Contacts of the helix formed by residues 409 - 423 (chain A) in PDB entry 1R6U
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 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A ARG* 3.6 1.8 + - - -
407A LEU* 3.4 8.1 - - + +
408A GLU* 1.3 79.6 + - - +
410A ASP* 1.3 56.8 + - - +
411A ASP* 3.0 14.6 + - - +
412A LYS* 2.7 47.3 + - + +
413A LEU* 3.0 26.5 + - - +
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Residues in contact with ASP 410 (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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127A ARG* 3.6 13.6 + - - +
133A ARG* 2.8 44.7 + - - +
134A ARG* 2.6 42.5 + - - +
408A GLU 3.2 0.6 + - - -
409A ASP* 1.3 70.3 + - - +
411A ASP* 1.3 65.4 + - - +
413A LEU* 3.1 5.9 + - - +
414A GLU* 2.9 28.8 + - - +
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Residues in contact with ASP 411 (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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409A ASP* 3.0 8.2 + - - +
410A ASP* 1.3 79.4 - - - +
412A LYS* 1.3 58.1 + - - +
414A GLU* 3.3 8.1 + - - +
415A GLN* 2.9 28.1 + - - +
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Residues in contact with LYS 412 (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 LEU* 4.0 27.8 - - + -
409A ASP* 2.7 33.8 + - + +
411A ASP* 1.3 73.1 - - - +
413A LEU* 1.3 63.8 + - - +
415A GLN* 3.2 16.3 + - - +
416A ILE* 3.0 43.5 + - + +
433A ALA* 5.8 5.0 - - - +
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Residues in contact with LEU 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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134A ARG* 3.5 39.0 - - + +
400A PHE* 3.9 17.5 - - + -
403A LEU* 3.8 31.4 - - + +
404A THR* 3.8 15.5 - - + +
407A LEU* 3.7 22.2 - - + +
409A ASP 3.0 16.2 + - - +
410A ASP* 3.1 10.1 + - - +
412A LYS* 1.3 77.6 - - - +
414A GLU* 1.3 56.4 + - - +
416A ILE* 3.2 5.5 + - + +
417A ARG* 2.9 27.1 + - - +
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Residues in contact with GLU 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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410A ASP 2.9 12.6 + - - +
411A ASP* 3.3 11.2 + - - +
413A LEU* 1.3 74.6 - - - +
415A GLN* 1.3 60.4 + - - +
417A ARG* 2.5 45.5 + - - +
418A LYS* 2.9 48.7 + - - +
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Residues in contact with GLN 415 (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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411A ASP 2.9 16.6 + - - +
412A LYS* 3.5 17.0 + - - +
413A LEU 3.2 0.2 - - - -
414A GLU* 1.3 73.8 - - - +
416A ILE* 1.3 76.2 + - - +
418A LYS* 4.0 4.8 - - - +
419A ASP* 2.6 61.0 + - - +
425A MSE 4.1 6.1 - - - +
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Residues in contact with ILE 416 (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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400A PHE* 4.5 7.2 - - + -
403A LEU* 4.1 15.0 - - + -
407A LEU* 3.7 29.6 - - + -
412A LYS* 3.0 26.8 + - + +
413A LEU* 3.2 6.3 + - - +
415A GLN* 1.3 83.3 - - - +
417A ARG* 1.3 61.4 + - - +
420A TYR* 3.0 28.3 + - + +
425A MSE 3.2 33.1 - - + +
430A LEU* 3.5 18.8 - - + -
433A ALA* 4.5 12.3 - - + -
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Residues in contact with ARG 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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394A CYS* 3.8 13.9 - - + -
400A PHE* 3.5 29.6 - - + -
413A LEU 2.9 15.5 + - - +
414A GLU* 2.5 49.0 + - - +
415A GLN 3.2 0.2 - - - -
416A ILE* 1.3 78.2 - - - +
418A LYS* 1.3 72.2 + - - +
420A TYR* 3.3 1.9 + - - +
421A THR* 2.8 52.9 + - - +
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Residues in contact with LYS 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 GLU* 2.9 47.6 + - - +
415A GLN* 4.0 5.6 - - - +
417A ARG* 1.3 90.6 - - - +
419A ASP* 1.3 65.5 + - - +
421A THR* 3.4 8.0 + - - -
422A SER* 2.8 33.0 + - - -
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Residues in contact with ASP 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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415A GLN* 2.6 42.6 + - - +
418A LYS* 1.3 81.6 - - - +
420A TYR* 1.3 61.9 + - - +
422A SER* 2.7 21.7 + - - -
423A GLY 2.8 11.6 + - - -
424A ALA* 3.1 20.6 + - - +
425A MSE 3.1 25.7 + - + +
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Residues in contact with TYR 420 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A GLY* 3.3 7.3 + - - -
387A HIS* 3.5 10.4 - - - -
391A GLY 3.7 0.5 - - - -
392A GLY* 2.8 39.8 + - - -
393A ASN 4.2 4.5 - - - -
394A CYS* 3.8 22.0 - - - -
397A ASP* 3.1 33.0 + - + -
400A PHE* 5.4 0.7 - - + -
416A ILE* 3.0 20.0 + - + +
417A ARG 3.7 2.7 - - - +
419A ASP* 1.3 76.5 - - - +
421A THR* 1.3 59.4 + - - +
422A SER 3.4 0.2 + - - -
423A GLY 3.5 5.5 + - - -
425A MSE 3.6 24.4 - - + +
426A LEU 3.9 0.4 - - - -
427A THR* 2.6 47.5 + - - +
430A LEU* 3.3 34.0 - - + +
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Residues in contact with THR 421 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A PHE 4.4 3.6 - - - +
391A GLY* 4.0 9.4 - - - -
392A GLY 3.6 16.2 + - - +
394A CYS* 3.9 13.2 + - - +
417A ARG* 2.8 43.2 + - - +
418A LYS* 3.6 8.3 - - - +
420A TYR* 1.3 76.7 - - - +
422A SER* 1.3 60.1 + - - +
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Residues in contact with SER 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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388A ARG 4.0 11.1 - - - +
389A GLN 5.6 0.3 - - - +
390A PHE 5.3 0.9 - - - -
391A GLY* 4.2 4.9 + - - -
418A LYS* 2.8 17.2 + - - -
419A ASP* 2.7 22.5 + - - -
421A THR* 1.3 80.0 - - - +
423A GLY* 1.3 57.9 + - - +
424A ALA* 3.0 20.0 + - - +
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Residues in contact with GLY 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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387A HIS* 3.7 27.1 + - - -
388A ARG* 3.3 26.3 + - - -
391A GLY* 3.9 5.2 - - - -
419A ASP 2.8 5.0 + - - -
420A TYR 3.5 5.6 + - - -
422A SER* 1.3 79.6 - - - +
424A ALA* 1.3 63.8 + - - +
425A MSE 3.0 10.4 + - - +
426A LEU* 4.0 3.6 - - - +
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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