Contacts of the helix formed by residues 418 - 432 (chain A) in PDB entry 3PE3
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 PHE 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A ALA* 3.9 16.6 - - + -
386A ASP* 3.6 39.7 - - + -
389A SER* 3.6 20.9 - - - -
411A ALA* 4.6 2.2 - - + +
415A ASN* 3.0 38.9 + - + +
416A PRO 3.4 1.6 + - - -
417A ALA* 1.3 73.5 - - - +
419A ALA* 1.3 65.6 + - - +
420A ASP* 3.7 22.2 - - + -
421A ALA* 3.3 32.5 + - + +
422A HIS* 3.3 16.9 - - - -
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Residues in contact with ALA 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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417A ALA 3.2 6.0 + - - +
418A PHE* 1.3 72.7 - - - +
420A ASP* 1.3 66.4 + - - +
422A HIS* 2.9 17.0 + - - +
423A SER 3.1 8.8 + - - -
445A ALA* 3.5 18.7 - - - +
448A LEU* 3.9 17.7 - - + -
449A LYS* 3.5 35.4 - - + -
452A PHE* 4.0 8.5 - - + -
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Residues in contact with ASP 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ASP* 5.6 2.9 - - - +
389A SER* 4.1 7.6 - - - +
418A PHE* 3.4 28.7 + - + -
419A ALA* 1.3 76.2 + - - +
421A ALA* 1.3 56.8 + - - +
423A SER* 3.2 3.6 + - - -
424A ASN* 3.0 33.8 + - - +
449A LYS* 3.3 26.0 + - - -
452A PHE* 3.9 23.3 - - - -
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Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A SER* 3.9 10.5 - - - +
408A TYR* 4.1 9.6 - - - +
411A ALA* 3.9 14.8 - - + -
412A ILE* 3.6 25.3 - - + +
418A PHE* 3.3 26.7 + - + +
419A ALA 3.2 1.0 - - - -
420A ASP* 1.3 78.2 - - - +
422A HIS* 1.3 58.3 + - - +
424A ASN* 3.8 3.8 - - - +
425A LEU* 2.9 28.8 + - - +
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Residues in contact with HIS 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ILE* 3.4 44.3 - - + +
416A PRO 3.4 16.9 + - - -
418A PHE 3.3 24.2 - - - -
419A ALA 2.9 7.4 + - - +
421A ALA* 1.3 76.2 - - - +
423A SER* 1.3 63.8 + - - +
425A LEU* 3.3 5.9 + - - +
426A ALA* 3.0 23.6 + - - +
441A SER* 3.6 26.3 + - - +
444A THR* 3.3 27.1 - - + +
445A ALA* 3.8 7.6 - - + -
448A LEU* 3.8 11.2 - - + +
416B PRO* 6.4 2.2 - - + -
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Residues in contact with SER 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ALA 3.1 5.3 + - - -
420A ASP 3.5 7.9 - - - -
422A HIS* 1.3 77.8 - - - +
424A ASN* 1.3 64.6 + - - +
426A ALA* 3.2 5.2 + - - +
427A SER* 3.1 24.7 + - - -
442A TYR* 3.4 23.0 - - - -
445A ALA* 3.7 5.7 - - - +
452A PHE* 3.6 30.6 - - - -
454A ASP* 4.7 3.3 - - - +
455A ALA* 3.7 14.3 + - - +
458A ASN* 5.4 0.9 + - - -
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Residues in contact with ASN 424 (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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389A SER* 2.9 30.1 + - - -
390A ASN* 5.5 0.2 + - - -
393A ASN* 3.2 34.4 + - - +
396A LYS* 4.9 0.4 + - - +
408A TYR* 3.4 33.8 + - + +
420A ASP* 3.0 16.5 + - - +
421A ALA 3.8 1.3 - - - +
423A SER* 1.3 75.9 + - - +
425A LEU* 1.3 66.2 + - - +
427A SER* 3.2 19.2 + - - -
428A ILE* 3.2 9.5 + - - +
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Residues in contact with LEU 425 (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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405A LEU* 3.4 31.6 - - + -
408A TYR* 3.8 15.4 - - + -
409A THR* 4.4 12.8 - - + -
412A ILE* 4.3 17.3 - - + -
421A ALA 2.9 18.1 + - - +
422A HIS* 3.6 7.0 - - + +
423A SER 3.3 0.2 - - - -
424A ASN* 1.3 75.4 - - - +
426A ALA* 1.3 62.4 + - - +
