Contacts of the strand formed by residues 448 - 454 (chain F) in PDB entry 6M17
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 ASN 448 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442F ASP* 2.5 31.9 + - - +
444F LYS* 3.9 24.5 + - + +
447F GLY* 1.3 69.8 - - - -
449F TYR* 1.3 58.8 + - - +
450F ASN* 3.2 29.6 + - - +
451F TYR* 3.4 27.9 + - - -
495F TYR 2.8 19.7 - - - +
497F PHE* 2.9 23.3 + - + +
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Residues in contact with TYR 449 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ASP* 3.0 32.7 + - - -
42D GLN* 3.4 16.9 + - - -
444F LYS* 5.5 1.4 - - - +
446F GLY 3.6 13.2 + - - -
447F GLY* 3.2 32.1 + - - -
448F ASN* 1.3 70.9 + - - +
450F ASN* 1.3 65.4 + - - +
451F TYR 3.5 2.6 + - - -
452F LEU* 4.8 4.7 - - - +
494F SER* 3.6 32.1 - - - +
495F TYR 4.0 3.8 - - - -
496F GLY* 4.0 17.0 - - - -
498F GLN* 5.3 0.3 + - - -
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Residues in contact with ASN 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346F ARG* 5.8 1.9 + - - -
349F SER* 4.6 6.2 + - - -
444F LYS* 4.7 9.5 + - - -
448F ASN* 3.2 19.1 + - - +
449F TYR* 1.3 84.4 + - - +
451F TYR* 1.3 66.3 + - + +
452F LEU* 3.9 13.8 + - - +
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Residues in contact with TYR 451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346F ARG* 4.8 11.5 - - + +
347F PHE* 4.2 20.2 + - - +
348F ALA 4.6 11.9 - - - -
349F SER* 4.6 13.5 - - - -
401F VAL* 4.0 29.4 - - + +
442F ASP* 2.4 37.3 + - + -
448F ASN* 3.4 32.0 + - - +
449F TYR 3.5 1.6 - - - -
450F ASN* 1.3 83.8 - - + +
452F LEU* 1.3 62.2 + - - +
494F SER* 3.5 1.4 - - - -
495F TYR* 3.0 35.2 + - + +
497F PHE* 4.1 29.8 - + + -
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Residues in contact with LEU 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349F SER* 4.4 6.6 + - - +
350F VAL* 3.2 24.8 + - - +
351F TYR* 4.0 28.8 - - + +
449F TYR 4.8 3.8 - - - +
450F ASN* 3.9 15.9 + - - +
451F TYR* 1.3 77.9 - - - +
453F TYR* 1.3 62.7 + - - +
490F PHE* 6.5 0.2 - - + -
492F LEU* 4.4 19.5 - - + +
493F GLN 3.0 20.4 - - - +
494F SER* 4.0 15.0 - - - -
495F TYR* 4.5 1.7 - - - -
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Residues in contact with TYR 453 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D HIS* 3.1 36.8 - - - +
350F VAL* 3.2 27.1 - - + -
351F TYR* 4.3 3.1 - - - -
406F GLU* 5.4 2.7 - - - -
417F LYS* 4.6 17.3 - - + +
418F ILE* 4.8 5.8 - - + -
422F ASN* 4.0 6.3 - - - +
452F LEU* 1.3 72.0 - - - +
454F ARG* 1.3 70.6 + - - +
455F LEU* 3.8 19.0 + - + +
492F LEU* 3.5 7.4 - - - -
493F GLN* 2.9 52.7 + - + +
494F SER 4.3 0.9 - - - -
495F TYR* 3.8 41.5 - + - +
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Residues in contact with ARG 454 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351F TYR* 4.0 15.2 - - + +
417F LYS* 3.9 4.7 - - - +
421F TYR* 3.7 19.4 - - + +
422F ASN* 3.0 35.6 - - - +
453F TYR* 1.3 79.0 - - - +
455F LEU* 1.3 62.7 + - - +
456F PHE 3.5 21.3 + - - +
457F ARG* 4.1 20.2 - - - +
467F ASP* 2.9 42.1 + - - +
468F ILE* 4.0 1.6 - - - +
469F SER* 2.9 30.3 + - - +
491F PRO* 3.5 29.1 - - - +
492F LEU* 3.6 10.2 - - + +
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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