1 5.1 - - + +
433A PRO 3.0 18.0 + - - +
434A VAL* 2.9 45.3 + - + +
436A GLU* 1.3 75.7 - - - +
438A LEU* 1.3 89.8 + - + +
440A VAL* 2.9 17.8 - - + +
441A MSE 2.9 24.1 + - - +
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Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ILE* 5.4 7.0 - - + +
392A CYS* 3.6 49.1 - - + +
396A PHE* 3.8 23.3 - - + -
410A MSE 4.7 12.3 - - + +
414A LEU* 4.4 13.2 - - + +
417A VAL* 3.9 26.9 - - + -
434A VAL* 3.0 10.8 + - + +
435A LEU* 3.1 12.1 + - - +
437A HIS* 1.3 84.8 - - + +
439A VAL* 1.3 67.2 + - - +
441A MSE 3.3 4.7 + - + +
442A GLN* 3.1 19.8 + - - +
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Residues in contact with VAL 439 (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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414A LEU* 6.0 0.7 - - - -
421A LEU* 6.3 0.2 - - + -
435A LEU* 2.9 22.3 + - + +
436A GLU* 3.1 10.8 - - - +
438A LEU* 1.3 77.7 - - - +
440A VAL* 1.3 64.6 + - - +
442A GLN* 3.0 5.1 + - - +
443A ILE* 2.9 47.6 + - + +
461A ILE* 6.0 0.2 - - + -
464A VAL* 4.5 16.2 - - + -
465A PHE* 3.7 12.8 - - + -
468A LEU* 3.7 29.8 - - + -
479A ILE* 3.5 23.8 - - + -
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Residues in contact with VAL 440 (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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436A GLU* 3.1 23.1 - - + +
437A HIS* 2.9 26.3 + - + +
439A VAL* 1.3 75.1 - - + +
441A MSE 1.3 66.0 + - + +
443A ILE* 3.3 5.1 + - - +
444A ASP* 2.9 26.4 + - - +
479A ILE* 5.3 2.5 - - + -
482A VAL* 5.4 10.3 - - + -
483A VAL* 3.6 34.1 - - + +
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Residues in contact with MSE 441 (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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396A PHE* 3.2 48.5 - - + +
399A GLN* 5.3 11.9 - - + -
407A VAL* 5.7 5.4 - - + -
410A MSE 3.2 32.5 - - + +
437A HIS 2.9 12.8 + - - +
438A LEU* 3.6 9.9 - - - +
439A VAL 3.1 0.2 + - - -
440A VAL* 1.3 81.7 - - + +
442A GLN* 1.3 50.3 + - - +
444A ASP* 2.7 27.0 + - + +
445A SER* 2.5 25.3 + - - +
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Residues in contact with GLN 442 (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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410A MSE 3.9 11.7 - - - +
411A PRO* 3.4 19.0 - - - +
414A LEU* 3.5 26.5 - - + -
438A LEU 3.1 8.0 + - - +
439A VAL* 3.0 9.1 + - - +
441A MSE 1.3 78.9 - - - +
443A ILE* 1.3 57.1 + - - +
445A SER* 2.9 32.2 + - - -
446A PHE* 3.5 4.9 + - - +
449A TYR* 2.8 30.4 + - - -
457A CYS* 3.2 13.7 - - - +
461A ILE* 3.1 36.9 - - + +
464A VAL* 5.7 0.7 - - + -
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Residues in contact with ILE 443 (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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439A VAL* 2.9 29.5 + - + +
440A VAL* 3.5 7.0 - - - +
441A MSE 3.2 0.2 - - - -
442A GLN* 1.3 73.5 - - - +
444A ASP* 1.3 56.9 + - - +
446A PHE* 2.8 36.2 - - + -
461A ILE* 4.2 20.4 - - + -
465A PHE* 3.5 34.8 - - + -
483A VAL* 3.5 43.1 - - + +
487A LEU* 5.5 2.9 - - + -
534A LEU* 5.3 10.5 - - + -
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Residues in contact with ASP 444 (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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440A VAL* 2.9 13.0 + - - +
441A MSE 2.7 25.9 + - + +
443A ILE* 1.3 72.5 - - - +
445A SER* 1.3 53.5 + - - -
446A PHE* 3.2 15.8 - - - -
447A PRO* 3.3 14.7 - - - +
486A GLY* 5.1 12.7 - - - -
487A LEU* 5.2 2.1 + - - -
490A ILE* 5.0 13.0 - - - +
525A LYS* 3.4 27.1 + - - +
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Residues in contact with SER 445 (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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407A VAL* 4.1 22.7 - - - +
410A MSE 3.0 19.0 - - - +
441A MSE 2.5 24.4 + - - -
442A GLN* 2.9 17.1 + - - -
444A ASP* 1.3 72.2 - - - +
446A PHE* 1.3 51.2 + - - +
447A PRO* 3.2 7.9 - - - -
448A GLN* 3.1 16.3 + - - +
449A TYR* 2.9 36.0 - - - -
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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