Contacts of the helix formed by residues 406 - 424 (chain A) in PDB entry 6DEE
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 406 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A GLU* 1.3 78.4 + - - +
407A GLU* 1.3 66.3 + - - +
408A GLY* 3.2 3.8 - - - +
409A VAL* 3.2 31.0 + - + +
410A ILE* 3.4 12.3 + - - +
453A ARG* 3.9 0.2 - - - -
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Residues in contact with GLU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ASP* 1.3 72.4 - - - +
408A GLY* 1.3 57.0 + - - +
410A ILE 3.6 0.5 + - - -
411A ARG* 2.9 29.4 + - - +
453A ARG* 3.3 37.7 - - - +
456A LEU* 3.6 12.0 - - + +
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Residues in contact with GLY 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ASP* 3.2 3.6 - - - +
407A GLU* 1.3 76.9 - - - +
409A VAL* 1.3 58.4 + - - +
411A ARG* 3.2 23.7 + - - +
412A CYS* 2.9 37.1 + - - -
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Residues in contact with VAL 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLU* 5.2 7.4 - - + +
406A ASP* 3.2 31.2 + - + +
408A GLY* 1.3 75.7 - - - +
410A ILE* 1.3 62.9 + - + +
412A CYS* 3.0 10.1 + - + +
413A TYR* 2.9 52.4 + - + -
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Residues in contact with ILE 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU* 4.6 11.2 - - + -
402A ALA* 3.7 40.2 - - + +
405A GLU* 4.3 12.6 - - + -
406A ASP 3.6 12.8 - - - +
407A GLU 4.0 1.1 - - - +
408A GLY 3.4 0.2 - - - -
409A VAL* 1.3 78.5 - - + +
411A ARG* 1.3 57.6 + - - +
413A TYR* 3.2 11.6 + - + +
414A LEU* 2.9 41.9 + - + +
447A TYR* 3.2 24.7 - - + +
453A ARG* 4.3 7.2 - - - +
456A LEU* 3.7 20.4 - - + -
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Residues in contact with ARG 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A GLU 2.9 19.2 + - - +
408A GLY* 3.3 23.9 + - - +
409A VAL 3.1 0.2 - - - -
410A ILE* 1.3 77.3 - - - +
412A CYS* 1.3 65.7 + - - +
414A LEU 3.4 0.2 + - - -
415A GLU* 2.9 74.3 + - - +
455A SER* 5.5 9.4 - - - -
456A LEU* 3.5 12.5 - - + +
459A LEU* 3.6 15.5 - - + +
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Residues in contact with CYS 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A GLY 2.9 20.3 + - - -
409A VAL* 3.0 9.6 + - - +
411A ARG* 1.3 86.7 - - - +
413A TYR* 1.3 60.8 - - + +
415A GLU* 3.7 16.3 - - - +
416A GLU* 2.9 31.7 + - - +
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Residues in contact with TYR 413 (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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381A ARG* 5.7 5.2 - - - -
384A VAL* 5.0 7.0 - - + +
385A ILE* 4.0 31.8 - - + +
388A ASP* 3.9 28.4 - - + +
389A LEU* 4.3 25.4 - - + -
409A VAL* 2.9 47.7 + - + -
410A ILE* 3.3 17.7 - - + +
412A CYS* 1.3 78.2 - - + +
414A LEU* 1.3 58.8 + - + +
416A GLU* 3.3 5.9 + - - +
417A LEU* 2.9 27.8 + - - +
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Residues in contact with LEU 414 (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 LEU* 3.7 24.7 - - + -
410A ILE* 2.9 30.2 + - + +
413A TYR* 1.3 72.4 - - + +
415A GLU* 1.3 61.0 + - - +
417A LEU* 4.1 11.0 - - + -
418A LEU* 2.9 30.3 + - - +
447A TYR* 4.9 2.0 - - + -
456A LEU* 3.2 43.7 - - + +
459A LEU* 3.6 25.1 - - + +
460A LEU* 3.7 28.7 - - + -
463A CYS* 3.5 8.2 - - - -
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Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ARG* 2.9 62.4 + - - +
412A CYS* 3.7 14.4 - - - +
414A LEU* 1.3 76.5 - - - +
416A GLU* 1.3 57.7 + - - +
418A LEU* 3.3 6.3 + - + +
419A HIS* 2.9 50.8 + - + +
459A LEU* 4.2 19.1 - - + +
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ARG* 2.6 48.8 + - - +
385A ILE* 3.3 15.5 - - + +
412A CYS 2.9 17.8 + - - +
413A TYR* 3.7 5.6 - - - +
415A GLU* 1.3 73.8 - - - +
