Contacts of the helix formed by residues 460 - 470 (chain A) in PDB entry 3N51
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 460 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A SER* 1.3 72.7 - - - +
461A THR* 1.3 56.8 + - - +
463A LEU* 3.3 13.7 + - - +
464A ALA* 2.9 28.8 + - - +
477A TRP* 3.8 20.0 - - - -
481A LEU* 4.8 4.7 - - - +
490A GLY* 3.0 31.8 + - - -
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Residues in contact with THR 461 (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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459A SER* 3.8 10.3 - - - -
460A SER* 1.3 78.9 - - - +
462A GLU* 1.3 62.7 + - + +
464A ALA* 3.3 8.7 + - - +
465A THR* 3.2 26.8 + - - +
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Residues in contact with GLU 462 (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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450A PHE* 3.6 30.7 - - + +
457A LYS 4.4 2.6 - - - +
458A ILE* 3.3 21.6 - - + +
459A SER* 3.0 32.7 + - - +
461A THR* 1.3 76.9 - - + +
463A LEU* 1.3 60.9 + - - +
465A THR* 3.3 8.4 + - - -
466A ILE* 2.8 34.7 + - - +
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Residues in contact with LEU 463 (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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458A ILE* 3.8 16.3 - - + +
459A SER 2.9 16.7 + - - +
460A SER* 3.5 14.1 - - - +
462A GLU* 1.3 77.0 - - - +
464A ALA* 1.3 56.1 + - - +
466A ILE* 4.3 4.5 - - + -
467A PHE* 2.8 47.8 + - + +
477A TRP* 3.9 25.4 - - + -
481A LEU* 4.3 8.1 - - + -
491A GLU* 5.5 1.6 - - - +
492A VAL* 4.0 30.3 - - + -
497A PHE* 3.7 36.8 - - + -
500A MET* 4.5 4.9 - - - -
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Residues in contact with ALA 464 (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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253A ALA* 4.5 3.2 - - - +
460A SER 2.9 14.6 + - - +
461A THR* 3.5 13.2 - - - +
462A GLU 3.2 0.4 - - - -
463A LEU* 1.3 73.9 - - - +
465A THR* 1.3 57.3 + - - +
467A PHE* 3.9 0.3 - - - +
468A GLY* 2.9 26.2 + - - -
477A TRP* 3.7 21.0 + - + +
478A LYS* 6.1 0.9 - - - -
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Residues in contact with THR 465 (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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253A ALA* 4.9 3.5 - - - +
336A THR* 3.8 22.2 - - + +
450A PHE* 6.3 0.4 - - - -
461A THR* 3.2 15.5 + - - +
462A GLU* 3.5 10.2 - - - -
463A LEU 3.2 0.2 - - - -
464A ALA* 1.3 75.8 - - - +
466A ILE* 1.3 67.7 + - - +
468A GLY* 3.2 1.4 + - - -
469A VAL* 3.0 36.3 + - + +
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Residues in contact with ILE 466 (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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336A THR* 4.2 21.3 - - + +
339A LEU* 3.7 27.6 - - + -
340A ALA* 3.7 22.6 - - - +
343A ALA* 5.2 2.0 - - + -
450A PHE* 3.9 12.1 - - + -
458A ILE* 3.8 19.7 - - + -
462A GLU 2.8 32.6 + - - +
463A LEU* 3.8 8.7 - - + +
465A THR* 1.3 73.6 - - - +
467A PHE* 1.3 63.4 + - + +
469A VAL* 3.6 4.5 + - - +
470A SER* 3.0 31.1 + - - +
497A PHE* 4.3 21.5 - - + -
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Residues in contact with PHE 467 (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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343A ALA* 5.6 2.9 - - + -
347A MET* 5.8 0.7 - - + -
463A LEU* 2.8 43.9 + - + +
466A ILE* 1.3 76.5 - - + +
468A GLY* 1.3 59.3 + - - +
470A SER* 3.0 5.8 + - - -
471A ASP 2.9 23.7 + - - -
472A VAL* 2.9 37.4 + - + +
477A TRP* 3.4 39.5 - + + +
497A PHE* 3.8 21.8 - + - -
500A MET* 3.7 28.5 - - + -
501A LEU* 3.9 16.4 - - + -
504A LEU* 3.7 26.5 - - + -
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Residues in contact with GLY 468 (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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253A ALA 2.9 26.2 - - - -
254A ASN* 3.6 17.1 - - - +
255A GLU 4.5 1.7 + - - -
464A ALA 2.9 18.0 + - - -
465A THR 3.7 0.2 - - - -
467A PHE* 1.3 75.1 - - - +
469A VAL* 1.3 63.0 + - - +
471A ASP* 2.9 16.2 + - - -
472A VAL 4.6 2.9 + - - -
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Residues in contact with VAL 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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208A MET* 4.2 7.4 - - - +
212A ILE* 3.3 22.3 - - + +
213A GLY 5.3 1.8 - - - +
216A TYR* 3.8 20.9 - - + +
253A ALA 3.9 4.2 + - - +
254A ASN* 5.1 3.8 - - - +
255A GLU* 5.7 1.1 + - - +
258A ILE* 5.9 3.8 - - + -
336A THR* 4.7 5.4 - - + -
337A GLN* 4.1 27.1 - - - +
340A ALA* 3.6 20.0 - - + -
465A THR* 3.0 28.1 + - + +
466A ILE* 3.6 5.2 - - - +
468A GLY* 1.3 73.1 - - - +
470A SER* 1.3 57.8 + - - +
471A ASP 3.6 0.5 + - - -
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Residues in contact with SER 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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208A MET* 3.6 11.2 - - - +
212A ILE* 4.3 0.7 - - - -
340A ALA* 3.1 29.3 + - - +
343A ALA* 4.7 3.7 - - - +
344A LEU* 3.8 30.1 - - - +
347A MET* 5.9 0.2 - - - -
466A ILE* 3.0 19.3 + - - +
467A PHE* 3.0 13.9 + - - -
469A VAL* 1.3 74.5 - - - +
471A ASP* 1.3 69.8 + - - +
472A VAL* 3.2 10.1 + - - +
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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