Contacts of the helix formed by residues 444 - 455 (chain A) in PDB entry 3UON
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 ASN 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.6 7.5 - - - +
59A ASN* 5.2 5.9 + - - +
384A LYS* 3.5 30.9 - - + +
388A THR* 4.5 8.6 + - - +
440A TYR* 2.9 23.5 + - - +
441A ALA 3.1 11.3 - - - +
442A LEU 3.3 0.6 - - - -
443A CYS* 1.3 81.3 - - - +
445A ALA* 1.3 63.0 + - - +
446A THR* 2.7 40.7 + - - -
447A PHE* 3.3 22.4 + - + -
448A LYS 3.4 8.1 + - - -
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Residues in contact with ALA 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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384A LYS* 3.7 16.5 - - - +
387A ARG* 5.5 0.2 - - - +
441A ALA 4.6 1.6 - - - -
442A LEU 5.4 0.4 + - - -
443A CYS 4.3 0.2 - - - -
444A ASN* 1.3 73.5 + - - +
446A THR* 1.3 57.9 + - - +
448A LYS* 3.8 9.5 - - + +
449A LYS* 3.0 29.5 + - - +
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Residues in contact with THR 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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51A ASN* 3.7 14.8 - - - +
53A HIS* 4.5 11.7 - - + -
54A LEU* 3.5 26.9 - - + -
384A LYS* 4.4 10.7 - - - +
444A ASN* 2.7 19.2 + - - -
445A ALA* 1.3 71.2 - - - +
447A PHE* 1.3 55.0 + - - -
449A LYS* 3.5 17.2 + - + +
450A THR* 2.5 37.6 + - - -
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Residues in contact with PHE 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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44A VAL* 4.2 12.1 - - + -
47A SER* 4.1 14.4 - - - -
48A ILE* 3.4 40.6 - - + -
54A LEU* 3.5 22.2 - - + -
59A ASN* 3.9 22.7 - - - -
62A LEU* 3.9 17.5 - - + -
440A TYR* 3.6 42.0 - - + +
444A ASN* 3.3 17.6 + - + -
445A ALA 3.4 0.2 - - - -
446A THR* 1.3 75.8 - - - +
448A LYS* 1.3 58.9 + - - +
450A THR* 3.2 3.2 + - - -
451A PHE* 2.9 49.0 + + + -
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Residues in contact with LYS 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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441A ALA* 3.3 37.7 - - + +
442A LEU* 4.8 14.1 - - - +
444A ASN 3.4 3.0 + - - -
445A ALA* 3.8 11.2 - - - +
446A THR 3.4 0.2 - - - -
447A PHE* 1.3 78.4 - - - +
449A LYS* 1.3 64.5 + - - +
451A PHE* 3.1 13.9 + - - +
452A LYS* 2.9 24.3 + - + +
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Residues in contact with LYS 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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51A ASN* 4.8 11.9 + - - +
53A HIS* 5.8 6.3 - - - -
445A ALA 3.0 19.2 + - - +
446A THR* 3.6 15.8 - - + +
448A LYS* 1.3 76.8 - - - +
450A THR* 1.3 66.9 + - - +
452A LYS* 3.1 10.3 + - - +
453A HIS* 2.6 55.6 + - + +
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Residues in contact with THR 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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47A SER* 3.3 39.7 - - - +
50A VAL* 4.6 4.7 - - + -
51A ASN* 3.3 18.0 + - + +
54A LEU* 3.2 15.3 - - + +
446A THR 2.5 26.8 + - - -
447A PHE 3.5 3.8 - - - -
449A LYS* 1.3 78.1 - - - +
451A PHE* 1.3 57.7 + - - +
453A HIS* 3.2 7.2 + - + +
454A LEU* 2.8 38.3 + - + +
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Residues in contact with PHE 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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40A GLY 4.8 1.3 - - - -
43A LEU* 3.3 42.0 - - + -
44A VAL* 3.4 25.4 - - + -
47A SER* 2.9 30.3 - - - -
437A PRO* 3.9 13.0 - - + -
440A TYR* 5.0 0.9 - - + -
441A ALA* 3.9 22.7 - - + -
447A PHE* 2.9 36.6 + + + -
448A LYS* 3.4 10.5 - - - +
450A THR* 1.3 74.6 - - - +
452A LYS* 1.3 57.8 + - - +
454A LEU* 2.8 22.4 + - - +
455A LEU* 3.0 21.2 + - + +
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Residues in contact with LYS 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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448A LYS* 2.9 15.2 + - + +
449A LYS* 3.2 12.8 - - - +
451A PHE* 1.3 77.4 - - - +
453A HIS* 1.3 78.4 + - + +
455A LEU* 3.6 21.4 + - - +
456A MET* 4.0 6.6 + - - +
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Residues in contact with HIS 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 LYS* 2.6 58.0 + - + +
450A THR* 3.8 5.8 - - - +
452A LYS* 1.3 95.7 - - + +
454A LEU* 1.3 62.3 + - - +
455A LEU 3.3 0.2 - - - -
456A MET* 3.3 23.3 + - - +
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Residues in contact with LEU 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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43A LEU* 3.7 22.1 - - + +
46A VAL* 3.6 35.0 - - + -
47A SER* 3.0 35.9 - - - +
50A VAL* 4.2 12.8 - - + -
450A THR* 2.8 21.6 + - + +
451A PHE* 2.8 7.2 + - - +
453A HIS* 1.3 75.8 - - + +
455A LEU* 1.3 64.4 + - - +
456A MET 3.1 7.7 + - - +
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Residues in contact with LEU 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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39A ILE* 5.7 3.8 - - + -
43A LEU* 3.8 33.2 - - + -
451A PHE* 3.0 18.8 + - + +
452A LYS* 3.8 14.1 - - - +
453A HIS 3.3 0.4 - - - -
454A LEU* 1.3 76.2 - - - +
456A MET* 1.3 58.3 + - - +
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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