Contacts of the helix formed by residues 468 - 480 (chain A) in PDB entry 1YHV
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 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466A ASN 4.3 0.4 + - - -
467A GLU* 1.3 73.8 - - - +
469A PRO* 1.3 77.5 - - - +
470A LEU* 2.7 51.8 + - - +
471A ARG* 2.8 38.1 + - + +
472A ALA* 2.9 10.2 + - - +
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Residues in contact with PRO 469 (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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428A PRO* 3.9 24.5 - - + -
429A TYR* 3.4 28.7 - - + +
467A GLU 3.3 0.6 - - - -
468A ASN* 1.3 94.8 - - - +
470A LEU* 1.3 68.2 + - + +
472A ALA* 3.1 13.2 + - + +
473A LEU* 3.2 21.9 + - - +
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Residues in contact with LEU 470 (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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468A ASN* 2.7 26.2 + - - +
469A PRO* 1.3 84.0 - - + +
471A ARG* 1.3 58.8 + - - +
473A LEU* 3.7 10.4 + - + +
474A TYR* 3.7 15.9 + - - +
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Residues in contact with ARG 471 (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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467A GLU* 3.3 28.5 + - + +
468A ASN* 2.8 27.9 + - + +
470A LEU* 1.3 78.0 - - - +
472A ALA* 1.3 66.4 + - - +
474A TYR* 3.2 12.9 + - + +
475A LEU* 3.0 35.4 + - + +
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Residues in contact with ALA 472 (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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428A PRO* 5.1 3.1 - - + -
429A TYR* 3.7 36.1 - - + -
464A TYR* 4.1 17.7 - - + +
467A GLU* 4.5 1.3 - - + +
468A ASN 2.9 7.8 + - - +
469A PRO* 3.1 9.8 + - + +
471A ARG* 1.3 76.9 - - - +
473A LEU* 1.3 50.5 + - - +
475A LEU* 3.0 9.3 + - - +
476A ILE* 2.7 45.3 + - + +
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Residues in contact with LEU 473 (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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424A MET* 3.8 11.4 - - + -
428A PRO* 3.6 33.2 - - + +
431A MET* 3.8 24.7 - - + -
436A VAL* 2.8 40.5 - - + +
469A PRO 3.2 24.4 + - - +
470A LEU* 4.0 10.3 - - + +
472A ALA* 1.3 77.8 - - - +
474A TYR* 1.3 57.7 + - - +
476A ILE* 3.3 9.3 + - + +
477A ALA* 2.9 31.1 + - - +
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Residues in contact with TYR 474 (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 VAL* 6.0 1.1 - - - -
470A LEU 3.7 9.4 + - - +
471A ARG* 3.2 16.2 + - + +
473A LEU* 1.3 78.0 - - - +
475A LEU* 1.3 74.0 + - + +
477A ALA* 3.3 4.8 + - - +
478A THR* 2.8 69.0 + - + +
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Residues in contact with LEU 475 (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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464A TYR* 3.9 35.4 - - + -
467A GLU* 4.4 14.6 - - + +
471A ARG* 3.0 34.3 + - + +
472A ALA* 3.0 7.2 + - - +
474A TYR* 1.3 92.2 - - + +
476A ILE* 1.3 58.6 + - - +
478A THR* 3.8 4.9 - - - +
479A ASN* 2.6 54.3 + - - +
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Residues in contact with ILE 476 (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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428A PRO 3.1 28.7 - - - +
429A TYR* 4.1 14.8 - - - +
431A MET* 3.5 25.4 - - + +
432A ALA 4.5 0.2 - - - -
433A PRO* 3.9 24.9 - - + +
448A TRP* 4.3 11.2 - - + +
464A TYR* 3.8 23.8 - - + -
472A ALA* 2.7 29.8 + - + +
473A LEU* 3.6 9.0 - - + +
475A LEU* 1.3 70.9 - - - +
477A ALA* 1.3 59.7 + - - +
480A GLY* 3.0 31.3 + - - +
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Residues in contact with ALA 477 (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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433A PRO* 4.4 6.1 - - + +
436A VAL* 4.2 17.0 - - + -
437A THR* 3.4 36.0 - - + +
473A LEU 2.9 18.1 + - - +
474A TYR* 3.7 5.4 - - + +
476A ILE* 1.3 79.1 - - - +
478A THR* 1.3 61.6 + - + +
480A GLY 4.6 1.7 + - - -
504A MET* 4.7 8.1 - - - +
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Residues in contact with THR 478 (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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474A TYR* 2.8 67.5 + - + +
475A LEU* 3.6 9.5 + - - +
477A ALA* 1.3 77.0 - - + +
479A ASN* 1.3 71.1 + - - +
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Residues in contact with ASN 479 (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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464A TYR* 3.1 30.8 + - - +
475A LEU* 2.6 42.3 + - - +
478A THR* 1.3 82.5 + - - +
480A GLY* 1.3 62.5 + - - +
481A THR* 3.6 8.6 + - - +
482A PRO* 6.3 0.4 - - + -
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Residues in contact with GLY 480 (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 TRP* 3.8 8.2 - - - -
464A TYR* 4.8 2.9 + - - -
476A ILE* 3.0 17.2 + - - +
478A THR 3.6 1.4 - - - -
479A ASN* 1.3 78.6 - - - +
481A THR* 1.3 66.2 + - - -
482A PRO* 3.2 10.2 - - - +
504A MET* 3.1 36.1 - - - +
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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