428A ILE* 3.3 13.5 + - - +
429A HIS* 3.3 25.3 + - + +
441A SER* 3.8 18.8 - - - +
413B GLN 4.0 17.0 - - - +
414B ILE* 4.2 11.2 - - - +
416B PRO* 5.1 7.0 - - + -
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Residues in contact with ALA 426 (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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422A HIS 3.0 13.2 + - - +
423A SER 3.3 10.1 - - - +
424A ASN 3.2 0.2 - - - -
425A LEU* 1.3 78.0 - - - +
427A SER* 1.3 56.5 + - - +
429A HIS* 3.0 4.7 + - - -
430A LYS* 2.8 24.9 + - - +
438A ALA* 3.3 35.5 - - - +
441A SER* 3.6 11.2 - - - -
442A TYR* 3.5 23.8 - - + +
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Residues in contact with SER 427 (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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396A LYS* 3.3 23.1 - - - -
423A SER* 3.1 12.6 + - - -
424A ASN* 3.2 13.6 + - - -
426A ALA* 1.3 75.5 - - - +
428A ILE* 1.3 56.3 + - - +
430A LYS* 3.1 6.6 + - - +
431A ASP* 2.9 35.3 + - - -
442A TYR* 2.8 22.9 + - - -
458A ASN* 3.9 9.2 + - - -
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Residues in contact with ILE 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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396A LYS* 4.0 28.5 - - + -
401A VAL* 3.9 31.0 - - + +
404A ALA* 4.5 7.2 - - + -
405A LEU* 3.6 17.3 - - + -
408A TYR* 3.6 31.6 - - + -
424A ASN 3.2 2.1 + - - +
425A LEU 3.4 9.0 - - - +
426A ALA 3.2 0.8 - - - -
427A SER* 1.3 78.5 - - - +
429A HIS* 1.3 62.4 + - + +
431A ASP* 3.4 6.0 + - + +
432A SER* 3.2 23.9 + - - +
383B THR* 3.5 24.7 - - + -
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Residues in contact with HIS 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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425A LEU* 3.3 31.5 + - + +
426A ALA* 3.0 8.3 + - - +
428A ILE* 1.3 76.7 - - + +
430A LYS* 1.3 64.7 + - - +
432A SER* 3.1 7.0 + - - -
434A ASN* 2.9 62.0 + - - +
437A GLU* 4.0 27.1 - - + +
438A ALA 3.8 7.0 - - - +
441A SER* 5.0 2.7 - - - -
383B THR* 4.0 19.8 - - + +
414B ILE* 3.0 45.7 + - + +
415B ASN* 5.0 2.9 - - + -
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Residues in contact with LYS 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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426A ALA 2.8 12.1 + - - +
427A SER* 3.1 12.1 + - - +
429A HIS* 1.3 76.6 - - - +
431A ASP* 1.3 66.7 + - - +
433A GLY* 3.4 10.6 + - - -
435A ILE* 4.2 14.9 - - + +
438A ALA* 3.7 11.6 - - + +
442A TYR* 4.0 14.4 - - - +
458A ASN* 3.6 23.1 - - + +
461A HIS* 2.8 37.2 + - - -
462A CYS* 3.5 30.3 - - - +
465A ILE* 4.2 5.8 - - + +
499A HIS* 4.5 6.0 - - - -
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Residues in contact with ASP 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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396A LYS* 3.2 34.8 + - - -
427A SER* 2.9 14.9 + - - +
428A ILE* 3.8 6.4 - - + +
430A LYS* 1.3 83.8 - - - +
432A SER* 1.3 59.0 + - - +
433A GLY* 3.1 3.7 + - - -
634A LYS* 4.9 12.3 + - - +
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Residues in contact with SER 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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401A VAL* 5.3 5.2 - - - +
428A ILE* 3.2 17.5 + - - +
429A HIS 3.1 2.4 + - - -
431A ASP* 1.3 77.2 - - - +
433A GLY* 1.3 55.9 + - - +
434A ASN* 3.2 30.8 + - - +
382B PRO* 6.1 0.7 - - - +
383B THR* 3.8 19.5 + - - +
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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