Contacts of the strand formed by residues 465 - 471 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B CYS* 2.8 33.9 - - + +
463B SER 3.1 2.4 - - - -
464B ASP* 1.3 80.4 - - - +
466B LYS* 1.3 63.5 + - - +
467B GLN* 3.4 23.1 + - + +
577B ILE* 4.0 20.4 - - + +
580B THR* 3.6 37.0 - - + +
581B GLY* 4.9 0.7 - - - -
587B GLY* 3.2 7.9 - - - +
589B ALA* 3.8 27.4 - - + +
614B GLN* 3.5 7.8 + - - -
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Residues in contact with LYS 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B ASP 4.1 1.4 + - - -
465B VAL* 1.3 70.3 - - - +
467B GLN* 1.3 69.7 + - - +
468B THR* 4.0 7.8 + - - +
587B GLY 3.0 11.9 + - - +
588B ARG* 3.6 8.5 - - + +
589B ALA 3.0 25.5 + - - +
613B GLY 4.4 7.5 + - - -
614B GLN* 3.2 27.8 + - - +
615B THR* 4.7 19.9 - - - +
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Residues in contact with GLN 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ALA* 3.8 5.9 - - - +
465B VAL* 3.5 22.2 + - + +
466B LYS* 1.3 80.1 - - - +
468B THR* 1.3 63.2 + - - +
469B ILE* 4.3 2.3 + - + +
573B TYR* 2.9 38.6 + - - +
577B ILE* 3.5 23.8 - - + +
589B ALA* 3.6 9.0 - - + +
608B ILE* 3.7 6.4 - - - +
609B LEU* 3.4 24.4 - - + +
612B SER* 3.4 23.1 + - - -
614B GLN* 2.7 31.1 + - - +
615B THR* 4.8 7.6 + - - +
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Residues in contact with THR 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B LYS* 4.7 9.2 + - - +
467B GLN* 1.3 73.6 + - - +
469B ILE* 1.3 66.4 + - - +
470B TYR* 3.7 40.6 + - + +
589B ALA 2.9 12.4 + - - +
590B THR* 3.5 8.8 - - - +
591B SER 2.9 26.0 + - - +
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Residues in contact with ILE 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467B GLN 4.3 0.6 + - - +
468B THR* 1.3 84.7 - - - +
470B TYR* 1.3 65.3 + - - +
573B TYR* 3.8 17.0 - - - +
589B ALA 5.7 0.4 - - - +
591B SER* 3.5 28.5 - - - +
593B PHE* 3.7 27.4 - - + +
605B LEU* 3.9 31.4 - - + -
609B LEU* 4.3 22.2 - - + -
617B PRO* 3.6 22.4 - - + +
619B PHE* 3.2 25.9 - - + -
620B LEU* 4.3 1.8 - - + -
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Residues in contact with TYR 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B THR* 3.7 21.0 - - + +
469B ILE* 1.3 78.6 - - - +
471B GLU* 1.3 61.2 + - - +
472B VAL* 4.0 15.0 - - + -
480B LYS* 4.0 27.6 - - + +
484B ILE* 4.6 10.8 - - + -
590B THR* 3.8 31.9 - - + -
591B SER 3.0 9.5 + - - +
592B PHE* 3.9 11.3 - + + -
593B PHE* 2.9 31.0 + - - +
619B PHE* 3.7 2.5 - - - -
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Residues in contact with GLU 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B TYR* 1.3 71.2 - - - +
472B VAL* 1.3 68.2 + - - +
480B LYS* 5.0 3.8 - - - -
593B PHE* 3.6 3.5 - - - +
595B PRO* 3.2 35.8 - - + +
619B PHE* 3.4 49.1 - - + +
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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