Contacts of the strand formed by residues 458 - 466 (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 SER 458 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450B PRO* 4.4 4.9 - - - -
457B ARG* 1.3 86.7 + - - +
459B VAL* 1.3 73.3 + - - +
473B HIS 4.5 0.8 + - - -
474B VAL* 3.4 1.7 - - - +
475B THR* 2.4 58.8 + - - +
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Residues in contact with VAL 459 (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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446B LEU* 3.4 28.0 - - + +
447B ARG* 3.8 16.1 - - + +
450B PRO* 3.8 11.3 - - + +
456B TYR* 3.3 35.2 - - + -
458B SER* 1.3 84.8 - - - +
460B GLU* 1.3 62.6 + - - +
472B TYR* 3.4 34.3 - - + -
473B HIS 3.5 3.6 - - - +
474B VAL* 4.2 4.0 - - + -
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Residues in contact with GLU 460 (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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459B VAL* 1.3 75.3 - - - +
461B LEU* 1.3 69.1 + - - +
462B VAL* 5.7 2.0 - - + +
472B TYR* 3.2 7.5 - - - -
473B HIS* 2.7 67.2 + - + +
516B HIS* 5.9 0.7 + - - -
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Residues in contact with LEU 461 (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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447B ARG* 5.0 22.5 - - - +
459B VAL* 4.5 0.4 + - - +
460B GLU* 1.3 76.9 - - - +
462B VAL* 1.3 64.0 + - - +
463B GLN 3.8 11.4 - - - +
464B GLN* 3.5 29.2 - - + +
470B ALA* 3.7 24.9 - - + -
471B ILE 3.3 19.1 - - - +
472B TYR* 4.0 20.0 - - + +
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Residues in contact with VAL 462 (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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460B GLU* 4.2 2.7 - - + +
461B LEU* 1.3 75.8 - - - +
463B GLN* 1.3 69.4 + - + +
471B ILE* 2.8 20.9 + - + +
472B TYR 4.0 3.1 - - - -
473B HIS* 3.7 32.3 - - + +
489B VAL* 5.3 2.0 - - + -
513B LEU* 3.9 19.1 - - + -
516B HIS* 3.6 42.0 - - + +
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Residues in contact with GLN 463 (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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379B TRP* 3.4 33.9 - - - +
381B PRO* 6.3 0.2 - - - +
461B LEU* 3.6 4.1 - - - +
462B VAL* 1.3 93.4 - - + +
464B GLN* 1.3 70.9 + - - +
465B VAL* 3.3 6.7 + - + +
470B ALA* 3.4 0.9 - - - -
471B ILE* 2.9 46.9 + - + +
513B LEU* 5.1 6.5 - - - +
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Residues in contact with GLN 464 (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* 3.5 31.9 - - + +
463B GLN* 1.3 77.0 - - - +
465B VAL* 1.3 60.9 + - - +
466B ASP* 2.7 30.8 + - - +
467B GLU* 4.2 8.7 + - - +
469B ASP 3.4 12.0 + - - +
470B ALA* 4.1 8.7 - - - +
472B TYR* 5.5 0.7 + - - -
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Residues in contact with VAL 465 (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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379B TRP* 3.6 42.2 - - + -
384B GLN* 3.6 33.3 + - + +
463B GLN* 3.8 18.4 - - - +
464B GLN* 1.3 74.3 - - - +
466B ASP* 1.3 70.2 + - - +
469B ASP* 2.9 22.8 + - + +
470B ALA* 4.2 3.8 - - - +
471B ILE* 4.1 14.4 - - + -
491B LEU* 4.6 1.6 - - + -
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Residues in contact with ASP 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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384B GLN* 4.4 9.2 + - - +
385B VAL* 6.1 1.2 - - - +
388B SER* 5.8 0.2 - - - -
464B GLN* 2.7 32.4 + - - -
465B VAL* 1.3 83.5 - - - +
467B GLU* 1.3 60.3 + - - +
468B ASP* 3.1 5.6 + - - +
469B ASP* 2.5 46.7 + - - +
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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