Contacts of the strand formed by residues 444 - 451 (chain A) in PDB entry 2YA6
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 LYS 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439A LYS 3.5 1.2 - - - +
440A LYS* 3.2 2.6 - - - -
441A ILE 2.8 31.3 + - - +
442A ASP 3.2 10.7 + - - +
443A GLY* 1.3 86.7 + - - +
445A THR* 1.3 62.5 + - - +
446A TYR* 3.5 32.5 + - + +
462A GLU* 4.2 13.7 - - - +
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Residues in contact with THR 445 (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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438A TYR* 3.9 29.8 - - + -
439A LYS 3.6 6.1 - - - +
440A LYS* 4.0 22.9 - - - +
443A GLY 4.2 1.9 + - - -
444A LYS* 1.3 71.9 - - - +
446A TYR* 1.3 69.4 + - - +
541A PRO* 4.1 23.5 - - + +
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Residues in contact with TYR 446 (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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438A TYR* 3.2 7.3 - - - -
439A LYS* 2.8 37.0 + - - +
441A ILE* 3.9 31.2 + - + -
444A LYS* 3.5 37.7 - - + +
445A THR* 1.3 78.4 - - - +
447A GLN* 1.3 60.7 + - - +
459A THR* 3.9 15.7 - - + -
460A ILE 3.2 23.6 - - - +
461A ARG* 3.7 43.3 + - + -
462A GLU* 3.4 27.3 + - - -
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Residues in contact with GLN 447 (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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437A ALA 3.6 10.5 - - - +
438A TYR* 3.7 18.7 - - + -
445A THR 4.5 0.2 + - - -
446A TYR* 1.3 73.3 - - - +
448A ILE* 1.3 73.9 + - - +
459A THR* 3.5 2.4 - - - -
460A ILE* 2.9 50.2 + - + +
503A ILE* 4.8 3.8 - - - +
504A TYR* 4.9 8.3 + - - -
515A ILE* 3.4 32.2 - - + +
516A ALA 6.0 0.2 - - - +
520A TYR* 3.7 21.1 + - - -
538A ASP* 4.2 11.4 + - - +
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Residues in contact with ILE 448 (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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436A GLU* 3.7 27.6 - - + +
437A ALA 2.8 16.1 + - - +
438A TYR 3.4 34.3 - - - +
439A LYS* 3.9 19.3 - - + +
447A GLN* 1.3 85.3 - - - +
449A LEU* 1.3 72.8 + - - +
450A TYR* 3.7 22.2 - - + +
457A ALA* 3.5 33.2 - - + -
458A TYR 3.3 5.4 - - - +
459A THR* 4.5 1.6 - - + +
515A ILE* 3.7 15.1 - - - -
516A ALA 4.2 2.2 + - - +
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Residues in contact with LEU 449 (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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448A ILE* 1.3 80.1 - - - +
450A TYR* 1.3 61.8 + - - +
457A ALA* 3.9 1.9 - - - -
458A TYR* 2.7 47.5 + - + +
459A THR 5.0 0.7 - - - +
460A ILE* 3.5 35.4 - - + +
466A VAL* 3.7 30.1 - - + -
478A VAL* 4.0 5.6 - - + -
503A ILE* 3.5 24.7 - - + -
513A PHE* 4.0 18.4 - - + -
514A ARG 3.4 26.7 - - - +
515A ILE* 3.8 3.8 - - + +
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Residues in contact with TYR 450 (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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435A GLU* 3.9 12.6 - - + +
436A GLU* 2.6 48.0 + - - +
448A ILE* 3.7 18.1 - - + +
449A LEU* 1.3 74.1 - - - +
451A ARG* 1.3 62.5 + - - +
452A GLU 4.1 0.5 + - - -
454A GLU 5.1 4.3 - - - +
455A LYS 4.5 2.5 - - - -
456A GLY 3.9 18.6 - - - -
457A ALA* 4.6 5.3 - - + +
512A PRO 3.4 1.0 - - - +
513A PHE* 3.3 6.9 - - - -
514A ARG* 2.7 71.8 + - - +
516A ALA* 3.8 22.2 - - + -
610B ASN* 4.2 27.9 - - + +
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Residues in contact with ARG 451 (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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449A LEU 4.2 1.0 + - - -
450A TYR* 1.3 74.7 - - - +
452A GLU* 1.3 78.1 + - + +
453A GLY 3.3 0.3 + - - -
454A GLU* 3.0 39.4 + - + +
456A GLY 5.0 1.0 + - - -
458A TYR* 3.2 49.3 + - + -
474A THR* 5.7 2.8 - - - +
476A TYR* 3.4 30.9 + - - -
512A PRO* 3.1 29.0 - - + +
513A PHE* 3.8 23.7 - - + -
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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