Contacts of the strand formed by residues 465 - 471 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462C CYS* 3.1 23.5 + - + +
463C SER 3.1 2.6 - - - -
464C ASP* 1.3 80.8 - - - +
466C LYS* 1.3 62.9 + - - +
467C GLN* 3.3 21.9 + - + +
577C ILE* 3.6 28.5 - - + +
578C GLY* 4.8 0.2 - - - -
580C THR* 3.4 33.4 - - + +
581C GLY* 3.9 7.9 - - - -
587C GLY 3.4 2.9 - - - -
588C ARG 4.2 0.7 - - - -
589C ALA* 3.7 31.6 - - + +
614C GLN* 3.5 8.0 + - - +
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Residues in contact with LYS 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B ASN* 3.5 49.5 + - - +
262B LYS* 5.5 0.8 - - - +
264B GLY* 4.3 12.5 - - - -
266B LYS* 5.6 6.8 - - - +
463C SER 5.4 0.2 - - - -
464C ASP 3.6 2.4 + - - +
465C VAL* 1.3 69.4 - - - +
467C GLN* 1.3 67.8 + - - +
468C THR* 3.8 8.2 + - - +
587C GLY 2.8 16.4 + - - +
588C ARG* 3.5 8.7 - - + +
589C ALA 2.9 29.1 + - - +
614C GLN* 3.3 18.2 - - - +
615C THR* 6.1 6.7 - - - +
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Residues in contact with GLN 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461C ALA* 3.9 3.4 - - - +
462C CYS 4.2 3.2 + - - -
465C VAL* 3.4 19.3 + - + +
466C LYS* 1.3 77.0 - - - +
468C THR* 1.3 61.9 + - - +
469C ILE* 4.3 1.9 + - + +
573C TYR* 2.7 40.5 + - - +
577C ILE* 3.4 23.7 - - + +
589C ALA* 3.6 6.1 - - + +
608C ILE* 3.9 5.2 - - - +
609C LEU* 3.5 21.8 - - + +
612C SER* 3.0 28.5 + - - -
614C GLN* 2.6 34.9 + - - +
615C THR* 4.9 7.1 + - - +
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Residues in contact with THR 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B LYS* 2.9 37.9 + - - +
466C LYS* 4.8 7.3 + - - +
467C GLN* 1.3 75.1 + - - +
469C ILE* 1.3 69.1 + - - +
470C TYR* 3.8 32.3 - - + -
589C ALA 2.8 14.6 + - - +
590C THR* 3.3 10.2 - - - +
591C SER* 2.9 24.4 + - - -
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Residues in contact with ILE 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467C GLN 5.0 0.9 - - - +
468C THR* 1.3 85.6 - - - +
470C TYR* 1.3 67.9 + - - +
573C TYR* 3.8 22.0 - - - +
591C SER* 3.6 20.0 - - - +
593C PHE* 3.8 25.6 - - + -
605C LEU* 4.2 24.7 - - + -
609C LEU* 4.1 27.6 - - + -
615C THR 5.8 0.4 - - - +
617C PRO* 3.9 21.8 - - + +
619C PHE* 3.7 22.0 - - + -
620C LEU* 4.6 3.6 - - + -
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Residues in contact with TYR 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B LYS* 3.9 17.2 + - - +
468C THR* 3.8 14.5 - - + +
469C ILE* 1.3 79.9 - - - +
471C GLU* 1.3 56.4 + - - +
472C VAL* 3.4 16.1 + - + -
480C LYS* 4.0 29.2 - - - -
484C ILE* 4.3 10.4 - - + +
590C THR* 3.5 33.2 - - + -
591C SER 3.0 9.2 + - - +
592C PHE* 3.6 6.8 - + + -
593C PHE* 2.6 35.2 + - - +
619C PHE* 3.8 3.8 - - - -
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Residues in contact with GLU 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470C TYR* 1.3 72.3 - - - +
472C VAL* 1.3 61.8 + - - +
593C PHE* 3.4 5.7 - - + +
595C PRO* 3.5 31.8 - - + +
599C ARG* 5.7 1.7 + - - -
619C PHE* 3.5 54.4 - - + +
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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