Contacts of the helix formed by residues 398 - 412 (chain P) in PDB entry 5A31
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 398 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365P LEU* 4.5 10.9 - - + +
366P GLY* 5.3 0.2 - - - -
369P THR* 3.4 29.3 - - - +
391P ALA* 4.8 4.2 - - + +
392P ILE* 5.9 1.1 - - - -
395P ASN* 3.6 29.1 + - - +
396P LYS 3.5 3.2 - - - -
397P ARG* 1.3 71.6 - - - +
399P TYR* 1.3 66.7 + - - +
400P ARG* 3.0 39.6 + - - +
401P ALA* 3.2 17.8 + - + +
402P TRP* 3.5 11.7 + - - -
428P LEU* 4.1 1.8 - - - -
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Residues in contact with TYR 399 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277P ARG* 4.7 18.3 + - - +
397P ARG 3.1 6.9 + - - -
398P ASP* 1.3 73.3 + - - +
400P ARG* 1.3 103.0 + - + +
402P TRP* 3.3 5.6 + - - +
403P TYR* 2.9 23.8 + - + +
425P ALA* 4.2 6.8 - - - +
428P LEU* 3.7 30.5 - - + -
429P ARG* 3.3 42.0 - - - +
432P ASP* 4.0 7.0 - - - -
434P ARG* 5.7 4.0 + - - -
435P MET* 3.4 31.4 - - + -
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Residues in contact with ARG 400 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274P HIS* 5.5 7.2 + - - -
305P ASN* 5.3 10.9 + - - -
366P GLY* 5.3 5.1 - - - -
369P THR* 4.0 24.8 - - - +
370P LEU* 5.6 5.8 - - - +
373P HIS* 4.1 24.4 - - + +
398P ASP* 3.0 30.1 + - - +
399P TYR* 1.3 119.6 + - + +
401P ALA* 1.3 58.6 + - - +
403P TYR* 3.3 7.6 + - + +
404P GLY* 2.8 26.0 + - - -
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Residues in contact with ALA 401 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369P THR* 3.9 11.2 + - - +
388P TYR* 3.8 38.0 - - + +
391P ALA* 3.9 19.1 - - + -
392P ILE* 4.4 7.6 - - + +
398P ASP* 3.2 12.6 + - + +
400P ARG* 1.3 78.3 - - - +
402P TRP* 1.3 65.4 + - - +
404P GLY* 3.3 1.4 + - - -
405P LEU* 2.9 23.9 + - - +
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Residues in contact with TRP 402 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503J HIS* 5.1 5.2 - + - -
392P ILE* 2.9 43.3 - - + +
395P ASN 4.8 0.6 + - - -
396P LYS* 3.0 29.1 + - + -
398P ASP 3.5 15.5 + - - -
399P TYR 3.3 6.2 + - - +
401P ALA* 1.3 78.1 - - - +
403P TYR* 1.3 63.8 + - - +
405P LEU* 3.1 8.9 + - + +
406P GLY 3.0 17.8 + - - -
420P TYR* 4.0 6.5 - + - -
421P TYR* 3.5 42.7 - + - +
424P ARG* 3.1 53.7 - - + +
425P ALA* 3.7 17.0 - - + -
428P LEU* 3.5 25.3 - - + +
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Residues in contact with TYR 403 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399P TYR* 2.9 11.9 + - + +
400P ARG* 3.5 10.5 - - + +
402P TRP* 1.3 78.4 - - - +
404P GLY* 1.3 61.5 + - - +
406P GLY* 3.1 4.2 + - - -
407P GLN* 2.9 55.3 + - + +
422P TYR* 3.2 37.2 + + - -
425P ALA* 3.8 7.2 - - + +
434P ARG* 4.6 36.8 + - + +
435P MET* 4.0 33.0 - - + -
438P ALA* 4.1 14.0 - - + +
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Residues in contact with GLY 404 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373P HIS* 5.4 2.5 - - - -
376P MET* 4.8 0.9 - - - +
388P TYR* 3.8 26.2 - - - -
400P ARG 2.8 15.5 + - - -
401P ALA 3.7 3.4 - - - -
403P TYR* 1.3 80.8 - - - +
405P LEU* 1.3 56.7 + - - +
407P GLN* 3.3 12.3 + - - +
408P THR* 2.9 31.8 + - - +
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Residues in contact with LEU 405 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385P ILE* 3.6 34.8 - - + +
