Contacts of the helix formed by residues 427 - 444 (chain A) in PDB entry 3PU3
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 LYS 427 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A EDO 2.6 23.4 + - - +
425A HIS 4.8 4.5 - - - +
426A PHE* 1.3 76.9 - - - +
428A PRO* 1.3 70.8 - - + +
429A SER* 3.2 4.3 - - - +
430A GLN* 3.1 19.4 + - + +
431A LEU* 3.0 20.1 + - - +
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Residues in contact with PRO 428 (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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371A TRP* 4.3 14.1 - - + -
410A THR* 3.8 30.1 - - + -
422A LEU* 3.2 31.0 - - + -
426A PHE* 3.1 15.2 - - + +
427A LYS* 1.3 84.9 - - + +
429A SER* 1.3 64.6 + - - +
431A LEU* 3.4 2.9 + - + +
432A ILE* 3.1 31.4 + - - +
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Residues in contact with SER 429 (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 THR* 6.2 0.2 - - - -
427A LYS* 3.2 2.8 + - - -
428A PRO* 1.3 79.9 - - - +
430A GLN* 1.3 63.0 + - - +
432A ILE* 3.7 9.6 + - - +
433A LYS* 3.3 22.5 + - - +
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Residues in contact with GLN 430 (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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9A EDO 5.0 1.3 - - - +
427A LYS* 3.1 25.2 + - + +
429A SER* 1.3 77.8 - - - +
431A LEU* 1.3 59.8 + - - +
433A LYS* 3.4 8.8 + - - +
434A ASP* 2.9 58.3 + - - +
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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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9A EDO 4.2 14.9 + - - +
371A TRP* 3.9 30.7 - - + +
374A GLY 4.0 4.7 - - - +
375A LYS* 4.3 11.4 - - - +
378A LEU* 3.8 29.2 - - + -
406A PHE* 4.2 7.9 - - + -
426A PHE* 4.0 19.5 - - + -
427A LYS 3.0 15.1 + - - +
428A PRO* 3.8 4.0 - - + +
430A GLN* 1.3 76.3 - - - +
432A ILE* 1.3 57.3 + - - +
434A ASP* 3.1 6.7 + - - +
435A LEU* 2.8 59.7 + - + +
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Residues in contact with ILE 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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371A TRP* 4.7 2.0 - - + -
403A ASN* 3.1 28.6 + - - +
406A PHE* 3.8 28.5 - - + +
407A ARG* 3.5 37.9 - - + +
410A THR* 3.5 25.4 - - - +
428A PRO* 3.1 24.9 + - + +
429A SER* 3.8 7.9 - - - +
431A LEU* 1.3 75.1 - - - +
433A LYS* 1.3 60.1 + - - +
435A LEU* 4.7 0.2 - - - -
436A ALA* 2.9 26.5 + - - +
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Residues in contact with LYS 433 (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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429A SER 3.3 14.6 + - - +
430A GLN* 4.0 10.1 - - - +
432A ILE* 1.3 82.6 - - + +
434A ASP* 1.3 64.3 + - - +
436A ALA* 3.9 6.1 - - - +
437A LYS* 3.2 24.4 + - - +
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Residues in contact with ASP 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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378A LEU* 3.7 31.1 - - + +
382A LYS* 4.9 10.2 + - - -
430A GLN* 2.9 52.3 + - - +
431A LEU* 3.4 5.6 + - - +
433A LYS* 1.3 79.2 - - - +
435A LEU* 1.3 58.3 + - - +
437A LYS* 3.7 3.5 + - - +
438A GLU* 3.0 32.2 + - - +
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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
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374A GLY* 3.9 8.1 - - - +
377A LEU* 4.2 11.0 - - + -
378A LEU* 3.9 30.5 - - + +
381A PHE* 4.3 14.6 - - + -
399A ALA* 4.6 9.9 - - + +
402A LEU* 6.4 0.2 - - + -
403A ASN* 3.7 25.1 - - + +
406A PHE* 4.2 14.1 - - + -
431A LEU* 2.8 48.9 + - + +
434A ASP* 1.3 75.8 - - - +
436A ALA* 1.3 60.2 + - - +
437A LYS 3.2 0.2 - - - -
438A GLU* 3.1 3.1 + - - +
