Contacts of the helix formed by residues 450 - 457 (chain A) in PDB entry 1ZDT
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 ASN 450 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A CYS* 3.7 27.3 + - - +
270A ASP* 3.4 21.2 + - - -
446A MET* 3.8 17.2 - - - +
447A PRO* 3.3 27.0 + - + +
448A ARG 3.5 1.2 + - - -
449A ASN* 1.3 77.3 - - - +
451A LEU* 1.3 63.8 + - - +
452A LEU* 3.0 28.9 + - - +
453A ILE* 3.0 26.3 + - + +
454A GLU* 3.4 20.3 + - - +
1001A PEF 6.1 0.4 - - - +
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Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ASP* 3.0 38.2 + - + +
271A GLN* 5.4 2.7 - - - +
273A PHE* 4.7 10.3 - - + -
274A ILE* 3.7 30.7 - - + -
449A ASN 3.7 13.9 - - - +
450A ASN* 1.3 71.1 - - - +
452A LEU* 1.3 67.2 + - - +
453A ILE 3.2 0.2 - - - -
454A GLU* 3.3 9.9 + - - +
455A MET* 3.0 27.3 + - - +
744P LEU* 3.8 34.8 - - + +
748P LEU* 5.5 0.2 - - + -
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Residues in contact with LEU 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A CYS 5.7 0.2 - - - +
269A ALA* 4.1 24.0 - - + +
270A ASP* 3.5 14.6 - - - +
273A PHE* 3.9 20.9 - - + -
302A TRP* 3.7 16.2 - - + -
306A LEU* 3.6 23.3 - - + -
437A LEU* 4.2 14.1 - - + -
450A ASN* 3.0 10.9 + - - +
451A LEU* 1.3 79.1 - - - +
453A ILE* 1.3 59.0 + - - +
455A MET* 3.3 6.9 + - + +
456A LEU* 3.0 27.5 + - - +
1001A PEF 4.0 39.7 - - + -
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Residues in contact with ILE 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A LEU* 3.8 34.1 - - + +
441A HIS* 3.7 30.5 - - + +
446A MET* 3.8 27.1 - - + -
447A PRO 5.4 0.4 - - - +
450A ASN* 3.0 29.2 + - + +
451A LEU 3.2 0.2 - - - -
452A LEU* 1.3 75.6 - - - +
454A GLU* 1.3 63.5 + - - +
456A LEU* 3.3 14.3 + - + +
457A GLN* 2.7 43.0 + - + +
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Residues in contact with GLU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A ASN* 5.3 2.9 + - - +
450A ASN 3.4 11.7 + - - +
451A LEU* 3.3 17.5 + - - +
453A ILE* 1.3 79.6 - - - +
455A MET* 1.3 59.8 + - - +
457A GLN* 3.6 12.2 + - - +
458A ALA* 3.7 15.2 + - - +
742P ASN* 4.3 4.6 + - - +
743P ALA* 4.7 6.8 + - - +
744P LEU* 3.6 46.4 + - + +
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Residues in contact with MET 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A PHE* 3.7 35.4 - - + -
298A LEU 4.6 0.7 - - - +
299A GLN* 3.0 17.3 + - - +
302A TRP* 3.7 40.8 - - + -
451A LEU 3.0 18.6 + - - +
452A LEU* 3.5 9.2 - - - +
454A GLU* 1.3 74.8 - - - +
456A LEU* 1.3 62.1 + - - +
457A GLN 3.5 0.2 + - - -
458A ALA* 3.7 2.9 + - - +
460A GLN* 2.9 20.5 - - - +
742P ASN* 3.3 26.5 - - - +
744P LEU* 3.9 12.3 - - + -
745P LEU* 3.8 28.3 - - + -
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Residues in contact with LEU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A TRP* 3.8 13.4 - - + -
434A LYS* 3.6 46.9 - - + +
437A LEU* 4.1 9.4 - - + -
438A TYR* 3.9 37.0 - - + +
441A HIS* 5.2 0.9 - - + -
452A LEU 3.0 11.8 + - - +
453A ILE* 3.4 20.4 - - + +
455A MET* 1.3 76.6 - - - +
457A GLN* 1.3 75.4 + - - +
458A ALA 3.4 0.5 + - - -
459A LYS 4.8 0.3 + - - -
460A GLN* 3.4 18.9 + - - +
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Residues in contact with GLN 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A TYR* 4.7 7.1 - - - -
441A HIS* 3.2 41.8 + - - -
453A ILE* 2.7 32.5 + - + +
454A GLU* 3.6 6.5 + - - +
455A MET 3.3 0.6 - - - -
456A LEU* 1.3 95.2 - - - +
458A ALA* 1.3 57.0 + - - +
459A LYS* 3.6 6.9 + - - +
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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