Contacts of the helix formed by residues 409 - 423 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B ARG* 3.9 1.3 - - - -
407B LEU* 3.4 11.8 - - + +
408B GLU* 1.3 76.4 - - - +
410B ASP* 1.3 56.6 + - - +
411B ASP* 3.1 16.4 + - - +
412B LYS* 2.7 47.6 + - + +
413B LEU* 2.9 29.6 + - - +
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Residues in contact with ASP 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ARG* 2.8 17.3 + - - -
133B ARG* 2.8 35.3 + - - -
134B ARG* 2.9 35.0 + - - +
408B GLU 3.3 2.6 + - - -
409B ASP* 1.3 70.7 + - - +
411B ASP* 1.3 62.6 + - - +
413B LEU* 3.0 7.8 + - - +
414B GLU* 2.8 31.2 + - - +
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Residues in contact with ASP 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ASP* 3.1 9.3 + - - +
410B ASP* 1.3 79.7 + - - +
412B LYS* 1.3 58.6 + - - +
414B GLU* 3.3 5.6 + - - +
415B GLN* 2.9 31.8 + - - +
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Residues in contact with LYS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B LEU* 4.1 20.3 - - + +
409B ASP* 2.7 35.4 + - + +
411B ASP* 1.3 73.1 - - - +
413B LEU* 1.3 58.9 + - - +
415B GLN* 3.6 15.2 + - - +
416B ILE* 3.0 41.8 + - + +
433B ALA* 5.6 5.3 - - - +
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Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ARG* 3.2 40.6 - - + +
400B PHE* 3.4 34.7 - - + -
403B LEU* 3.8 29.4 - - + +
404B THR* 4.1 11.9 - - + +
407B LEU* 3.7 13.0 - - + +
409B ASP 2.9 18.0 + - - +
410B ASP* 3.0 6.7 + - - +
412B LYS* 1.3 75.6 - - - +
414B GLU* 1.3 65.4 + - - +
416B ILE* 3.3 7.1 + - + +
417B ARG* 3.1 17.0 + - - +
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Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B ASP 2.8 15.7 + - - +
411B ASP* 3.8 5.6 - - - +
413B LEU* 1.3 74.9 - - - +
415B GLN* 1.3 67.9 + - - +
417B ARG* 2.5 53.0 + - - +
418B LYS* 2.9 49.4 + - - +
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Residues in contact with GLN 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B ASP 2.9 18.8 + - - +
412B LYS* 3.6 23.6 + - - +
413B LEU 3.3 0.2 - - - -
414B GLU* 1.3 76.9 - - - +
416B ILE* 1.3 65.7 + - - +
418B LYS* 3.5 8.2 + - - +
419B ASP* 2.7 54.9 + - - +
425B MSE 3.5 20.2 - - - +
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Residues in contact with ILE 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B PHE* 4.2 11.2 - - + -
403B LEU* 3.9 11.4 - - + -
407B LEU* 3.9 21.3 - - + -
412B LYS* 3.0 28.2 + - - +
413B LEU 3.3 7.2 + - - +
414B GLU 3.1 0.4 - - - -
415B GLN* 1.3 83.3 - - - +
417B ARG* 1.3 66.1 + - - +
419B ASP* 3.4 0.9 + - - +
420B TYR* 2.9 24.1 + - + +
425B MSE 3.8 24.0 - - + +
430B LEU* 3.4 29.8 - - + -
433B ALA* 4.2 16.2 - - + -
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Residues in contact with ARG 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B CYS* 3.7 29.8 - - + -
400B PHE* 3.5 27.8 - - + -
413B LEU 3.1 8.0 + - - +
414B GLU* 2.5 52.3 + - - +
416B ILE* 1.3 77.1 - - - +
418B LYS* 1.3 65.8 + - - +
421B THR* 2.6 48.5 + - - +
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Residues in contact with LYS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B GLU* 2.9 49.9 + - + +
415B GLN* 3.8 7.4 - - - +
417B ARG* 1.3 85.5 - - - +
419B ASP* 1.3 59.1 + - - +
421B THR* 3.2 6.1 + - - -
422B SER* 2.9 32.4 + - - -
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Residues in contact with ASP 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B GLN* 2.7 44.1 + - - +
418B LYS* 1.3 78.9 - - - +
420B TYR* 1.3 58.5 + - - +
422B SER* 2.9 20.1 + - - -
423B GLY 3.0 12.0 + - - -
424B ALA* 3.0 22.2 + - - +
425B MSE 3.2 28.1 + - + +
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Residues in contact with TYR 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B SER* 3.1 1.4 + - - -
379B GLY 4.4 0.2 - - - -
380B GLY 3.0 22.8 + - - -
387B HIS* 3.3 25.5 - - - -
392B GLY* 2.8 37.4 + - - -
393B ASN 4.2 0.9 - - - -
394B CYS* 3.8 20.6 - - - -
397B ASP* 3.1 26.0 + - + -
416B ILE* 2.9 19.7 + - + +
417B ARG 3.9 2.7 - - - +
419B ASP* 1.3 76.6 - - - +
421B THR* 1.3 59.8 + - - +
423B GLY 3.4 5.7 + - - -
425B MSE 3.6 22.3 - - + +
426B LEU 4.0 4.5 - - - -
427B THR* 3.1 26.8 + - - +
430B LEU* 3.5 37.0 - - + -
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Residues in contact with THR 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B PHE 3.8 5.0 - - - +
391B GLY* 3.1 20.1 - - - -
392B GLY 3.5 16.0 + - - +
394B CYS* 3.6 14.6 + - - +
417B ARG* 2.6 35.4 + - - +
418B LYS* 3.6 5.8 - - - -
420B TYR* 1.3 78.1 - - - +
422B SER* 1.3 57.7 + - - +
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Residues in contact with SER 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B ARG 4.0 11.3 - - - +
389B GLN 5.5 0.2 - - - -
390B PHE 4.9 1.4 - - - -
391B GLY* 4.0 4.7 + - - -
418B LYS 2.9 14.8 + - - -
419B ASP* 2.9 17.7 + - - -
421B THR* 1.3 77.6 - - - +
423B GLY* 1.3 57.9 + - - +
424B ALA* 3.2 16.3 + - - +
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Residues in contact with GLY 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B HIS* 3.6 30.7 + - - -
388B ARG* 3.2 31.1 + - - +
391B GLY* 3.7 2.9 - - - -
419B ASP 3.0 4.7 + - - -
420B TYR 3.4 2.6 + - - -
421B THR 3.2 3.4 - - - -
422B SER* 1.3 78.7 - - - +
424B ALA* 1.3 64.8 + - - +
425B MSE 3.3 8.1 + - - +
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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