Contacts of the helix formed by residues 430 - 445 (chain A) in PDB entry 6PAU
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 PRO 430 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A HIS* 5.4 1.1 - - - +
428A GLU 3.6 7.2 - - - +
429A THR* 1.3 93.6 - - + +
431A LEU* 1.3 66.9 + - - +
432A LEU* 3.1 7.1 + - + +
433A ASP* 3.2 24.8 + - - +
434A LEU* 3.0 19.6 + - - +
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Residues in contact with LEU 431 (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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356A TYR* 5.0 1.3 - - - +
424A ASN* 4.4 11.2 - - + +
426A HIS* 3.8 36.5 + - + +
429A THR 3.4 3.3 + - - -
430A PRO* 1.3 72.5 - - - +
432A LEU* 1.3 56.7 + - - +
434A LEU* 3.3 17.2 + - + +
435A MET* 2.9 47.8 + - + +
457A GLU* 3.8 26.5 - - + +
458A ASN* 5.2 1.3 - - - +
460A THR* 3.7 22.7 - - - +
461A PHE* 3.8 17.5 - - + -
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Residues in contact with LEU 432 (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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430A PRO* 3.1 5.0 - - + +
431A LEU* 1.3 80.1 - - - +
433A ASP* 1.3 61.8 + - - +
435A MET* 3.8 1.1 - - - -
436A SER* 2.9 29.2 + - - -
460A THR 4.8 1.1 - - - +
461A PHE* 3.5 28.0 - - + +
464A LYS* 3.9 32.3 - - + -
465A LEU* 3.5 30.7 - - + +
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Residues in contact with ASP 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LYS* 3.3 35.1 + - + +
335A THR* 4.5 7.0 - - - +
429A THR* 4.2 11.9 - - + -
430A PRO* 3.2 35.6 + - - +
432A LEU* 1.3 76.9 - - - +
434A LEU* 1.3 66.3 + - - +
436A SER* 3.3 7.8 + - - -
437A ASP* 2.9 28.9 + - - +
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Residues in contact with LEU 434 (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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335A THR* 4.9 2.9 - - - +
338A LEU* 4.9 2.0 - - + -
387A VAL* 4.2 14.4 - - + -
396A ASP* 4.2 17.3 - - + -
397A PHE 3.5 24.2 - - - +
398A LEU* 3.6 29.8 - - + +
424A ASN* 4.3 13.5 - - + -
425A ILE 3.6 19.5 - - - +
426A HIS* 4.4 6.1 - - + -
429A THR* 4.2 12.0 - - + +
430A PRO 3.0 13.4 + - - +
431A LEU* 3.4 18.4 - - + +
432A LEU 3.3 0.2 - - - -
433A ASP* 1.3 78.3 - - - +
435A MET* 1.3 59.1 + - - +
437A ASP* 3.1 6.7 + - + +
438A ALA 2.9 22.0 + - - -
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Residues in contact with MET 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LEU* 5.2 0.2 - - - -
421A SER* 4.0 2.9 - - - +
424A ASN* 3.5 45.3 - - - +
431A LEU* 2.9 25.2 + - + +
434A LEU* 1.3 74.3 - - - +
436A SER* 1.3 61.2 - - - +
438A ALA* 3.2 9.6 + - + +
439A LEU* 2.9 32.7 + - + +
450A PHE* 4.0 30.7 - - + -
461A PHE* 3.5 39.7 - - + -
465A LEU* 3.4 22.7 - - + -
467A PHE* 5.5 0.9 - - + -
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Residues in contact with SER 436 (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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329A LEU* 5.2 3.9 - - - +
330A PRO* 5.4 5.0 - - - +
432A LEU* 2.9 18.5 + - - -
433A ASP* 3.5 9.4 - - - -
435A MET* 1.3 76.8 - - - +
437A ASP* 1.3 59.0 + - - +
439A LEU* 3.2 10.0 + - - +
440A ILE* 2.9 42.2 + - - +
465A LEU* 3.8 16.2 - - - +
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Residues in contact with ASP 437 (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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333A THR* 3.4 13.4 - - + -
334A LYS* 2.9 28.5 + - - +
335A THR* 2.5 40.2 + - - -
338A LEU* 3.5 19.2 - - + +
398A LEU* 4.5 1.8 - - + -
433A ASP 2.9 13.8 + - - +
434A LEU* 3.5 9.0 - - + +
436A SER* 1.3 78.2 + - - +
438A ALA* 1.3 63.0 + - - +
440A ILE* 3.2 7.4 + - - +
441A LEU* 2.9 31.1 + - - +
