Contacts of the helix formed by residues 431 - 450 (chain A) in PDB entry 1DG3
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 GLY 431 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A PRO* 1.3 71.9 - - - +
432A GLY* 1.3 61.6 + - - +
433A TYR 3.2 1.0 + - - -
434A ARG* 3.5 16.3 + - - +
435A LEU* 3.6 18.4 + - - +
479A ASP* 3.0 24.7 + - - -
481A THR* 3.3 14.2 - - - +
482A LEU* 6.4 0.2 - - - -
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Residues in contact with GLY 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A TYR* 3.3 42.1 - - - +
429A LYS* 2.8 22.1 + - - -
430A PRO 3.1 1.4 + - - -
431A GLY* 1.3 79.5 - - - +
433A TYR* 1.3 61.2 + - - +
434A ARG 3.5 0.2 - - - -
435A LEU* 3.6 2.6 + - - -
436A PHE* 3.2 18.5 + - - +
475A ILE* 4.1 1.1 - - - -
479A ASP* 2.9 0.6 + - - -
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Residues in contact with TYR 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLY* 1.3 77.0 - - - +
434A ARG* 1.3 64.1 + - + +
436A PHE* 3.1 5.9 + + - +
437A VAL* 2.9 53.8 + - + +
472A THR* 3.7 28.6 - - + +
475A ILE* 3.8 14.5 - - + +
476A LEU* 3.4 47.8 - - + +
479A ASP* 2.8 27.1 + - + +
482A LEU* 4.2 9.9 - - + -
490A GLU* 2.7 39.9 + - + +
493A ARG* 4.6 0.3 + - - -
494A VAL* 4.2 10.6 - - - +
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Residues in contact with ARG 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A GLY* 3.5 10.7 + - - +
432A GLY 3.5 0.2 - - - -
433A TYR* 1.3 88.6 - - + +
435A LEU* 1.3 63.9 + - + +
437A VAL* 4.2 5.3 - - - +
438A GLN* 3.3 24.1 + - - +
479A ASP* 5.7 0.4 - - - +
482A LEU* 3.9 26.1 - - + +
486A GLU* 4.1 20.4 + - - +
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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
----------------------------------------------------------
426A ILE* 6.1 2.0 - - + -
427A TYR* 3.8 15.5 - - + -
429A LYS* 4.2 29.2 - - - +
431A GLY 3.6 12.2 + - - +
432A GLY 3.6 6.9 + - - +
433A TYR 3.2 0.8 - - - -
434A ARG* 1.3 77.4 - - + +
436A PHE* 1.3 63.8 + - - +
438A GLN* 4.0 10.4 - - + +
439A LYS* 3.2 23.2 + - - +
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Residues in contact with PHE 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU* 3.7 35.0 - - + -
422A VAL* 3.6 21.8 - - + -
427A TYR* 3.6 21.3 - + + -
432A GLY 3.2 13.8 + - - +
433A TYR* 3.1 14.1 + + - +
435A LEU* 1.3 76.4 - - - +
437A VAL* 1.3 65.8 + - + +
439A LYS* 3.1 3.7 + - - +
440A LEU* 2.8 45.7 + - + +
468A LYS* 6.2 0.4 - - + -
471A MET* 4.1 14.6 - - + -
472A THR* 3.5 40.4 - - + -
475A ILE* 3.9 20.2 - - + -
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Residues in contact with VAL 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A TYR* 2.9 59.6 + - + +
434A ARG* 4.2 6.1 - - - +
435A LEU 3.5 0.2 - - - -
436A PHE* 1.3 81.8 - - + +
438A GLN* 1.3 58.7 + - - +
440A LEU* 3.3 10.3 + - + +
441A GLN* 2.9 45.3 + - + +
472A THR* 5.4 1.8 - - + -
490A GLU* 4.4 2.2 - - - +
493A ARG* 4.6 14.4 - - - +
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Residues in contact with GLN 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ARG 3.3 17.4 + - - +
435A LEU* 4.1 11.4 - - - +
436A PHE 3.2 0.4 - - - -
437A VAL* 1.3 76.9 - - - +
439A LYS* 1.3 66.4 + - - +
441A GLN* 3.5 5.6 + - + +
442A ASP* 2.7 46.2 + - - +
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Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A PRO* 6.4 1.6 - - - -
418A LEU* 3.8 17.0 - - + +
421A GLU* 4.1 18.5 + - - -
427A TYR* 3.7 18.4 - - - +
435A LEU 3.2 16.1 + - - +
436A PHE* 3.1 5.6 + - - +
438A GLN* 1.3 78.0 - - - +
440A LEU* 1.3 64.2 + - - +
442A ASP* 3.2 10.7 + - + +
443A LEU* 3.0 45.4 + - + +
446A LYS* 6.1 0.8 - - - +
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Residues in contact with LEU 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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415A PHE* 3.9 23.6 - - + -
418A LEU* 4.1 20.6 - - + +
436A PHE* 2.8 37.7 + - + +
437A VAL* 3.5 9.2 - - + +
439A LYS* 1.3 77.5 - - - +
441A GLN* 1.3 68.7 + - - +
443A LEU* 3.0 5.6 + - - +
444A LYS* 2.9 44.7 + - - +
