Contacts of the strand formed by residues 465 - 471 (chain D) in PDB entry 2DB3
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 465 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462D CYS* 2.7 33.3 - - + +
463D SER 3.0 2.6 - - - +
464D ASP* 1.3 78.5 - - - +
466D LYS* 1.3 64.8 + - - +
467D GLN* 3.2 10.7 + - + +
577D ILE* 3.7 40.4 - - + +
580D THR* 4.6 11.7 - - - +
581D GLY* 5.0 0.9 - - - -
587D GLY 3.4 12.6 - - - +
588D ARG* 4.0 3.4 - - - +
589D ALA* 3.9 31.4 - - + +
614D GLN* 3.4 11.5 + - - -
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Residues in contact with LYS 466 (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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464D ASP 3.7 3.2 + - - +
465D VAL* 1.3 69.7 - - - +
467D GLN* 1.3 68.8 + - - +
468D THR* 4.0 10.5 + - - +
587D GLY 2.9 15.0 + - - +
588D ARG* 3.4 10.3 - - + +
589D ALA 2.9 26.9 + - - +
614D GLN* 3.5 12.6 - - - +
615D THR* 5.3 8.3 - - - +
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Residues in contact with GLN 467 (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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461D ALA* 3.6 13.3 - - - +
462D CYS 4.4 0.2 + - - -
465D VAL* 3.3 20.4 + - + +
466D LYS* 1.3 76.6 - - - +
468D THR* 1.3 61.7 + - - +
469D ILE* 4.3 0.9 + - - +
573D TYR* 2.7 41.2 + - - +
577D ILE* 3.5 18.7 - - + +
589D ALA* 3.5 7.0 - - + +
608D ILE* 4.0 3.5 - - - +
609D LEU* 3.6 17.7 - - + +
612D SER* 3.2 27.1 + - - -
614D GLN* 2.7 37.5 + - + +
615D THR* 4.8 9.4 + - - +
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Residues in contact with THR 468 (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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466D LYS* 4.7 12.3 + - - +
467D GLN* 1.3 75.5 + - - +
469D ILE* 1.3 68.5 + - - +
470D TYR* 3.9 33.7 - - + +
588D ARG* 6.1 0.7 - - - +
589D ALA 3.0 11.7 + - - +
590D THR* 3.3 12.4 + - - +
591D SER* 2.9 24.9 + - - -
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Residues in contact with ILE 469 (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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467D GLN 4.3 0.4 + - - +
468D THR* 1.3 87.0 - - - +
470D TYR* 1.3 69.6 + - - +
566D MET* 5.8 0.4 - - - -
573D TYR* 3.7 23.6 - - - +
591D SER* 3.5 19.5 - - - +
593D PHE* 3.9 17.5 - - + -
605D LEU* 3.9 27.4 - - + -
609D LEU* 4.1 26.9 - - + -
615D THR 5.8 0.4 - - - +
617D PRO* 4.0 19.8 - - + +
619D PHE* 3.7 29.3 - - + -
620D LEU* 4.4 2.7 - - + -
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Residues in contact with TYR 470 (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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468D THR* 3.9 22.1 - - + +
469D ILE* 1.3 79.5 - - - +
471D GLU* 1.3 59.1 + - - +
472D VAL* 3.5 16.3 + - + -
480D LYS* 3.8 34.1 + - - -
484D ILE* 4.5 4.5 - - + -
590D THR* 3.7 32.5 - - + -
591D SER 2.8 9.4 + - - +
592D PHE* 3.6 6.1 - + + -
593D PHE* 2.7 34.8 + - - +
619D PHE* 3.7 4.5 - - - -
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Residues in contact with GLU 471 (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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470D TYR* 1.3 72.4 - - - +
472D VAL* 1.3 61.9 + - - +
593D PHE* 3.4 4.8 - - - -
595D PRO* 3.4 34.7 - - + +
619D PHE* 3.6 53.2 - - + +
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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