439A ILE* 2.9 39.2 + - + +
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Residues in contact with ALA 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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403A ASN* 3.3 5.9 - - - +
407A ARG* 3.5 24.2 - - - +
432A ILE 2.9 16.4 + - - +
433A LYS* 3.9 7.0 - - - +
435A LEU* 1.3 75.6 - - - +
437A LYS* 1.3 62.2 + - - +
439A ILE* 3.8 7.2 - - - +
440A ARG* 3.0 22.9 + - - +
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Residues in contact with LYS 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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433A LYS 3.2 15.9 + - - +
434A ASP* 3.9 6.3 - - - +
436A ALA* 1.3 79.8 - - - +
438A GLU* 1.3 61.0 + - + +
440A ARG* 3.1 29.4 + - - +
441A LEU* 2.8 28.4 + - - +
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Residues in contact with GLU 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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378A LEU* 3.9 13.2 - - + -
381A PHE* 3.6 40.5 - - + +
382A LYS* 4.0 19.3 - - - +
385A HIS* 2.9 39.0 + - - -
434A ASP 3.0 19.3 + - - +
435A LEU* 3.1 6.3 + - - +
437A LYS* 1.3 77.5 - - + +
439A ILE* 1.3 62.5 + - - +
441A LEU* 3.5 9.6 + - - +
442A SER* 3.2 17.3 + - - -
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Residues in contact with ILE 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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381A PHE* 3.7 24.0 - - + -
396A VAL* 4.3 8.5 - - + +
399A ALA* 3.6 26.5 - - + +
400A LYS* 3.8 29.6 - - + +
403A ASN* 4.4 7.4 - - + +
435A LEU* 2.9 29.3 + - + +
436A ALA* 3.8 7.9 - - - +
438A GLU* 1.3 73.4 - - - +
440A ARG* 1.3 63.8 + - - +
442A SER* 3.5 2.4 + - - -
443A GLU* 2.9 54.0 + - + +
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Residues in contact with ARG 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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436A ALA 3.0 14.2 + - - +
437A LYS* 3.1 28.5 + - - +
439A ILE* 1.3 77.5 - - - +
441A LEU* 1.3 67.8 + - - +
442A SER 3.2 0.2 + - - -
443A GLU* 3.3 10.0 + - - +
444A ASN* 3.2 42.4 + - - +
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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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381A PHE* 6.4 0.7 - - + -
385A HIS* 3.4 41.3 - - + +
437A LYS 2.8 15.3 + - - +
438A GLU* 3.7 11.7 - - - +
440A ARG* 1.3 78.8 - - - +
442A SER* 1.3 66.4 + - - +
444A ASN* 3.1 23.6 + - - +
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Residues in contact with SER 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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381A PHE* 4.0 18.2 - - - -
390A GLN* 2.9 43.4 + - - +
391A LEU 6.1 0.4 - - - -
396A VAL* 3.9 20.5 - - - +
438A GLU 3.2 10.2 + - - -
439A ILE* 3.7 8.5 - - - -
440A ARG 3.3 0.2 - - - -
441A LEU* 1.3 79.0 - - - +
443A GLU* 1.3 65.7 + - - +
444A ASN 2.9 13.7 + - - +
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Residues in contact with GLU 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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390A GLN* 5.0 0.2 - - - +
396A VAL* 5.0 6.5 - - + -
400A LYS* 4.1 14.5 + - - +
439A ILE* 2.9 41.0 + - + +
440A ARG* 3.8 6.3 - - - +
442A SER* 1.3 76.2 - - - +
444A ASN* 1.3 69.9 + - - +
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Residues in contact with ASN 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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390A GLN* 5.1 2.3 + - - +
440A ARG* 3.2 33.1 + - - +
441A LEU* 3.1 17.0 + - - +
442A SER 2.9 13.9 + - - +
443A GLU* 1.3 92.2 - - - +
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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