Contacts of the helix formed by residues 491 - 501 (chain N) in PDB entry 6AH0
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 ILE 491 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480N THR* 4.9 7.6 - - - +
484N GLU* 5.6 7.0 - - - +
490N ALA* 1.3 75.7 - - - +
492N THR* 1.3 68.0 + - - +
494N LEU* 3.6 1.3 + - - +
495N ARG* 3.4 15.8 + - - -
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Residues in contact with THR 492 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481N GLN* 4.8 21.2 + - - +
484N GLU* 5.5 3.9 - - - +
490N ALA* 3.4 2.2 - - - +
491N ILE* 1.3 79.8 - - - +
493N SER* 1.3 62.5 + - - +
495N ARG* 3.1 8.8 + - - -
496N ALA* 3.3 10.9 + - - -
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Residues in contact with SER 493 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490N ALA* 4.1 4.2 + - - +
492N THR* 1.3 72.5 - - - +
494N LEU* 1.3 60.8 + - - +
495N ARG 3.4 0.2 - - - -
496N ALA* 4.3 2.0 - - - +
497N ASN* 4.0 13.5 + - - -
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Residues in contact with LEU 494 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490N ALA 3.5 16.2 + - - -
491N ILE* 3.6 1.5 + - - +
492N THR 3.2 1.0 - - - -
493N SER* 1.3 80.6 - - - +
495N ARG* 1.3 59.5 + - - +
498N GLY* 3.7 15.4 + - - -
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Residues in contact with ARG 495 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477N ASN* 4.2 8.8 - - - -
480N THR* 5.0 11.4 - - - +
491N ILE 3.4 9.4 + - - -
492N THR 3.1 6.6 + - - -
494N LEU* 1.3 75.1 - - - +
496N ALA* 1.3 59.7 + - - +
498N GLY* 3.4 1.5 + - - -
499N VAL* 2.9 27.9 + - - -
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Residues in contact with ALA 496 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477N ASN* 4.0 22.6 + - - +
492N THR 3.3 12.2 + - - -
493N SER* 4.1 2.0 + - - +
494N LEU 3.5 0.2 - - - -
495N ARG* 1.3 76.1 - - - +
497N ASN* 1.3 61.8 + - - +
499N VAL* 3.2 2.6 + - - -
500N GLU* 3.0 19.9 + - - -
523N GLN* 6.0 0.2 - - - -
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Residues in contact with ASN 497 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493N SER 4.0 11.9 + - - -
495N ARG 3.5 0.2 - - - -
496N ALA* 1.3 74.4 - - - +
498N GLY* 1.3 53.5 + - - +
500N GLU* 3.1 2.4 + - - +
501N ILE* 2.7 35.9 + - - -
523N GLN* 4.8 18.2 - - - +
526N MET* 4.4 16.4 - - - +
527N ARG 4.0 10.2 + - - +
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Residues in contact with GLY 498 (chain N).
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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494N LEU 3.7 13.0 + - - -
495N ARG* 3.4 5.3 + - - -
496N ALA 3.2 0.6 - - - -
497N ASN* 1.3 76.4 - - - +
499N VAL* 1.3 59.4 + - - +
501N ILE* 3.8 7.2 + - - -
526N MET* 5.0 4.6 - - - +
530N ILE* 6.0 3.6 - - - -
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Residues in contact with VAL 499 (chain N).
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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475N GLU 5.0 7.4 - - - +
476N ALA* 4.8 4.4 - - - -
477N ASN* 4.5 17.0 - - - +
495N ARG 2.9 15.9 + - - -
496N ALA 3.2 4.0 + - - -
498N GLY* 1.3 77.4 - - - +
500N GLU* 1.3 57.6 + - - +
501N ILE 3.7 0.3 + - - -
502N ASN 4.6 2.6 + - - -
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Residues in contact with GLU 500 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477N ASN 5.2 0.8 - - - +
496N ALA 3.0 13.6 + - - -
497N ASN* 3.5 3.1 - - - +
499N VAL* 1.3 73.1 - - - +
501N ILE* 1.3 64.5 + - - +
502N ASN 3.0 5.0 + - - -
503N ARG* 3.3 13.9 + - - +
504N GLU 4.6 2.9 + - - -
527N ARG* 5.0 1.6 - - - -
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Residues in contact with ILE 501 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497N ASN 2.7 14.2 + - - -
498N GLY* 3.8 6.0 + - - -
499N VAL 3.4 3.0 - - - -
500N GLU* 1.3 72.7 - - - +
502N ASN* 1.3 60.2 + - - +
504N GLU 4.7 3.6 + - - -
526N MET 5.0 0.9 - - - -
527N ARG* 3.4 38.6 - - - +
530N ILE* 5.2 6.5 - - - +
531N GLY* 4.6 8.2 + - - -
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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