Contacts of the helix formed by residues 402 - 410 (chain A) in PDB entry 2CDZ
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 ALA 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A GLY 4.5 3.3 - - - +
401A GLY* 1.3 74.5 - - - -
403A LEU* 1.3 65.8 + - - +
404A THR* 3.2 12.0 + - - +
405A ASP* 3.5 18.9 + - + +
406A ILE* 4.0 6.6 + - - +
443A SER 4.2 0.4 - - - +
444A ASP* 4.0 17.3 - - - +
446A ILE 3.3 10.1 - - - +
447A LEU* 4.0 5.1 - - + +
448A LEU* 5.1 2.2 - - - -
1591A 23D 3.9 24.5 + - - +
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Residues in contact with LEU 403 (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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402A ALA* 1.3 72.7 - - - +
404A THR* 1.3 64.7 + - - +
406A ILE* 2.9 32.5 + - + +
407A VAL* 3.0 19.0 + - + +
412A MET* 4.1 28.3 - - + -
420A VAL* 3.8 31.9 - - + -
443A SER* 3.4 23.9 + - - +
446A ILE* 2.9 23.1 + - + +
448A LEU* 4.9 8.2 - - + +
504A MET* 4.1 14.6 - - + -
508A MET* 4.1 14.1 - - + -
581A ILE* 6.4 0.4 - - + -
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Residues in contact with THR 404 (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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402A ALA* 3.2 6.2 - - - -
403A LEU* 1.3 77.2 - - - +
405A ASP* 1.3 59.8 + - - +
407A VAL* 3.3 3.9 - - + +
408A THR* 3.0 47.1 + - + +
443A SER* 2.9 26.3 + - - +
444A ASP* 2.9 37.9 + - - +
507A GLU* 5.2 0.9 - - - +
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Residues in contact with ASP 405 (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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402A ALA* 3.5 14.2 + - + +
403A LEU 3.1 0.6 - - - -
404A THR* 1.3 76.9 - - - +
406A ILE* 1.3 67.4 + - + +
408A THR* 3.9 4.0 - - - -
409A HIS* 3.0 36.4 + - - +
586A ARG* 2.8 47.3 + - - +
589A ARG* 3.1 23.6 + - - -
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Residues in contact with ILE 406 (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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400A GLY 5.7 0.2 - - - +
402A ALA 4.7 3.4 - - - +
403A LEU* 2.9 19.5 + - + +
405A ASP* 1.3 77.8 - - + +
407A VAL* 1.3 59.7 + - - +
409A HIS 3.2 1.2 + - - -
410A THR* 2.9 48.5 + - - +
412A MET* 3.7 29.8 - - + -
448A LEU* 3.2 34.8 - - + -
581A ILE* 4.3 7.6 - - + -
584A LEU* 3.7 38.8 - - + +
585A MET* 4.5 5.8 - - + +
589A ARG* 3.9 7.4 - - - +
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Residues in contact with VAL 407 (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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403A LEU* 3.0 31.4 + - + +
404A THR* 3.3 17.5 - - - +
406A ILE* 1.3 78.5 - - - +
408A THR* 1.3 67.7 + - + +
410A THR 3.5 13.2 - - - +
412A MET* 4.2 8.3 - - - -
443A SER* 4.2 2.9 - - - +
507A GLU* 3.6 31.6 - - + +
508A MET* 3.9 30.0 - - + +
511A GLY* 3.6 24.5 - - - +
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Residues in contact with THR 408 (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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404A THR* 3.0 31.8 + - + +
405A ASP* 3.9 1.6 - - - -
407A VAL* 1.3 84.9 - - + +
409A HIS* 1.3 84.6 + - - +
511A GLY* 4.1 12.3 - - - +
512A GLU* 6.1 1.1 - - + -
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Residues in contact with HIS 409 (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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405A ASP* 3.0 45.1 + - - +
406A ILE 3.2 1.6 + - - -
408A THR* 1.3 101.3 + - - +
410A THR* 1.3 62.0 + - - +
586A ARG* 3.9 12.2 + - - -
589A ARG* 3.7 23.5 + - - +
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Residues in contact with THR 410 (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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406A ILE* 2.9 37.4 + - - +
407A VAL* 3.5 14.4 - - - +
408A THR 3.9 0.2 - - - -
409A HIS* 1.3 82.5 - - - +
411A ARG* 1.3 66.8 + - - +
412A MET 4.1 1.4 + - - -
508A MET 5.6 1.0 - - - +
584A LEU* 3.5 25.9 - - + +
589A ARG* 3.3 35.7 - - - +
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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