Contacts of the helix formed by residues 492 - 503 (chain A) in PDB entry 3NYN
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 GLU 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A LYS* 3.7 18.0 + - - +
490A GLU* 3.9 16.2 - - + +
491A LEU* 1.3 79.4 - - - +
493A PRO* 1.3 67.8 - - + +
494A THR* 3.1 7.8 + - - +
495A ASP* 2.7 39.4 + - - +
496A GLN* 3.6 8.3 + - - +
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Residues in contact with PRO 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 LEU 4.8 0.2 - - - +
492A GLU* 1.3 89.7 - - + +
494A THR* 1.3 61.7 + - - +
496A GLN* 3.1 35.5 + - + +
497A ASP* 3.5 12.6 + - - +
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Residues in contact with THR 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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223A LYS* 5.9 1.1 - - - -
492A GLU* 2.9 7.0 + - - +
493A PRO* 1.3 80.1 - - - +
495A ASP* 1.3 66.6 + - - +
496A GLN 3.7 0.3 + - - -
497A ASP* 3.8 17.7 + - + +
498A PHE* 3.8 9.2 + - - +
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Residues in contact with ASP 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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223A LYS* 3.0 47.2 + - - +
228A GLU* 5.4 3.6 - - - +
491A LEU* 3.7 7.1 - - + +
492A GLU* 2.7 29.1 + - - +
494A THR* 1.3 77.3 - - - +
496A GLN* 1.3 59.5 + - + +
498A PHE* 3.1 10.8 + - + +
499A TYR* 2.9 56.4 + - + +
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Residues in contact with GLN 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 GLU 4.3 6.9 - - - +
493A PRO* 3.1 26.1 + - + +
495A ASP* 1.3 77.9 - - - +
497A ASP* 1.3 59.0 + - - +
499A TYR* 3.3 18.3 + - + +
500A GLN* 3.0 29.0 + - - +
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Residues in contact with ASP 497 (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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493A PRO 3.5 12.4 + - - +
494A THR* 3.9 13.3 - - - +
495A ASP 3.2 0.4 - - - -
496A GLN* 1.3 78.1 - - - +
498A PHE* 1.3 61.5 + - - +
500A GLN* 3.4 16.3 - - - +
501A LYS* 3.2 20.3 + - - +
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Residues in contact with PHE 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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222A ILE* 4.9 5.6 - - + -
228A GLU* 3.7 51.4 - - + -
231A ALA* 4.4 9.4 - - + -
232A LEU* 4.1 20.4 - - + -
259A LEU* 3.7 30.3 - - + -
494A THR 3.8 6.6 + - - +
495A ASP* 3.1 13.0 + - + +
497A ASP* 1.3 78.2 - - - +
499A TYR* 1.3 85.5 + + - +
500A GLN 3.1 0.2 - - - -
501A LYS* 2.9 28.2 + - + +
502A PHE* 2.9 18.3 + - + +
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Residues in contact with TYR 499 (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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219A LYS* 3.5 56.3 + - + +
222A ILE* 5.7 1.8 - - + -
223A LYS* 5.8 1.0 - - - +
254A GLU* 3.8 24.7 - - - +
259A LEU* 3.6 21.5 - - + +
491A LEU* 4.1 15.0 - - + +
495A ASP* 2.9 47.9 + - + +
496A GLN* 3.3 15.7 + - + +
498A PHE* 1.3 99.0 - + - +
500A GLN* 1.3 57.2 + - - +
502A PHE* 3.7 4.2 - - - +
503A ALA* 2.9 35.0 + - - +
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Residues in contact with GLN 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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254A GLU* 5.5 2.0 - - - -
496A GLN 3.0 12.0 + - - +
497A ASP* 3.4 19.2 - - - +
498A PHE 3.1 0.2 - - - -
499A TYR* 1.3 78.4 - - - +
501A LYS* 1.3 61.9 + - - +
502A PHE 3.3 0.2 + - - -
503A ALA* 3.8 14.6 + - - +
504A THR* 5.4 0.5 - - - -
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Residues in contact with LYS 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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232A LEU* 4.1 36.3 - - + +
235A LYS* 4.0 12.0 + - - -
236A GLN* 5.4 4.9 - - - +
497A ASP 3.2 8.9 + - - +
498A PHE* 2.9 20.0 + - + +
500A GLN* 1.3 78.8 - - - +
502A PHE* 1.3 59.7 + - - +
504A THR* 4.1 3.5 + - - -
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Residues in contact with PHE 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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217A LEU* 5.1 4.3 - - + -
231A ALA* 3.9 19.5 - - + -
232A LEU* 4.4 14.6 - - - -
235A LYS* 3.4 37.9 - - + +
252A ALA* 3.8 7.1 - - + +
253A TYR 3.9 6.3 - - - -
259A LEU* 3.6 48.9 - - + -
260A CYS 3.7 17.0 - - - -
261A LEU* 3.3 36.1 - - + -
498A PHE* 2.9 18.5 + + + +
499A TYR* 3.2 9.6 + - - +
501A LYS* 1.3 76.9 - - - +
503A ALA* 1.3 60.1 + - - +
504A THR 2.7 16.4 + - - -
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Residues in contact with ALA 503 (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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252A ALA 3.5 13.9 - - - +
253A TYR* 4.1 17.9 - - - -
254A GLU* 4.2 20.6 - - + +
499A TYR 2.9 19.7 + - - +
500A GLN* 3.8 9.8 + - - +
501A LYS 3.7 0.4 - - - -
502A PHE* 1.3 74.0 - - + +
504A THR* 1.3 60.9 - - - +
505A GLY 3.8 0.2 + - - -
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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