464A TYR* 5.6 1.6 - - + -
465A LEU* 4.2 18.4 - - + -
472A THR* 5.0 7.6 - - + +
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Residues in contact with GLN 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A VAL* 2.9 36.0 + - + +
438A GLN* 3.8 7.0 - - + +
439A LYS 3.4 0.2 - - - -
440A LEU* 1.3 80.7 - - - +
442A ASP* 1.3 67.0 + - - +
444A LYS* 3.2 38.6 + - - +
445A LYS* 3.0 23.2 + - - +
493A ARG* 5.2 5.6 + - - -
497A GLU* 4.5 10.8 + - - +
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Residues in contact with ASP 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A GLN* 2.7 39.2 + - - +
439A LYS* 3.4 14.4 - - + +
441A GLN* 1.3 79.1 - - - +
443A LEU* 1.3 60.0 + - + +
445A LYS* 3.4 10.9 - - - +
446A LYS* 3.1 36.3 + - - +
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Residues in contact with LEU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ILE* 3.8 30.0 - - + +
415A PHE* 3.5 26.7 - - + -
417A PRO* 6.4 0.2 - - + -
418A LEU* 3.8 40.4 - - + +
439A LYS* 3.0 34.8 + - + +
440A LEU 3.0 2.9 + - - +
442A ASP* 1.3 75.5 - - + +
444A LYS* 1.3 66.3 + - - +
445A LYS 3.2 0.2 - - - -
446A LYS* 3.1 25.8 + - + +
447A TYR* 2.9 23.0 + - - +
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Residues in contact with LYS 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A PHE* 4.0 15.9 - - + -
440A LEU* 2.9 29.8 + - + +
441A GLN* 3.4 40.7 + - - +
443A LEU* 1.3 75.4 - - - +
445A LYS* 1.3 64.0 + - - +
447A TYR* 3.1 6.5 + - - +
448A TYR* 2.9 41.4 + - + -
461A LEU* 4.8 7.0 - - + -
465A LEU* 3.5 39.7 - - + +
497A GLU* 3.9 22.4 + - - -
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Residues in contact with LYS 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A GLN 3.0 12.4 + - - +
442A ASP* 3.4 13.5 - - - +
444A LYS* 1.3 77.3 - - - +
446A LYS* 1.3 62.3 + - + +
448A TYR* 3.3 10.5 + - - +
449A GLU* 2.9 54.4 + - + +
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Residues in contact with LYS 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ILE* 4.1 15.0 - - + -
439A LYS* 6.1 0.8 - - - +
442A ASP* 3.1 21.0 + - - +
443A LEU* 3.1 29.3 + - + +
445A LYS* 1.3 76.1 - - + +
447A TYR* 1.3 63.7 + - - +
449A GLU* 3.1 24.4 + - - +
450A GLU* 3.3 19.2 + - - +
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Residues in contact with TYR 447 (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 CYS* 3.4 36.7 - - + +
410A LEU* 4.5 6.3 - - + -
411A LEU* 3.9 24.7 - - + -
414A ILE* 3.6 23.0 - - + +
415A PHE* 4.4 6.7 - + + -
443A LEU 2.9 12.0 + - - +
444A LYS* 3.1 11.4 + - - +
446A LYS* 1.3 75.5 - - - +
448A TYR* 1.3 71.9 + + - +
450A GLU* 3.1 17.0 + - - +
453A LYS* 3.1 40.4 + - + +
457A ALA* 2.9 29.7 + - + -
460A ILE* 3.8 5.7 - - - +
461A LEU* 3.7 31.4 + - + -
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Residues in contact with TYR 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A LYS* 2.9 33.3 + - + -
445A LYS* 3.7 8.7 - - - +
447A TYR* 1.3 87.4 - + - +
449A GLU* 1.3 60.5 + - + +
450A GLU 3.8 1.4 - - - +
453A LYS* 3.1 19.9 + - - +
457A ALA* 5.8 2.9 - - + -
458A GLU* 2.5 35.6 + - + -
461A LEU* 3.3 30.7 - - + +
462A GLN* 4.3 5.0 + - - -
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Residues in contact with GLU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A LYS* 2.9 54.5 + - + +
446A LYS* 3.1 24.0 - - - +
447A TYR 3.1 0.4 - - - -
448A TYR* 1.3 78.3 - - + +
450A GLU* 1.3 64.2 + - - +
451A PRO* 3.5 6.1 - - - +
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Residues in contact with GLU 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ARG* 4.4 3.2 + - - +
410A LEU* 3.8 42.8 - - + +
414A ILE* 4.0 18.5 - - + +
446A LYS* 3.3 17.5 + - - +
447A TYR 3.1 12.7 + - - +
448A TYR 3.8 1.4 - - - +
449A GLU* 1.3 78.8 - - - +
451A PRO* 1.3 78.6 - - + +
452A ARG 4.0 0.3 + - - -
453A LYS* 2.9 23.9 + - + -
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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
------------------------------------------------------------
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