Contacts of the helix formed by residues 443 - 452 (chain D) in PDB entry 1ZM9
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 PHE 443 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442D THR* 1.3 83.1 + - - +
444D LEU* 1.3 68.3 + - - +
445D GLU* 3.7 22.2 - - + -
446D ALA* 2.8 47.2 + - + -
447D ALA* 3.1 10.1 + - - -
481D TYR 4.5 1.0 + - - -
483D GLN 4.3 5.2 - - - +
484D ASP* 3.7 35.0 - - - +
485D GLN* 5.6 6.7 - - + -
496D GLY* 4.1 5.4 - - - -
701D P34 6.3 3.6 - - - -
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Residues in contact with LEU 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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409D PHE* 4.1 27.7 - - + +
410D SER* 3.7 15.5 - - - +
411D THR* 3.5 29.8 - - - +
443D PHE* 1.3 72.2 - - - +
445D GLU* 1.3 80.9 + - - +
447D ALA* 3.4 5.9 + - - +
448D GLN* 3.3 19.2 + - - +
484D ASP* 5.1 0.6 + - - +
494D ARG* 3.6 23.1 - - - +
495D ASN 3.8 11.6 + - - +
496D GLY* 3.9 26.5 - - - +
497D ALA* 4.4 3.1 - - + +
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Residues in contact with GLU 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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443D PHE* 3.0 19.7 + - + -
444D LEU* 1.3 87.7 - - - +
446D ALA* 1.3 67.6 + - - +
448D GLN* 3.2 8.1 + - - +
449D SER* 3.0 18.3 + - - -
494D ARG* 2.4 36.1 + - - -
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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 THR* 3.3 24.0 - - + +
443D PHE* 2.8 37.4 + - + +
445D GLU* 1.3 72.9 - - - +
447D ALA* 1.3 67.0 + - - +
449D SER* 2.7 21.1 + - - -
450D ILE* 2.8 17.9 + - + +
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Residues in contact with ALA 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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409D PHE* 3.4 27.9 - - + -
442D THR* 3.4 9.4 - - + +
443D PHE 3.1 4.6 + - - +
444D LEU 3.6 7.2 - - - +
446D ALA* 1.3 75.3 - - - +
448D GLN* 1.3 66.8 + - - +
450D ILE* 2.7 15.2 + - - +
451D VAL* 2.8 13.0 + - - +
497D ALA* 4.5 9.9 - - + -
499D LEU* 3.7 31.0 - - + -
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Residues in contact with GLN 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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407D VAL 4.8 0.8 + - - +
408D SER* 4.3 8.5 - - - +
409D PHE* 3.2 31.8 + - + +
444D LEU 3.3 7.3 + - - +
445D GLU* 3.2 13.2 + - - +
447D ALA* 1.3 77.6 - - - +
449D SER* 1.3 65.4 + - - +
452D PHE* 3.0 57.8 + - + +
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Residues in contact with SER 449 (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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445D GLU 3.0 7.7 + - - -
446D ALA* 2.7 21.9 + - - -
448D GLN* 1.3 77.9 - - - +
450D ILE* 1.3 62.0 + - - +
452D PHE 2.9 25.2 - - - +
453D GLY* 3.8 1.9 - - - -
454D GLY 3.6 6.3 + - - +
458D ARG* 3.4 24.6 + - - -
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Residues in contact with ILE 450 (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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440D HIS* 3.8 23.6 - - + +
442D THR* 4.4 5.8 - - + -
446D ALA* 2.8 18.2 + - + +
447D ALA 2.7 11.1 + - - +
449D SER* 1.3 73.7 - - - +
451D VAL* 1.3 57.7 + - - +
454D GLY* 2.9 36.0 + - - -
455D VAL* 3.7 17.7 - - + -
469D PHE* 4.2 11.2 - - + -
499D LEU* 3.6 22.7 - - + -
566D VAL* 3.4 43.0 + - + +
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Residues in contact with VAL 451 (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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401D LEU* 4.1 23.9 - - + +
407D VAL* 5.6 0.4 - - + -
409D PHE* 4.0 22.7 - - + -
447D ALA 2.8 14.7 + - - +
448D GLN 4.2 0.2 - - - +
450D ILE* 1.3 71.9 - - - +
452D PHE* 1.3 89.7 + - + +
453D GLY 3.9 0.8 + - - -
499D LEU* 4.3 4.9 - - + -
566D VAL* 3.4 39.3 - - + +
567D ILE* 4.0 10.3 - - - -
568D PRO* 4.7 3.4 - - + -
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Residues in contact with PHE 452 (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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401D LEU* 4.0 20.4 - - + -
407D VAL* 3.3 35.7 - - + -
409D PHE* 4.8 5.8 - + - -
448D GLN* 3.0 46.3 + - + +
449D SER* 2.9 14.8 - - - +
451D VAL* 1.3 100.8 - - + +
453D GLY* 1.3 56.7 + - - +
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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