Contacts of the helix formed by residues 442 - 456 (chain A) in PDB entry 3PEY
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 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A VAL* 4.0 2.8 - - - +
441A HIS* 1.3 102.2 + - + +
443A LYS* 1.3 64.6 + - - +
444A ASN* 3.9 12.4 + - - +
445A SER* 2.7 40.4 + - - -
446A PHE* 3.0 23.4 + - - +
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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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442A ASP* 1.3 76.0 - - - +
444A ASN* 1.3 59.3 + - - +
446A PHE* 3.3 10.8 + - + +
447A ASN* 2.8 53.0 + - - +
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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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413A GLY 4.9 5.9 + - - +
442A ASP* 3.3 13.1 + - - +
443A LYS* 1.3 80.3 - - - +
445A SER* 1.3 58.9 + - - +
447A ASN* 3.1 12.4 + - - +
448A ILE* 2.9 51.0 + - - +
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Residues in contact with SER 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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407A LEU* 3.2 27.9 - - - +
439A PHE 4.6 0.2 - - - -
440A VAL* 4.2 5.4 - - - -
441A HIS* 2.9 41.2 + - - -
442A ASP* 2.7 27.9 + - - -
444A ASN* 1.3 75.2 - - - +
446A PHE* 1.3 65.8 + - - +
448A ILE* 3.2 7.2 + - - -
449A LEU* 2.9 22.3 + - - +
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Residues in contact with PHE 446 (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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308A TYR* 6.6 0.4 - + - -
440A VAL* 3.6 20.1 - - + +
442A ASP 3.0 15.5 + - - +
443A LYS* 3.5 14.8 - - + +
445A SER* 1.3 77.1 + - - +
447A ASN* 1.3 78.2 + - - +
449A LEU* 3.5 1.4 + - + +
450A SER* 2.8 49.0 + - - -
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Residues in contact with ASN 447 (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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443A LYS* 2.8 44.1 + - - +
444A ASN* 3.5 12.2 + - - +
446A PHE* 1.3 93.5 - - - +
448A ILE* 1.3 59.2 + - + +
450A SER* 3.4 5.5 + - - -
451A ALA* 2.9 30.2 + - - +
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Residues in contact with ILE 448 (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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407A LEU* 4.0 21.1 - - + -
408A PRO 4.2 4.7 - - - +
409A THR* 3.6 22.9 - - + -
413A GLY 4.0 5.6 - - - +
415A ALA* 3.8 32.7 - - + +
444A ASN* 2.9 46.4 + - - +
445A SER* 3.6 8.3 - - - +
447A ASN* 1.3 78.1 - - + +
449A LEU* 1.3 63.5 + - - +
451A ALA* 3.2 3.8 + - - +
452A ILE* 3.0 35.8 + - + +
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Residues in contact with LEU 449 (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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308A TYR* 3.7 29.2 - - + -
407A LEU* 4.0 11.4 - - + -
420A TYR* 4.0 21.8 - - + +
438A SER* 4.1 15.0 - - - -
440A VAL* 3.6 24.9 - - + -
445A SER 2.9 15.8 + - - +
446A PHE* 4.1 2.2 - - + +
448A ILE* 1.3 78.8 - - - +
450A SER* 1.3 57.0 + - - +
452A ILE* 3.2 8.7 + - + +
453A GLN* 2.9 27.3 + - - +
461A MET* 3.8 31.4 - - + -
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Residues in contact with SER 450 (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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446A PHE* 2.8 49.0 + - - -
447A ASN* 3.7 6.1 - - - -
449A LEU* 1.3 78.7 - - - +
451A ALA* 1.3 60.8 + - - +
453A GLN* 3.3 14.5 + - - +
454A LYS* 3.0 23.7 + - - +
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Residues in contact with ALA 451 (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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415A ALA* 4.2 15.5 - - + -
417A PRO* 5.6 0.7 - - - -
447A ASN 2.9 18.4 + - - +
448A ILE* 3.6 5.2 - - - +
450A SER* 1.3 72.9 - - - +
452A ILE* 1.3 61.7 + - - +
454A LYS* 3.3 7.9 + - - +
455A TYR* 2.9 30.4 + - - +
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Residues in contact with ILE 452 (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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407A LEU* 5.4 0.9 - - + -
408A PRO* 4.4 14.4 - - + +
415A ALA* 4.1 10.1 - - + -
416A ASP 4.6 1.1 - - - +
417A PRO* 4.0 14.1 - - + -
420A TYR* 3.5 57.9 - - + -
448A ILE* 3.0 34.9 + - + +
449A LEU* 3.5 12.6 - - + +
451A ALA* 1.3 75.9 - - - +
453A GLN* 1.3 62.8 + - - +
455A TYR* 3.2 13.5 + - - +
456A PHE* 3.3 28.3 + - + -
461A MET* 4.3 5.8 - - + -
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Residues in contact with GLN 453 (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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449A LEU 2.9 13.5 + - - +
450A SER* 3.5 17.5 + - - +
452A ILE* 1.3 77.4 - - - +
454A LYS* 1.3 59.5 + - - +
456A PHE 3.5 3.8 + - - -
458A ASP* 2.9 44.1 + - - +
459A ILE* 2.9 37.9 + - - +
460A GLU* 4.7 0.4 - - - +
461A MET* 3.8 39.5 + - + +
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Residues in contact with LYS 454 (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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450A SER 3.0 16.5 + - - +
451A ALA* 3.7 7.2 - - - +
453A GLN* 1.3 74.2 - - - +
455A TYR* 1.3 68.3 + - - +
457A GLY* 2.9 15.6 + - - -
458A ASP* 3.8 6.2 + - - +
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Residues in contact with TYR 455 (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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275A ALA* 3.6 30.1 - - - +
276A ASP 4.9 0.7 + - - -
296A THR* 3.4 39.4 + - + +
417A PRO* 3.4 36.1 - - + -
418A ALA* 5.2 3.9 - - + +
451A ALA 2.9 17.9 + - - +
452A ILE 3.2 5.4 + - - +
454A LYS* 1.3 79.1 - - - +
456A PHE* 1.3 80.5 + + - +
457A GLY 3.4 2.1 + - - -
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Residues in contact with PHE 456 (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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273A THR* 5.0 3.8 - - + -
296A THR* 3.6 21.0 - - + +
297A ASN* 3.6 21.7 - - - +
299A VAL* 4.0 25.4 - - + -
300A ASN* 4.9 4.5 - - + +
417A PRO* 3.3 42.6 - - + -
418A ALA* 4.3 2.2 - - - -
421A ILE* 3.6 33.4 - - + -
452A ILE* 3.3 28.2 + - + +
453A GLN 3.5 0.4 + - - -
454A LYS 3.1 0.8 - - - -
455A TYR* 1.3 99.9 - + - +
457A GLY* 1.3 58.9 + - - +
458A ASP 3.7 1.3 - - - -
459A ILE* 3.5 32.2 - - + +
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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