Contacts of the helix formed by residues 469 - 477 (chain A) in PDB entry 1VF9
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 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465A TYR* 3.8 34.8 - - + +
466A GLY 3.6 1.0 + - - -
467A GLU 3.5 4.8 - - - +
468A GLY* 1.3 78.8 - - - +
470A TRP* 1.3 62.8 + - - +
471A ALA* 3.5 2.5 - - - +
472A ALA* 3.9 15.6 + - + +
473A ILE* 3.3 26.6 + - - +
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Residues in contact with TRP 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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458A VAL* 4.3 2.9 - - + -
462A VAL* 3.6 27.8 - - + -
467A GLU* 4.3 17.7 - - + -
468A GLY* 3.3 26.3 + - - +
469A ASN* 1.3 72.0 - - - +
471A ALA* 1.3 65.3 + - - +
472A ALA 3.1 1.8 - - - -
473A ILE* 3.2 21.3 + - + +
474A SER* 3.0 22.9 + - - -
484A ALA* 3.1 32.8 - - + +
487A ILE* 3.7 28.7 - - + +
488A LYS* 3.5 40.7 - - + +
491A TRP* 3.6 40.4 - + + -
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Residues in contact with ALA 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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469A ASN* 3.5 0.9 - - - -
470A TRP* 1.3 80.8 - - - +
472A ALA* 1.3 60.4 + - - +
474A SER* 3.4 4.8 + - - -
475A LYS* 2.9 39.0 + - + +
483A THR 5.6 0.2 - - - -
484A ALA* 3.4 14.3 - - + +
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Residues in contact with ALA 472 (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 TYR* 3.4 37.9 + - + -
469A ASN* 3.9 21.1 + - + +
470A TRP 3.1 0.8 - - - -
471A ALA* 1.3 79.6 - - - +
473A ILE* 1.3 57.9 + - - +
475A LYS* 3.3 5.0 + - - +
476A ASN* 2.9 33.2 + - - +
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Residues in contact with ILE 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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457A TRP 4.2 3.6 - - - +
458A VAL* 4.7 4.7 - - - +
461A GLY* 3.1 45.3 - - - +
462A VAL* 3.9 2.0 - - + +
465A TYR* 4.0 9.6 - - + -
466A GLY 5.1 1.8 - - - +
469A ASN 3.3 19.7 - - - +
470A TRP* 3.2 33.1 + - + +
472A ALA* 1.3 76.4 - - - +
474A SER* 1.3 58.4 + - - +
477A TYR* 2.8 55.5 + - + +
479A PHE* 3.8 19.3 - - + -
487A ILE* 5.1 4.9 - - + -
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Residues in contact with SER 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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470A TRP 3.0 13.9 + - - -
471A ALA* 3.8 6.7 + - - -
473A ILE* 1.3 78.2 - - - +
475A LYS* 1.3 65.5 + - - +
477A TYR 3.4 11.8 - - - +
479A PHE* 3.7 26.2 - - - +
480A VAL 5.0 2.6 + - - -
483A THR* 3.3 39.9 + - - -
487A ILE* 3.9 5.6 - - - +
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Residues in contact with LYS 475 (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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471A ALA* 2.9 26.2 + - - +
472A ALA* 3.8 4.9 - - - +
474A SER* 1.3 84.2 - - - +
476A ASN* 1.3 61.6 + - - +
477A TYR 4.4 1.6 - - - +
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Residues in contact with ASN 476 (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 TYR* 3.5 22.0 + - - +
472A ALA 2.9 17.7 + - - +
475A LYS* 1.3 80.5 - - - +
477A TYR* 1.3 78.1 + - + +
478A PRO* 4.6 0.7 - - - +
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Residues in contact with TYR 477 (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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457A TRP* 3.5 38.4 - + + -
460A ALA* 3.1 32.2 + - + +
461A GLY* 3.5 9.0 - - - -
464A LYS* 4.0 13.2 - - - +
465A TYR* 4.3 8.0 - + - -
473A ILE* 2.8 39.0 + - + +
474A SER 3.4 11.8 - - - +
475A LYS 4.4 1.6 - - - +
476A ASN* 1.3 100.8 - - + +
478A PRO* 1.3 64.2 - - + +
479A PHE* 2.7 32.7 + - + +
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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