Contacts of the helix formed by residues 443 - 451 (chain H) in PDB entry 6MZL
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 443 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442H PRO* 1.3 84.5 - - + +
444H ASN* 1.3 62.7 + - - +
445H GLN 3.5 2.2 - - - +
446H ASP* 3.7 21.1 - - + +
447H ALA* 2.9 25.7 + - - +
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Residues in contact with ASN 444 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442H PRO 3.7 1.0 - - - -
443H ASP* 1.3 72.1 - - - +
445H GLN* 1.3 62.2 + - - +
447H ALA* 3.2 5.5 + - - +
448H TYR* 2.9 26.0 + - - +
456H GLY* 4.8 0.7 - - - -
457H PRO* 3.9 24.0 - - + +
460H CYS* 3.7 30.0 - - + +
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Residues in contact with GLN 445 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443H ASP* 4.5 0.4 - - - +
444H ASN* 1.3 79.5 - - - +
446H ASP* 1.3 57.6 + - - +
448H TYR* 3.3 10.3 - - - +
449H ARG* 2.9 24.4 + - - +
457H PRO* 5.3 2.0 - - - +
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Residues in contact with ASP 446 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443H ASP* 3.6 24.0 + - + +
444H ASN 3.2 0.6 - - - -
445H GLN* 1.3 76.8 - - - +
447H ALA* 1.3 53.5 + - - +
449H ARG* 3.1 10.6 + - + +
450H ALA* 2.5 35.1 + - - +
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Residues in contact with ALA 447 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439H ARG* 3.1 39.5 + - - +
442H PRO 5.3 1.1 - - - +
443H ASP* 2.9 20.2 + - - +
444H ASN* 3.2 7.6 + - - +
446H ASP* 1.3 72.5 - - - +
448H TYR* 1.3 56.1 + - - +
450H ALA* 3.9 2.0 - - - -
451H GLU* 2.6 34.2 + - - +
456H GLY* 5.5 2.0 - - - -
459H LEU* 6.0 5.8 - - + -
460H CYS* 5.6 5.4 - - + -
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Residues in contact with TYR 448 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444H ASN 2.9 13.1 + - - +
445H GLN* 3.3 13.9 - - - +
447H ALA* 1.3 76.2 - - - +
449H ARG* 1.3 55.9 + - - +
451H GLU* 4.3 1.6 - - - +
452H PHE* 2.8 11.6 + - - -
453H GLY* 2.3 57.8 + - - +
456H GLY* 4.0 15.8 - - - +
457H PRO* 6.1 0.2 - - + -
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Residues in contact with ARG 449 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397H GLN* 5.1 1.2 + - - -
445H GLN 2.9 13.7 + - - +
446H ASP* 3.1 13.0 + - + +
448H TYR* 1.3 76.4 - - - +
450H ALA* 1.3 60.6 + - - +
451H GLU 3.5 0.3 + - - -
452H PHE* 4.0 4.8 + - - +
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Residues in contact with ALA 450 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397H GLN* 2.8 16.7 + - - -
439H ARG* 3.5 34.7 + - - +
446H ASP 2.5 19.7 + - - +
447H ALA* 3.1 1.8 + - - -
449H ARG* 1.3 73.4 - - - +
451H GLU* 1.3 58.6 + - - +
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Residues in contact with GLU 451 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393H LEU* 6.4 0.9 - - + -
396H LEU* 4.3 21.5 - - + +
397H GLN* 3.4 11.5 - - - +
435H LEU* 5.4 7.2 - - + -
439H ARG* 3.8 12.8 - - - +
447H ALA 2.6 18.3 + - - +
448H TYR* 3.3 4.1 - - - -
450H ALA* 1.3 77.1 - - - +
452H PHE* 1.3 69.2 + - - +
453H GLY 3.4 0.9 + - - -
455H LEU* 4.6 18.6 - - + +
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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