Contacts of the helix formed by residues 441 - 448 (chain F) in PDB entry 1ZMD
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 SER 441 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412F THR 4.5 4.3 - - - -
413F ASP* 3.0 28.3 - - - -
414F ARG* 4.0 2.0 - - - +
415F VAL* 3.6 1.8 - - - -
439F GLY 3.8 1.2 + - - -
440F ALA* 1.3 76.3 - - - +
442F CYS* 1.3 64.2 + - - +
443F GLU* 3.6 5.1 + - - +
444F ASP* 2.9 48.9 + - - +
445F ILE* 3.4 8.5 + - - +
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Residues in contact with CYS 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382F LYS* 4.8 0.2 - - - -
406F ILE* 3.8 20.4 - - - -
408F GLY* 4.1 15.7 - - - -
413F ASP* 2.7 34.7 + - - +
415F VAL* 3.7 13.9 - - - -
441F SER* 1.3 71.9 - - - +
443F GLU* 1.3 57.3 + - - +
445F ILE 3.2 2.4 + - - -
446F ALA* 3.0 23.4 + - - +
463F ASN* 3.4 38.9 - - - +
466F ALA* 4.0 10.1 - - - -
467F SER* 3.7 5.4 - - - +
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Residues in contact with GLU 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LYS* 4.2 24.2 + - - -
413F ASP* 2.9 12.0 + - - +
441F SER* 3.1 5.1 - - - +
442F CYS* 1.3 76.1 - - - +
444F ASP* 1.3 68.1 + - - +
446F ALA* 3.1 6.2 + - + +
447F ARG* 3.0 61.5 + - + +
467F SER* 3.2 22.2 + - - +
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Residues in contact with ASP 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A ASN* 5.3 2.9 + - - +
311A LYS* 5.1 13.2 - - - +
434E LEU* 5.5 0.4 - - - -
438E TYR* 2.7 39.3 + - + +
439F GLY 4.8 1.0 - - - +
440F ALA* 3.6 3.9 - - + -
441F SER* 2.9 42.7 + - - +
443F GLU* 1.3 76.8 - - - +
445F ILE* 1.3 65.1 + - + +
447F ARG* 3.2 11.6 + - - +
448F VAL* 3.4 17.5 + - - +
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Residues in contact with ILE 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434E LEU* 4.9 7.0 - - + -
415F VAL* 3.5 23.3 - - + -
431F GLU* 4.4 6.7 - - - +
435F ALA* 3.8 28.5 - - + -
440F ALA* 4.3 4.3 - - + -
441F SER 3.6 5.8 - - - +
442F CYS 3.2 5.8 + - - +
443F GLU 3.1 0.4 - - - -
444F ASP* 1.3 77.2 - - + +
446F ALA* 1.3 61.0 + - - +
448F VAL* 3.1 23.2 + - - +
450F HIS* 3.7 12.3 - - + -
459F PHE* 3.5 25.6 - - + -
460F ARG* 4.1 3.8 - - - +
463F ASN* 3.2 43.3 - - + +
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Residues in contact with ALA 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442F CYS 3.0 12.3 + - - +
443F GLU* 3.1 12.3 + - + +
445F ILE* 1.3 76.2 - - - +
447F ARG* 1.3 60.8 + - + +
460F ARG* 2.9 39.3 + - - +
463F ASN* 4.2 0.4 - - - +
464F LEU* 3.6 44.4 - - + +
467F SER* 5.3 0.9 - - - -
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Residues in contact with ARG 447 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LYS* 6.5 0.2 - - - +
333E ASP* 4.5 3.3 - - - +
336E ILE* 5.1 2.8 - - - +
337E ILE* 4.3 13.7 - - - +
340E GLU* 3.0 42.5 + - - -
437E GLU* 4.2 7.5 - - - +
443F GLU* 3.0 52.1 + - + +
444F ASP* 3.8 5.8 - - - +
445F ILE 3.1 0.4 - - - -
446F ALA* 1.3 79.7 - - + +
448F VAL* 1.3 62.0 + - - +
449F CYS 3.6 2.1 + - - -
460F ARG* 4.0 6.8 + - - +
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Residues in contact with VAL 448 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353E CYS 5.9 0.2 - - - +
430E ASN 4.9 0.7 - - - +
433E ALA* 3.8 9.4 - - + -
434E LEU* 3.6 50.3 - - + +
437E GLU* 3.5 28.5 - - + -
438E TYR* 5.7 0.4 - - + -
444F ASP* 3.4 15.7 + - + +
445F ILE* 3.1 10.4 + - - +
447F ARG* 1.3 76.4 - - - +
449F CYS* 1.3 70.8 + - - +
450F HIS* 2.9 30.8 + - + -
460F ARG* 3.0 14.5 + - - -
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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