Contacts of the helix formed by residues 413 - 420 (chain A) in PDB entry 1YUC
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 TYR 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A HIS* 5.5 1.9 + - - -
394A GLN* 5.2 4.9 + - - +
401A GLY* 3.1 33.9 + - - +
402A SER* 3.3 26.7 + - - -
403A ILE* 3.4 19.6 - - + +
412A ASP* 1.3 74.1 + - - +
414A SER* 1.3 66.8 + - - +
416A ILE* 3.0 12.3 + - + +
417A ALA* 3.0 22.8 + - - +
428A MET* 3.7 36.8 - - + +
431A ALA* 5.4 0.7 - - - +
432A GLN* 3.2 46.9 + - + +
435A VAL* 5.5 4.5 - - - +
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Residues in contact with SER 414 (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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412A ASP* 2.9 23.4 + - - +
413A TYR* 1.3 78.3 - - - +
415A ILE* 1.3 69.3 + - - +
417A ALA* 3.4 8.1 + - - +
418A SER* 3.2 21.8 + - - -
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Residues in contact with ILE 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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411A VAL* 4.7 7.4 - - + -
412A ASP* 3.5 27.6 - - + +
413A TYR 3.1 0.6 - - - -
414A SER* 1.3 90.3 + - - +
416A ILE* 1.3 61.5 + - + +
418A SER* 3.1 9.0 + - - -
419A GLN* 2.9 57.1 + - - +
1001A EPH 4.3 10.8 - - + +
336B HIS* 5.0 3.8 - - + +
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Residues in contact with ILE 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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403A ILE* 3.8 19.5 - - + -
411A VAL* 3.4 26.5 - - + -
412A ASP 3.5 11.7 - - - +
413A TYR* 3.0 10.7 + - + +
415A ILE* 1.3 76.4 - - + +
417A ALA* 1.3 63.2 + - - +
420A ALA* 3.0 43.4 + - + +
424A LEU* 4.9 5.8 - - + -
425A ASN* 3.2 10.7 - - - +
428A MET* 4.1 22.9 - - + -
1001A EPH 3.2 39.5 - - + +
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Residues in contact with ALA 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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413A TYR 3.0 14.4 + - - +
414A SER* 3.8 8.5 - - - +
415A ILE 3.3 0.2 - - - -
416A ILE* 1.3 77.0 - - - +
418A SER* 1.3 58.4 + - - +
420A ALA 4.6 2.1 - - - +
425A ASN* 3.2 24.7 + - - +
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Residues in contact with SER 418 (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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414A SER 3.2 11.3 + - - -
415A ILE* 3.1 13.7 + - - -
416A ILE 3.1 0.2 - - - -
417A ALA* 1.3 81.5 - - - +
419A GLN* 1.3 67.6 + - - +
420A ALA 3.6 2.7 - - - -
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Residues in contact with GLN 419 (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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415A ILE* 2.9 41.9 + - - +
416A ILE 3.8 0.4 - - - -
418A SER* 1.3 85.4 + - - +
420A ALA* 1.3 59.3 + - - +
1001A EPH 3.2 28.9 - - - +
334B SER* 3.8 13.6 + - - +
335B LYS* 3.1 26.1 + - + +
336B HIS* 2.7 32.3 + - + -
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Residues in contact with ALA 420 (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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416A ILE* 3.0 27.6 + - + +
417A ALA 4.6 2.8 - - - +
418A SER 3.6 1.3 - - - -
419A GLN* 1.3 81.1 + - - +
421A GLY* 1.3 63.3 + - - +
424A LEU* 3.8 27.8 - - + -
425A ASN* 3.1 18.6 + - - +
1001A EPH 3.8 13.2 - - - +
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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