Contacts of the strand formed by residues 458 - 466 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450A PRO* 4.3 4.7 - - - -
456A TYR 3.4 0.2 - - - -
457A ARG* 1.3 85.6 + - - +
459A VAL* 1.3 71.5 + - - +
473A HIS 4.4 0.7 + - - -
474A VAL* 3.3 2.8 - - - +
475A THR* 2.6 55.9 + - - +
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Residues in contact with VAL 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A LEU* 3.4 26.9 - - + +
447A ARG* 4.0 19.2 - - + +
450A PRO* 3.7 12.1 - - + +
456A TYR* 3.4 32.1 - - + -
458A SER* 1.3 82.8 - - - +
460A GLU* 1.3 62.9 + - - +
472A TYR* 3.5 36.1 - - + -
473A HIS 3.4 4.3 - - - +
474A VAL* 4.3 3.4 - - + -
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Residues in contact with GLU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A ARG* 5.6 0.2 - - - +
459A VAL* 1.3 76.2 - - - +
461A LEU* 1.3 74.1 + - - +
462A VAL* 3.3 7.3 + - - +
472A TYR* 3.3 7.5 - - - +
473A HIS* 2.9 51.9 + - + +
516A HIS* 3.7 24.8 + - - -
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Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A ARG* 3.8 46.5 - - - +
459A VAL 4.2 0.4 - - - -
460A GLU* 1.3 79.6 - - - +
462A VAL* 1.3 60.1 + - - +
463A GLN* 3.7 22.0 - - - +
464A GLN* 3.9 21.1 - - + +
470A ALA* 3.8 17.0 - - + -
471A ILE 3.7 12.8 - - - +
472A TYR* 3.8 16.6 - - + -
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Residues in contact with VAL 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A GLU* 4.0 6.7 - - - +
461A LEU* 1.3 76.1 - - - +
463A GLN* 1.3 65.6 + - + +
471A ILE* 2.8 20.5 + - + +
472A TYR 4.0 2.7 - - - -
473A HIS* 3.7 28.5 - - + +
489A VAL* 5.7 1.1 - - + -
513A LEU* 3.7 21.8 - - + -
515A THR* 4.8 2.0 - - - +
516A HIS* 3.7 41.1 - - + +
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Residues in contact with GLN 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A TRP* 3.9 24.0 - - - +
381A PRO* 6.1 0.6 - - - +
461A LEU* 3.8 6.1 - - - -
462A VAL* 1.3 87.3 - - + +
464A GLN* 1.3 70.3 - - - +
465A VAL* 3.4 15.9 + - - +
470A ALA* 3.2 4.0 - - - +
471A ILE* 2.8 45.8 + - + +
513A LEU* 5.7 2.0 - - + +
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Residues in contact with GLN 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A ARG* 4.7 5.4 + - - -
461A LEU* 3.9 26.8 - - + +
463A GLN* 1.3 78.5 - - - +
465A VAL* 1.3 66.0 + - - +
466A ASP* 3.0 26.5 + - - +
467A GLU* 3.8 14.8 + - - +
468A ASP 5.1 0.4 - - - -
469A ASP 3.5 10.0 + - - +
470A ALA* 3.8 13.5 - - - +
472A TYR* 5.0 2.6 + - - -
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Residues in contact with VAL 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A TRP* 3.7 27.4 - - + -
384A GLN* 3.6 42.6 - - + +
388A SER* 5.5 1.3 - - - +
463A GLN* 4.2 22.4 - - - +
464A GLN* 1.3 74.4 - - - +
466A ASP* 1.3 71.9 + - - +
469A ASP* 2.9 23.4 + - + +
471A ILE* 4.3 14.1 - - + -
491A LEU* 4.7 2.7 - - + -
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Residues in contact with ASP 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A GLN* 4.9 4.3 - - - +
388A SER* 5.2 0.9 + - - -
464A GLN* 3.0 24.3 + - - +
465A VAL* 1.3 85.3 - - + +
467A GLU* 1.3 65.6 + - - +
468A ASP* 2.9 13.3 + - - +
469A ASP* 2.6 40.0 + - - +
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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