Contacts of the helix formed by residues 441 - 447 (chain H) in PDB entry 1ZMC
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412H THR 4.2 4.9 - - - -
413H ASP* 3.1 31.6 + - - -
414H ARG* 3.8 2.9 - - - +
415H VAL* 3.7 3.1 - - - -
439H GLY 3.9 1.5 + - - -
440H ALA* 1.3 74.4 - - - +
442H CYS* 1.3 63.5 + - - +
443H GLU* 3.6 4.7 + - - +
444H ASP* 2.8 47.0 + - - +
445H ILE* 3.4 11.4 + - - +
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Residues in contact with CYS 442 (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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382H LYS* 5.3 0.2 - - - -
406H ILE* 3.7 27.6 - - - -
408H GLY* 4.0 14.1 - - - -
413H ASP* 2.9 34.4 + - - +
415H VAL* 3.9 7.6 - - - -
441H SER* 1.3 71.2 - - - +
443H GLU* 1.3 57.4 + - - +
445H ILE 3.3 2.1 + - - -
446H ALA* 3.0 24.8 + - - +
463H ASN* 3.2 39.9 - - - +
466H ALA* 3.8 9.4 - - - -
467H SER* 3.6 5.8 - - - +
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Residues in contact with GLU 443 (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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413H ASP* 2.9 18.4 + - - +
441H SER* 4.0 4.0 + - - +
442H CYS* 1.3 75.4 - - - +
444H ASP* 1.3 68.2 + - - +
446H ALA* 4.2 5.6 - - + -
447H ARG* 3.0 64.1 + - + +
467H SER* 3.4 15.4 + - - +
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Residues in contact with ASP 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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434G LEU* 5.3 1.6 - - + -
437G GLU* 5.2 3.1 - - + +
438G TYR* 2.6 38.6 + - + -
440H ALA* 3.3 9.2 - - + -
441H SER* 2.8 45.1 + - - +
443H GLU* 1.3 78.9 - - - +
445H ILE* 1.3 62.0 + - + +
447H ARG* 3.5 4.5 + - - +
448H VAL* 3.2 25.2 + - - +
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Residues in contact with ILE 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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434G LEU* 4.6 10.8 - - + -
415H VAL* 3.8 14.1 - - + -
431H GLU* 4.1 7.9 - - - +
435H ALA* 3.9 25.8 - - + -
440H ALA* 5.0 1.1 - - + -
441H SER 3.6 11.9 - - - +
442H CYS 3.3 6.6 + - - +
443H GLU 3.1 0.2 - - - -
444H ASP* 1.3 78.9 - - + +
446H ALA* 1.3 65.5 + - - +
448H VAL* 3.1 15.4 + - - +
450H HIS* 3.5 19.6 - - + -
459H PHE* 3.6 28.5 - - + -
460H ARG* 3.7 4.1 - - - +
463H ASN* 3.4 39.5 - - + +
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Residues in contact with ALA 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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442H CYS 3.0 16.8 + - - +
443H GLU* 3.1 8.7 + - + +
445H ILE* 1.3 76.2 - - - +
447H ARG* 1.3 62.7 + - + +
460H ARG* 2.8 39.7 + - - -
463H ASN* 4.3 0.2 - - - +
464H LEU* 3.7 43.7 - - + +
467H SER* 5.5 0.7 - - - -
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Residues in contact with ARG 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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333G ASP* 4.2 6.2 - - - +
336G ILE* 5.1 2.8 - - - +
337G ILE* 4.4 11.9 - - - +
340G GLU* 2.8 45.3 + - - -
346G ALA 6.0 0.4 - - - -
437G GLU* 5.1 5.6 - - - +
443H GLU* 3.0 50.3 + - + +
444H ASP* 4.0 4.3 - - - +
446H ALA* 1.3 81.8 - - + +
448H VAL* 1.3 62.4 + - - +
449H CYS* 3.4 2.6 + - - +
460H ARG* 4.1 3.1 - - - +
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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