Contacts of the helix formed by residues 466 - 474 (chain A) in PDB entry 2V9V
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 ARG 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A LEU 3.2 1.0 + - - -
465A ALA* 1.3 71.7 - - - +
467A GLU* 1.3 58.1 + - - +
470A ARG* 3.0 15.1 + - - +
482A TYR* 2.7 32.5 + - + +
483A GLN* 4.1 25.7 + - - +
486A LEU* 3.8 29.8 - - + +
487A GLU* 5.1 3.0 + - - +
497A LEU* 3.9 25.3 - - - +
498A ALA 2.9 37.6 + - - -
499A ALA* 3.5 19.3 + - - +
500A ASN* 2.9 18.9 + - - +
501A THR 3.7 14.8 - - - +
502A VAL* 4.1 7.0 - - + +
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Residues in contact with GLU 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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465A ALA* 3.2 5.2 - - + +
466A ARG* 1.3 79.0 - - - +
468A GLU* 1.3 58.5 + - - +
470A ARG* 2.7 49.1 + - - +
471A SER* 3.0 29.4 + - - -
482A TYR* 5.7 0.2 - - - -
500A ASN 4.8 0.2 + - - -
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Residues in contact with GLU 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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464A LEU* 3.8 16.2 - - + -
465A ALA* 3.1 23.3 + - + +
467A GLU* 1.3 75.9 - - - +
469A LEU* 1.3 65.3 + - - +
471A SER* 2.9 24.7 + - - -
472A ARG* 3.0 49.4 + - - +
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Residues in contact with LEU 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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447A VAL* 4.2 34.3 - - + -
450A ALA* 4.5 8.7 - - + -
451A LEU* 5.1 2.7 - - + -
464A LEU* 4.0 23.3 - - + +
465A ALA 3.0 13.4 + - - +
466A ARG 3.8 0.2 - - - +
468A GLU* 1.3 77.0 - - - +
470A ARG* 1.3 61.9 + - - +
472A ARG* 3.2 6.1 + - + +
473A TYR* 3.2 45.0 + - + -
474A PHE* 3.6 10.2 - - + -
482A TYR* 3.4 18.8 - - + +
486A LEU* 4.3 10.3 - - + -
502A VAL* 4.0 21.3 - - + -
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Residues in contact with ARG 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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466A ARG 3.0 17.2 + - - +
467A GLU* 2.7 45.7 + - - +
468A GLU 3.2 0.2 - - - -
469A LEU* 1.3 77.4 - - - +
471A SER* 1.3 57.1 + - - +
474A PHE* 2.8 39.5 + - - +
475A SER* 3.1 18.7 + - - +
477A LEU 4.3 15.6 + - - -
479A ALA* 4.4 22.1 - - - +
482A TYR* 3.4 45.9 + - + -
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Residues in contact with SER 471 (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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467A GLU* 3.0 16.2 + - - -
468A GLU* 2.9 28.1 + - - -
470A ARG* 1.3 76.5 - - - +
472A ARG* 1.3 62.6 + - - +
475A SER* 4.2 18.8 + - - -
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Residues in contact with ARG 472 (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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450A ALA* 4.1 23.0 + - - +
454A PHE* 5.1 7.5 - - - +
464A LEU* 3.9 27.2 - - - +
468A GLU* 3.0 48.1 + - - +
469A LEU* 3.2 8.7 + - - +
471A SER* 1.3 80.2 + - - +
473A TYR* 1.3 95.2 + - + +
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Residues in contact with TYR 473 (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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443A TRP* 4.4 12.2 + - + -
446A ALA* 3.9 42.7 + - + -
447A VAL 4.9 0.2 - - - -
450A ALA* 4.1 18.2 - - + +
469A LEU* 3.2 18.4 + - + -
472A ARG* 1.3 110.3 + - + +
474A PHE* 1.3 83.6 + + + +
475A SER 3.8 1.8 - - - -
1515A CL 3.7 12.3 - - - +
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Residues in contact with PHE 474 (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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443A TRP* 3.5 40.6 - + + -
447A VAL* 3.6 33.0 - - + -
469A LEU* 3.6 15.9 - - + -
470A ARG* 2.8 22.4 + - + +
473A TYR* 1.3 88.3 - - + +
475A SER* 1.3 65.2 + - - +
476A ARG 3.2 2.9 - - - -
477A LEU* 3.0 47.4 + - + +
482A TYR* 3.5 38.6 - + + -
485A LEU* 4.2 10.3 - - + -
489A TRP* 4.3 7.4 - + - -
1515A CL 3.7 4.3 - - - -
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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