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Residues in contact with ALA 438 (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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398A LEU* 3.9 30.0 - - + +
400A PHE* 4.1 5.3 - - + -
424A ASN* 5.3 0.7 - - - +
434A LEU 2.9 13.7 + - - +
435A MET* 3.2 27.8 + - + +
437A ASP* 1.3 77.0 - - - +
439A LEU* 1.3 56.2 + - - +
441A LEU* 3.3 3.6 + - - +
442A ALA* 2.9 30.0 + - - +
450A PHE* 4.2 14.5 - - + -
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Residues in contact with LEU 439 (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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299A ARG* 3.7 42.0 - - + +
301A LEU* 4.2 3.9 - - + +
329A LEU* 3.6 21.5 - - + +
435A MET* 2.9 19.7 + - + +
436A SER* 3.5 9.9 - - - +
438A ALA* 1.3 74.8 - - - +
440A ILE* 1.3 63.8 + - - +
442A ALA* 3.4 4.4 + - - +
443A LYS* 2.9 25.5 + - - +
450A PHE* 3.5 44.0 - - + -
465A LEU* 4.0 25.8 - - + -
467A PHE* 4.1 4.5 - - + -
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Residues in contact with ILE 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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329A LEU* 4.4 9.6 - - + -
330A PRO* 3.7 50.5 - - + +
331A ASP 4.2 4.9 - - - +
332A VAL* 3.4 39.0 - - - +
333A THR* 3.9 15.5 - - + +
334A LYS* 6.1 0.7 - - + -
436A SER* 2.9 26.1 + - - +
437A ASP* 3.2 13.7 + - - +
439A LEU* 1.3 75.1 - - - +
441A LEU* 1.3 59.1 + - + +
443A LYS* 3.3 4.3 + - - +
444A SER* 2.9 29.6 + - - -
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Residues in contact with LEU 441 (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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333A THR* 3.6 19.1 - - + -
338A LEU* 4.4 10.8 - - + -
385A PHE* 3.7 53.8 - - + -
398A LEU* 4.3 12.8 - - + -
400A PHE* 4.4 8.7 - - + -
437A ASP 2.9 22.8 + - - +
438A ALA 3.7 3.4 - - - +
440A ILE* 1.3 74.2 - - + +
442A ALA* 1.3 65.5 + - - +
444A SER* 2.6 25.9 + - - +
445A LYS* 3.0 18.6 + - - +
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Residues in contact with ALA 442 (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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301A LEU* 3.9 9.9 - - + -
400A PHE* 4.1 9.0 - - + -
419A ALA* 4.3 3.8 - - + -
438A ALA 2.9 17.8 + - - +
439A LEU 3.8 3.6 - - - +
441A LEU* 1.3 75.0 - - - +
443A LYS* 1.3 62.3 + - - +
445A LYS 3.2 4.5 + - - -
447A PHE* 3.1 48.5 + - + -
450A PHE* 3.8 24.5 - - + -
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Residues in contact with LYS 443 (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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301A LEU* 2.9 45.2 + - + +
302A ASN* 4.6 8.5 + - - +
329A LEU* 4.0 21.8 - - + -
330A PRO 5.9 1.8 - - - +
439A LEU 2.9 17.9 + - - +
440A ILE* 3.5 4.9 - - - +
441A LEU 3.2 0.2 - - - -
442A ALA* 1.3 75.8 - - - +
444A SER* 1.3 64.4 + - - +
446A GLY* 3.0 15.5 + - - -
447A PHE 4.6 5.3 + - - +
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Residues in contact with SER 444 (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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331A ASP 5.7 4.9 - - - -
440A ILE* 2.9 15.8 + - - -
441A LEU* 2.6 30.5 + - - +
443A LYS* 1.3 76.5 - - - +
445A LYS* 1.3 63.1 + - - +
446A GLY 3.3 1.0 + - - -
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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
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379A GLU* 6.2 2.0 - - - +
383A ASP* 3.3 31.7 + - - +
385A PHE* 4.0 24.5 - - - -
400A PHE* 4.3 14.4 - - + -
417A LYS* 3.1 21.8 + - - -
441A LEU* 3.0 21.1 + - - +
442A ALA 3.7 5.2 - - - +
443A LYS 3.0 0.8 - - - -
444A SER* 1.3 81.1 - - - +
446A GLY* 1.3 57.3 + - - +
447A PHE* 3.4 14.8 + - + -
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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