Contacts of the strand formed by residues 412 - 417 (chain A) in PDB entry 1YY9
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 PHE 412 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A PHE* 3.4 5.5 - - - +
407A LYS* 3.3 6.1 - - - +
408A GLN* 2.9 54.8 + - + +
409A HIS* 4.6 1.6 - + - -
411A GLN* 1.3 101.3 - - + +
413A SER* 1.3 59.7 + - - +
414A LEU 4.5 0.9 - - - +
415A ALA* 4.4 10.3 - - + -
436A ASP* 3.2 23.1 - - + +
437A VAL 5.5 0.2 - - - -
438A ILE* 3.6 35.9 - - + -
465A LYS* 5.8 5.8 - - + -
100D THR* 5.6 3.4 - - + -
101D TYR* 3.8 36.6 - + + -
102D TYR* 3.8 20.6 - + - -
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Residues in contact with SER 413 (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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380A PHE* 3.2 10.8 - - - -
381A LEU 2.9 24.0 + - - -
402A ILE* 3.3 10.8 - - - +
404A GLY* 3.8 19.5 - - - -
407A LYS* 4.7 1.3 - - - -
411A GLN 3.6 0.2 + - - -
412A PHE* 1.3 72.9 - - - +
414A LEU* 1.3 59.0 + - - +
415A ALA 4.4 0.2 - - - -
432A ILE* 3.1 20.1 - - - +
434A ASP 2.7 29.2 + - - -
435A GLY* 3.5 9.7 - - - -
436A ASP 3.0 10.0 + - - +
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Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LEU* 3.6 31.6 - - + +
383A ILE* 5.4 0.7 - - + -
393A LEU* 5.7 0.2 - - + -
402A ILE* 4.0 16.4 - - + -
412A PHE* 4.7 0.7 - - - -
413A SER* 1.3 81.1 + - - +
415A ALA* 1.3 64.0 + - - +
416A VAL* 3.7 24.9 - - + -
424A LEU* 5.9 0.4 - - + -
426A LEU* 4.1 24.9 - - + -
429A LEU* 4.5 1.1 - - + -
432A ILE* 4.2 8.1 - - + -
436A ASP 3.5 3.5 + - - +
437A VAL* 3.4 17.6 - - + -
438A ILE* 3.0 24.9 + - - +
439A ILE* 5.3 1.3 - - + -
453A TRP* 4.2 26.9 - - + -
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Residues in contact with ALA 415 (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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380A PHE* 6.3 0.7 - - + -
381A LEU 3.0 9.9 + - - +
382A LEU* 3.6 24.7 - - + +
383A ILE 2.8 29.6 + - - +
408A GLN* 4.4 1.8 - - + +
412A PHE* 4.4 9.2 - - + -
413A SER 4.4 0.2 - - - -
414A LEU* 1.3 73.0 - - - +
416A VAL* 1.3 64.1 + - - +
417A VAL* 4.2 1.8 - - + -
438A ILE* 3.4 22.0 - - + -
102D TYR* 4.2 11.4 - - + -
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Residues in contact with VAL 416 (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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383A ILE* 3.5 8.1 - - + +
393A LEU* 4.4 17.3 - - + -
414A LEU* 3.7 25.6 - - + -
415A ALA* 1.3 76.4 - - - +
417A VAL* 1.3 63.9 + - - +
419A LEU* 3.6 24.9 - - + -
421A ILE* 4.2 15.3 - - + -
424A LEU* 4.5 9.0 - - + -
438A ILE 2.8 8.5 + - - -
439A ILE* 3.4 17.3 - - + -
440A SER 3.0 23.9 + - - -
442A ASN* 3.1 15.6 + - - +
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Residues in contact with VAL 417 (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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383A ILE 3.1 10.9 + - - +
384A GLN* 3.6 27.8 - - + +
415A ALA* 4.7 3.1 - - + -
416A VAL* 1.3 85.2 - - - +
418A SER* 1.3 81.5 + - - +
419A LEU* 3.5 5.3 - - - +
438A ILE* 4.7 3.1 - - + +
440A SER* 3.3 13.7 - - - +
52D TRP* 4.4 21.1 - - + -
56D ASN* 4.7 0.9 + - - +
102D TYR* 3.5 55.0 - - + -
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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