Contacts of the strand formed by residues 430 - 434 (chain D) in PDB entry 1D00
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 VAL 430 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411D PHE* 4.0 42.2 - - + -
426D PHE* 4.1 8.1 - - + -
428D GLN 3.7 9.4 - - - +
429D LYS* 1.3 80.5 - - - +
431D THR* 1.3 65.1 + - - +
432D LEU* 4.0 21.0 - - + +
446D ALA* 3.1 4.4 - - - +
447D PHE* 2.9 69.2 + - + -
494D ALA* 5.6 1.6 - - + -
495D ILE 3.7 3.6 - - - +
496D VAL* 4.7 6.1 - - + -
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Residues in contact with THR 431 (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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429D LYS* 3.7 24.4 + - - +
430D VAL* 1.3 76.8 - - - +
432D LEU* 1.3 66.6 + - - +
433D MET* 4.3 9.2 - - + -
444D ILE* 3.4 32.3 - - + -
445D ASP 3.6 6.5 - - - +
446D ALA* 3.7 3.5 - - + +
493D LYS 3.8 0.4 - - - +
494D ALA* 3.2 5.9 - - - +
495D ILE* 2.9 53.5 + - + +
445H ASP* 4.7 2.9 - - - +
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Residues in contact with LEU 432 (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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392D LEU* 4.1 10.5 - - + -
409D LEU* 3.4 54.1 - - + +
410D PHE* 4.6 6.3 - - - -
411D PHE* 4.7 1.8 - - + +
430D VAL* 4.0 15.5 - - + -
431D THR* 1.3 82.2 - - - +
433D MET* 1.3 66.3 + - - +
444D ILE* 3.4 1.4 - - - -
445D ASP 2.9 33.2 + - - +
447D PHE* 4.3 14.8 - - + -
469D CYS* 4.2 16.4 - - - -
472D PHE* 3.5 10.9 - - + -
493D LYS 3.5 2.5 - - - +
494D ALA* 3.9 18.6 - - + -
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Residues in contact with MET 433 (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 LEU* 4.7 0.6 - - - +
431D THR* 4.3 4.0 - - + -
432D LEU* 1.3 81.6 - - - +
434D LEU* 1.3 59.4 + - - +
435D LEU* 3.9 16.2 - - + -
442D HIS* 4.1 29.6 - - + -
443D VAL 3.2 8.3 - - - +
444D ILE* 3.8 28.5 - - + -
472D PHE* 3.7 7.6 - - - -
492D ILE* 3.4 8.7 - - - +
493D LYS* 2.8 64.5 + - + +
495D ILE* 4.4 15.7 - - - -
444H ILE* 5.5 4.5 - - + +
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Residues in contact with LEU 434 (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 LEU* 4.2 10.8 - - + -
433D MET* 1.3 71.8 - - - +
435D LEU* 1.3 65.7 + - - +
436D ASP 3.6 1.2 + - - -
442D HIS* 3.8 1.2 - - - -
443D VAL* 3.0 40.1 + - + +
472D PHE* 3.8 12.2 - - + -
473D CYS* 3.9 16.4 - - + -
478D MET* 3.8 29.8 - - + -
484D TYR* 3.7 26.5 - - + -
490D ILE* 4.3 21.5 - - + -
491D PHE 3.7 14.1 - - - +
492D ILE* 3.8 16.4 - - + -
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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