Contacts of the helix formed by residues 441 - 448 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412D THR 4.4 4.9 - - - -
413D ASP* 3.2 26.5 - - - -
414D ARG* 3.9 3.8 - - - +
415D VAL* 3.8 3.6 - - - -
439D GLY 5.2 0.2 - - - -
440D ALA* 1.3 76.3 - - - +
442D CYS* 1.3 64.2 + - - +
443D GLU* 3.5 6.2 + - - +
444D ASP* 2.8 51.2 + - - +
445D ILE* 3.3 16.3 + - - +
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Residues in contact with CYS 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D LYS* 5.0 0.2 - - - -
406D ILE* 4.0 13.7 - - - -
408D GLY* 4.0 22.4 - - - -
413D ASP* 2.8 35.0 + - - +
415D VAL* 3.7 15.7 - - - -
441D SER* 1.3 71.9 - - - +
443D GLU* 1.3 62.2 + - - +
445D ILE 3.4 1.2 + - - -
446D ALA* 3.1 18.9 + - - +
463D ASN* 3.2 43.6 - - - +
466D ALA* 4.0 7.2 - - - -
467D SER* 3.9 4.0 - - - +
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Residues in contact with GLU 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413D ASP* 2.9 17.5 + - - +
441D SER* 3.7 4.3 - - - +
442D CYS* 1.3 75.1 - - - +
444D ASP* 1.3 66.9 + - - +
446D ALA* 3.1 5.5 + - + +
447D ARG* 3.1 59.0 + - - +
467D SER* 3.3 17.7 + - - +
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Residues in contact with ASP 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438C TYR* 3.1 38.2 + - + +
439D GLY 4.9 1.2 - - - +
440D ALA* 4.0 2.5 - - + -
441D SER* 2.8 40.0 + - - +
443D GLU* 1.3 77.3 - - - +
445D ILE* 1.3 61.8 - - - +
447D ARG* 3.5 5.9 + - - +
448D VAL* 3.4 25.1 + - - +
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Residues in contact with ILE 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C LEU* 4.9 8.5 - - + -
415D VAL* 3.6 20.9 - - + -
431D GLU* 4.7 1.1 - - - +
435D ALA* 3.9 23.3 - - + -
440D ALA* 4.3 9.4 - - + -
441D SER 3.3 6.8 + - - +
442D CYS 3.7 1.8 - - - +
443D GLU 3.2 0.6 - - - -
444D ASP* 1.3 75.7 - - - +
446D ALA* 1.3 65.4 + - - +
448D VAL* 3.1 24.3 + - - +
450D HIS* 4.0 10.2 - - + -
459D PHE* 3.6 25.1 - - + -
460D ARG* 4.0 8.0 - - - +
463D ASN* 3.2 48.5 - - + +
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Residues in contact with ALA 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442D CYS 3.1 16.5 + - - +
443D GLU* 3.1 9.4 + - + +
445D ILE* 1.3 76.8 - - - +
447D ARG* 1.3 63.3 + - - +
460D ARG* 2.9 36.8 + - - -
463D ASN* 4.4 0.4 - - - +
464D LEU* 3.7 44.2 - - + +
467D SER* 5.5 0.2 - - - -
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Residues in contact with ARG 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C ASP* 4.1 6.4 - - - +
336C ILE* 4.8 4.0 - - - +
337C ILE* 4.4 14.2 - - + +
340C GLU* 3.0 40.5 + - - -
346C ALA 5.7 1.4 + - - -
437C GLU* 4.4 5.7 - - - +
443D GLU* 3.1 48.2 + - - +
444D ASP* 3.9 5.8 - - - +
445D ILE 3.1 1.2 - - - -
446D ALA* 1.3 82.1 - - - +
448D VAL* 1.3 63.1 + - - +
449D CYS 3.4 2.8 + - - -
460D ARG* 3.9 6.9 + - - +
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Residues in contact with VAL 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C ASN 5.0 0.4 - - - +
433C ALA* 3.9 26.5 - - + +
434C LEU* 3.6 27.6 - - + +
437C GLU* 3.3 29.6 - - + -
438C TYR* 5.8 0.7 - - + -
444D ASP 3.4 15.5 + - - +
445D ILE 3.1 9.9 + - - +
447D ARG* 1.3 76.1 - - - +
449D CYS* 1.3 70.9 + - - +
450D HIS* 3.0 34.2 + - + -
460D ARG* 3.1 12.0 + - - -
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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