417A LEU* 1.3 61.2 + - - +
419A HIS* 3.3 10.2 + - + +
420A ILE* 2.9 45.3 + - + +
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Residues in contact with LEU 417 (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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382A LEU* 3.7 19.1 - - + -
385A ILE* 3.9 21.0 - - + +
386A PHE* 3.6 28.0 - - + -
389A LEU* 4.8 0.2 - - + -
413A TYR 2.9 17.2 + - - +
414A LEU* 3.6 11.9 - - + +
415A GLU 3.3 0.2 - - - -
416A GLU* 1.3 76.7 - - - +
418A LEU* 1.3 56.8 + - - +
420A ILE* 3.3 3.6 + - - +
421A LEU* 2.9 49.1 + - + +
444A LEU* 3.9 31.9 - - + -
463A CYS* 3.7 21.3 - - + -
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Residues in contact with LEU 418 (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 2.9 18.3 + - - +
415A GLU* 3.5 6.5 - - + +
417A LEU* 1.3 75.9 - - - +
419A HIS* 1.3 63.4 + - + +
421A LEU* 3.3 3.8 + - - -
422A THR* 2.8 47.1 + - - +
459A LEU* 4.8 13.2 - - + +
462A LYS* 3.7 59.7 - - + +
463A CYS* 3.9 10.1 - - - +
466A ALA* 4.2 6.3 - - + -
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Residues in contact with HIS 419 (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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321A ARG* 5.6 0.5 + - - -
415A GLU* 2.9 39.1 + - + +
416A GLU* 3.7 9.7 - - + +
418A LEU* 1.3 85.2 - - + +
420A ILE* 1.3 58.5 + - + +
422A THR* 4.6 2.5 - - - -
423A ASP* 2.9 46.1 + - - +
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Residues in contact with ILE 420 (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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321A ARG* 5.4 3.1 - - - +
378A ASP* 4.2 21.5 - - + +
381A ARG* 3.7 30.7 - - + -
382A LEU* 3.7 37.0 - - + -
385A ILE* 4.3 11.9 - - + -
416A GLU* 2.9 29.4 + - + +
417A LEU 3.6 4.3 - - - +
419A HIS* 1.3 75.3 - - + +
421A LEU* 1.3 62.9 + - - +
424A ALA* 3.0 49.2 + - + +
429A CYS* 3.7 4.3 - - - -
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Residues in contact with LEU 421 (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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382A LEU* 4.6 7.0 - - + -
417A LEU* 2.9 46.6 + - + +
418A LEU 3.9 2.0 - - - +
420A ILE* 1.3 76.8 - - - +
422A THR* 1.3 60.6 + - - +
424A ALA 5.3 1.4 - - - +
429A CYS* 3.8 30.3 - - + -
433A CYS* 4.2 13.2 - - - -
463A CYS* 3.7 26.9 - - + +
466A ALA* 3.8 22.7 - - + +
467A MET* 3.7 17.9 - - + -
470A LEU* 4.1 25.7 - - + +
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Residues in contact with THR 422 (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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418A LEU* 2.8 35.7 + - - +
419A HIS* 4.0 3.6 - - - -
421A LEU* 1.3 80.8 - - - +
423A ASP* 1.3 75.2 + - - +
424A ALA 3.7 3.6 - - - +
466A ALA* 4.5 5.3 - - - +
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Residues in contact with ASP 423 (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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321A ARG* 3.5 12.6 + - - +
327A SER* 3.8 21.4 - - - -
328A HIS* 2.9 30.8 + - - +
419A HIS* 2.9 28.2 + - - +
422A THR* 1.3 96.5 - - - +
424A ALA* 1.3 62.7 + - - +
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Residues in contact with ALA 424 (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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321A ARG* 3.8 7.6 - - - +
328A HIS* 4.1 6.4 - - - +
378A ASP* 3.3 37.9 - - + +
419A HIS 4.2 0.2 + - - -
420A ILE* 3.0 25.9 + - + +
421A LEU 5.3 1.2 - - - +
422A THR 4.6 3.1 - - - +
423A ASP* 1.3 83.2 + - - +
425A ASP* 1.3 67.1 + - - +
426A PRO* 3.3 9.2 - - - +
428A VAL* 5.7 0.9 - - + -
429A CYS* 4.4 7.3 - - - -
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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