Contacts of the strand formed by residues 469 - 476 (chain B) in PDB entry 3FO5
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 ASP 469 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388B SER* 2.6 33.8 + - - -
464B GLN* 3.4 2.0 + - - +
465B VAL* 2.9 35.5 + - + -
466B ASP* 2.5 45.8 + - - +
467B GLU 3.7 0.4 + - - -
468B ASP* 1.3 82.6 - - - +
470B ALA* 1.3 64.1 + - - +
491B LEU* 4.7 5.8 - - + -
492B ALA 3.2 6.3 - - - +
493B SER* 2.7 24.3 + - - +
495B ARG* 3.5 8.5 + - - -
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Residues in contact with ALA 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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461B LEU* 3.7 17.3 - - + -
463B GLN 3.4 7.2 - - - +
464B GLN* 4.1 12.1 - - - +
465B VAL* 4.1 1.8 - - - +
469B ASP* 1.3 76.7 - - - +
471B ILE* 1.3 62.1 + - - +
472B TYR* 3.6 26.7 - - + +
490B ILE 3.6 0.9 - - - +
491B LEU* 3.5 4.1 - - - +
492B ALA* 2.7 40.7 + - - +
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Residues in contact with ILE 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B TRP* 3.6 41.7 - - + +
461B LEU* 3.3 6.2 - - - +
462B VAL* 2.8 38.4 + - + -
463B GLN* 2.9 36.4 + - + +
465B VAL* 4.1 4.9 - - + -
470B ALA* 1.3 75.9 - - - +
472B TYR* 1.3 58.9 + - - +
489B VAL* 3.8 27.8 - - + -
490B ILE 3.2 6.7 - - - +
491B LEU* 4.0 16.4 - - + -
511B VAL* 4.1 8.5 - - + -
513B LEU* 4.2 12.8 - - + -
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Residues in contact with TYR 472 (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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444B SER 4.1 7.8 + - - -
445B ASP* 4.4 5.5 + - - -
446B LEU* 3.8 37.2 + - + -
447B ARG* 4.1 16.3 + - + +
459B VAL* 3.4 26.7 - - + -
460B GLU 3.2 10.5 - - - +
461B LEU* 4.0 17.9 - - + +
462B VAL* 4.0 4.7 - - - -
464B GLN* 5.5 1.0 + - - -
470B ALA* 3.6 32.5 - - + +
471B ILE* 1.3 75.8 - - - +
473B HIS* 1.3 59.5 + - - +
474B VAL* 3.9 17.0 + - + -
488B PHE 3.7 0.5 - - - +
489B VAL* 3.4 4.9 - - - +
490B ILE* 2.8 35.9 + - + +
492B ALA* 3.8 19.1 - - + -
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Residues in contact with HIS 473 (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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458B SER* 4.0 1.0 + - - +
459B VAL* 3.5 2.8 - - - -
460B GLU* 2.7 62.2 + - - +
462B VAL* 3.7 16.8 - - + +
472B TYR* 1.3 72.9 - - - +
474B VAL* 1.3 61.1 + - - +
475B THR* 4.1 18.9 + - + +
487B ASP* 2.7 34.0 + - + +
488B PHE 3.3 15.5 - - - -
489B VAL* 4.1 15.0 - - + +
516B HIS* 4.9 11.2 - + + -
522B TYR* 4.6 9.9 - + - -
524B ARG* 4.0 2.9 + - - -
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Residues in contact with VAL 474 (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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1B 1PE 5.5 2.2 - - - +
446B LEU* 5.2 2.0 - - + -
455B HIS 5.4 0.7 - - - +
456B TYR* 3.7 41.1 - - + +
458B SER 3.4 10.5 - - - +
459B VAL* 4.2 5.4 - - + -
472B TYR* 4.1 17.9 - - + +
473B HIS* 1.3 77.7 - - - +
475B THR* 1.3 73.7 + - - +
476B SER* 5.4 0.9 - - - -
487B ASP* 3.1 4.9 - - - +
488B PHE* 2.7 56.6 + - + +
490B ILE* 4.0 20.4 - - + -
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Residues in contact with THR 475 (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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456B TYR* 3.8 0.3 - - - -
457B ARG* 2.9 47.0 + - - -
458B SER* 2.4 37.9 + - - +
473B HIS* 4.1 13.0 - - + +
474B VAL* 1.3 84.5 - - - +
476B SER* 1.3 61.4 + - - +
486B GLN 3.3 8.1 - - - -
487B ASP* 4.0 8.7 - - + -
522B TYR* 3.7 30.1 - - + +
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Residues in contact with SER 476 (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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1B 1PE 4.2 11.1 + - - -
455B HIS* 2.8 22.6 + - - +
457B ARG* 4.3 2.7 - - - -
474B VAL* 5.4 0.4 - - - -
475B THR* 1.3 76.1 - - - +
477B PRO* 1.4 74.9 + - - +
479B LEU* 5.5 3.3 - - - +
485B PRO* 3.2 7.5 - - - +
486B GLN* 2.8 38.1 + - - -
488B PHE* 3.9 24.7 - - - -
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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