Contacts of the helix formed by residues 488 - 496 (chain A) in PDB entry 1R1H
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 488 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424A ARG* 4.9 1.1 - - - -
484A ASP* 2.8 28.7 + - - +
486A VAL 3.5 1.0 - - - -
487A SER* 1.3 82.0 - - - +
489A ASP* 1.3 62.6 + - - +
490A ASN* 3.4 11.4 + - - +
491A LYS* 3.0 40.4 + - + +
492A LEU* 3.3 17.7 + - - +
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Residues in contact with ASP 489 (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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129A ILE* 3.8 25.9 - - + +
424A ARG* 2.9 38.3 + - - +
486A VAL 3.9 5.5 - - - +
487A SER 3.9 3.1 + - - -
488A ASN* 1.3 71.7 + - - +
490A ASN* 1.3 64.9 + - - +
492A LEU* 3.2 3.0 + - - +
493A ASN* 2.9 35.4 + - - +
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Residues in contact with ASN 490 (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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488A ASN* 3.4 8.0 + - - +
489A ASP* 1.3 78.8 - - - +
491A LYS* 1.3 63.9 + - - +
493A ASN* 3.6 9.5 + - - +
494A ASN* 3.0 38.3 + - - +
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Residues in contact with LYS 491 (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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420A ASN* 6.4 0.2 - - - +
484A ASP* 2.1 46.6 + - + +
485A ILE* 6.6 0.2 - - - -
488A ASN* 3.0 30.6 + - + +
490A ASN* 1.3 75.6 - - - +
492A LEU* 1.3 57.6 + - - +
494A ASN* 3.3 8.0 + - - +
495A GLU* 3.1 26.7 + - - +
532A ASP* 5.3 12.7 + - - +
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Residues in contact with LEU 492 (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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129A ILE* 4.6 4.3 - - + -
131A ALA* 2.4 43.5 - - + -
132A VAL* 5.9 0.4 - - + -
420A ASN* 3.6 33.9 - - + +
421A ALA* 3.9 12.8 - - + +
424A ARG* 4.8 7.6 - - - +
485A ILE* 4.6 22.4 - - + +
488A ASN 3.3 9.0 + - - +
489A ASP* 3.2 10.3 + - - +
491A LYS* 1.3 77.1 - - - +
493A ASN* 1.3 66.0 + - - +
495A GLU* 3.2 17.0 + - - +
496A TYR* 3.3 24.9 - - + -
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Residues in contact with ASN 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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129A ILE* 3.7 16.4 - - - +
130A VAL* 3.6 18.7 + - + +
131A ALA* 3.0 34.1 + - - +
134A LYS* 5.3 0.7 + - - -
489A ASP* 2.9 27.4 + - - +
490A ASN* 3.8 11.3 - - - +
492A LEU* 1.3 76.5 - - - +
494A ASN* 1.3 60.2 + - - +
496A TYR* 3.0 20.8 + - - +
497A LEU* 3.1 12.5 + - + +
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Residues in contact with ASN 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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490A ASN* 3.0 33.9 + - - +
491A LYS* 3.3 7.2 + - - +
493A ASN* 1.3 80.0 - - - +
495A GLU* 1.3 62.1 - - - +
496A TYR 3.2 0.5 + - - -
497A LEU* 3.4 36.6 + - + +
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Residues in contact with GLU 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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419A GLU* 5.3 4.7 - - - +
420A ASN* 2.9 37.9 + - - +
491A LYS 3.1 11.6 + - - +
492A LEU* 3.4 16.3 - - - +
493A ASN 3.1 0.4 - - - -
494A ASN* 1.3 78.1 - - - +
496A TYR* 1.3 85.6 + - + +
497A LEU 3.9 0.3 + - - -
516A PHE* 3.7 11.4 - - - -
520A LYS* 3.7 28.5 + - - +
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Residues in contact with TYR 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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131A ALA* 3.8 6.3 - - + -
134A LYS* 2.7 39.6 + - + -
417A ASN 4.1 5.4 - - - -
418A MET* 3.4 57.1 - - + -
419A GLU 3.8 0.2 + - - -
420A ASN* 3.4 10.2 + - - +
421A ALA* 3.2 21.5 + - + -
492A LEU* 3.3 47.1 - - + -
493A ASN 3.0 6.6 + - - +
495A GLU* 1.3 101.9 + - + +
497A LEU* 1.3 57.8 + - - +
498A GLU 3.2 2.9 - - - -
499A LEU* 2.9 33.7 + - + +
501A TYR* 6.4 0.2 - - + -
516A PHE* 5.6 2.2 - + - -
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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