Contacts of the helix formed by residues 491 - 502 (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 SER 491 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A GLU* 2.7 35.6 + - - -
489A LYS 4.2 0.2 + - - -
490A LEU* 1.3 75.3 - - - +
492A ALA* 1.3 64.7 + - - +
493A ILE* 3.6 11.8 - - - +
494A PHE* 3.2 14.6 + - - +
495A ARG* 3.0 20.6 + - - +
523A ILE* 5.2 1.1 - - - +
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Residues in contact with ALA 492 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490A LEU 3.8 0.8 + - - -
491A SER* 1.3 73.1 - - - +
493A ILE* 1.3 56.6 + - - +
495A ARG* 3.4 27.3 + - - +
496A ASP* 3.0 27.5 + - - +
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Residues in contact with ILE 493 (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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491A SER* 3.6 12.6 - - - +
492A ALA* 1.3 76.9 - - - +
494A PHE* 1.3 63.9 + - - +
496A ASP* 3.4 7.4 + - + +
497A PHE* 3.0 22.9 + - - +
518A HIS* 3.4 24.0 - - + +
519A GLN* 3.9 22.2 - - + +
520A PHE* 3.5 36.2 - - + +
523A ILE* 5.0 13.7 - - + -
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Residues in contact with PHE 494 (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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363A GLU* 3.5 29.2 - - + +
366A ILE* 3.7 33.2 - - + -
454A ALA* 4.5 4.9 - - + -
458A ILE* 3.5 35.7 - - + -
490A LEU* 3.8 14.4 - - + -
491A SER* 3.2 19.2 + - - +
493A ILE* 1.3 79.1 - - - +
495A ARG* 1.3 66.9 + - - +
497A PHE* 3.2 5.8 + + - +
498A LEU* 3.0 42.8 + - + +
520A PHE* 3.4 38.8 - + + -
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Residues in contact with ARG 495 (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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484A LEU* 5.7 3.6 - - + -
487A PRO* 3.4 32.0 + - + +
488A GLU* 4.4 7.1 + - - +
490A LEU* 2.7 47.8 + - + -
491A SER 3.0 12.3 + - - +
492A ALA* 3.6 32.1 + - - +
494A PHE* 1.3 77.6 - - - +
496A ASP* 1.3 55.5 + - - +
498A LEU* 3.4 10.4 + - + +
499A ASN* 2.9 40.9 + - - +
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Residues in contact with ASP 496 (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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492A ALA 3.0 15.9 + - - +
493A ILE* 3.6 13.7 - - + +
494A PHE 3.2 0.2 - - - -
495A ARG* 1.3 76.3 - - - +
497A PHE* 1.3 63.5 + - - +
499A ASN* 3.2 14.0 + - - +
500A ARG* 3.0 37.4 + - - +
518A HIS* 2.8 25.9 + - + +
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Residues in contact with PHE 497 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A CYS* 4.0 30.7 - - + -
374A LEU* 3.9 30.3 - - + -
450A LEU* 4.5 4.5 - - + -
454A ALA* 5.1 6.5 - - + -
493A ILE 3.0 13.9 + - - +
494A PHE* 3.5 13.9 - + - +
496A ASP* 1.3 77.8 - - - +
498A LEU* 1.3 66.3 + - + +
500A ARG* 3.2 5.6 + - - +
501A CYS* 3.2 42.9 + - - -
515A LEU* 4.2 16.2 - - + -
518A HIS* 3.6 31.8 + + + -
520A PHE* 3.6 24.9 - + + -
521A LEU* 4.2 11.0 - - + -
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Residues in contact with LEU 498 (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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451A GLY* 4.2 10.1 - - - +
454A ALA* 3.5 33.0 - - + -
455A ILE* 4.8 4.9 - - + +
458A ILE* 3.8 13.2 - - + -
484A LEU* 4.0 20.9 - - + -
490A LEU* 3.6 30.1 - - + -
494A PHE* 3.0 27.5 + - + +
495A ARG* 3.7 9.2 - - - +
497A PHE* 1.3 79.2 - - + +
499A ASN* 1.3 59.0 + - - +
501A CYS* 3.1 3.7 + - - -
502A LEU* 2.9 42.7 + - + +
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Residues in contact with ASN 499 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A ARG* 2.9 31.4 + - - +
496A ASP* 3.2 15.8 + - - +
498A LEU* 1.3 79.3 - - - +
500A ARG* 1.3 62.3 + - + +
502A LEU* 3.8 2.1 - - - +
503A ASP* 3.3 29.6 + - - +
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Residues in contact with ARG 500 (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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496A ASP* 3.0 32.6 + - - +
497A PHE 3.6 5.6 - - - +
498A LEU 3.2 0.2 - - - -
499A ASN* 1.3 77.9 - - - +
501A CYS* 1.3 63.0 + - - +
503A ASP* 4.1 4.3 + - - -
508A LYS* 2.7 44.2 + - - +
509A ARG* 3.3 8.5 + - - +
510A GLY* 3.0 45.7 + - - +
514A GLU* 4.0 12.5 + - - +
515A LEU* 3.8 17.6 - - + +
518A HIS* 4.4 11.8 - - + -
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Residues in contact with CYS 501 (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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447A ILE* 3.8 23.6 - - - +
448A TRP* 3.5 13.9 - - - -
450A LEU* 4.6 6.1 - - - -
451A GLY* 3.8 18.4 - - - -
497A PHE* 3.2 46.6 + - - +
498A LEU* 3.1 8.6 + - - +
500A ARG* 1.3 78.9 - - - +
502A LEU* 1.3 59.8 + - - +
503A ASP 3.5 0.4 - - - -
509A ARG* 3.4 21.0 - - - -
515A LEU* 3.9 17.7 - - - -
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Residues in contact with LEU 502 (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* 3.3 45.7 - - + +
451A GLY* 3.9 15.9 - - - +
452A ILE* 3.7 19.7 - - + -
455A ILE* 3.8 28.0 - - + -
481A THR* 2.7 37.1 - - - +
482A PRO* 4.1 17.3 - - + +
484A LEU* 6.5 0.9 - - + -
498A LEU* 2.9 28.8 + - + +
499A ASN* 3.8 3.8 - - - -
501A CYS* 1.3 80.2 - - - +
503A ASP* 1.3 54.1 + - - +
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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