388P TYR* 3.6 25.7 - - + -
389P ARG* 3.9 25.6 - - - +
392P ILE* 4.1 28.3 - - + -
401P ALA 2.9 8.1 + - - +
402P TRP* 3.2 11.2 - - + +
404P GLY* 1.3 74.4 - - - +
406P GLY* 1.3 60.3 + - - +
408P THR* 3.1 6.7 - - + +
409P TYR* 3.0 38.1 + - + -
421P TYR* 3.9 22.9 - - + -
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Residues in contact with GLY 406 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402P TRP 3.0 8.5 + - - -
403P TYR 3.5 3.4 - - - -
405P LEU* 1.3 76.8 - - - +
407P GLN* 1.3 56.7 + - - +
409P TYR 3.0 1.2 + - - -
410P GLU* 2.8 35.2 + - - +
418P CYS* 3.5 11.1 - - - +
421P TYR* 3.4 20.7 - - - +
422P TYR* 3.2 18.2 - - - -
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Residues in contact with GLN 407 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376P MET* 3.6 26.4 - - + +
388P TYR* 5.5 1.2 + - - -
403P TYR* 2.9 40.6 + - + +
404P GLY* 3.4 13.2 - - - +
406P GLY* 1.3 76.8 - - - +
408P THR* 1.3 62.8 + - - +
410P GLU* 3.4 5.6 - - - +
411P ILE* 3.4 23.8 + - + +
422P TYR* 2.8 18.4 + - - +
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Residues in contact with THR 408 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376P MET* 4.0 20.2 - - - -
381P THR* 3.1 21.7 + - - -
384P ALA* 5.2 1.3 - - - -
385P ILE* 3.2 30.7 - - + +
388P TYR* 4.1 11.0 - - + -
404P GLY 2.9 20.9 + - - +
405P LEU* 3.1 21.1 - - + +
407P GLN* 1.3 74.7 - - - +
409P TYR* 1.3 64.0 + - + +
411P ILE* 3.4 7.5 + - - +
412P LEU* 3.4 19.9 + - - +
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Residues in contact with TYR 409 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D PRO* 3.5 9.3 - - + +
54D ILE* 3.1 38.7 + - + +
385P ILE* 3.6 29.8 - - + +
389P ARG* 3.0 26.3 + - - -
405P LEU* 3.0 28.1 + - + +
406P GLY 3.8 2.7 - - - +
408P THR* 1.3 75.6 - - - +
410P GLU* 1.3 54.9 + - - +
412P LEU* 2.8 46.9 + - + +
414P MET* 3.2 20.7 - - + +
417P TYR* 3.6 23.6 - + + -
418P CYS* 3.8 19.7 - - - +
421P TYR* 3.6 16.6 - + + -
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Residues in contact with GLU 410 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406P GLY 2.8 11.0 + - - +
407P GLN* 3.4 11.4 - - - +
409P TYR* 1.3 76.4 - - - +
411P ILE* 1.3 60.5 + - + +
412P LEU 2.9 11.7 - - - +
414P MET 4.7 0.7 - - - -
415P PRO* 5.9 0.2 - - - -
418P CYS* 3.2 23.3 - - + +
422P TYR* 3.0 28.5 + - - -
438P ALA* 4.8 3.1 - - - +
441P GLU* 3.5 22.9 - - - +
442P CYS* 4.1 9.6 - - - -
445P LYS* 3.2 36.5 + - + +
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Residues in contact with ILE 411 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376P MET* 4.4 13.7 - - + -
381P THR* 4.9 11.7 - - + +
407P GLN* 3.4 17.0 + - + +
408P THR* 3.4 12.8 - - - +
409P TYR 3.2 0.4 - - - -
410P GLU* 1.3 77.0 - - + +
412P LEU* 1.3 72.5 + - + +
413P LYS* 3.8 2.6 + - - +
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Residues in contact with LEU 412 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D PRO* 4.4 15.7 - - + -
381P THR* 4.1 22.4 - - + -
385P ILE* 3.4 30.3 - - + -
408P THR* 3.4 13.7 - - - +
409P TYR* 2.8 40.2 + - + +
410P GLU 2.9 12.0 - - - +
411P ILE* 1.3 81.9 - - + +
413P LYS* 1.3 67.8 + - - +
414P MET* 3.1 18.7 - - + +
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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