Contacts of the helix formed by residues 56 - 63 (chain I) in PDB entry 1VYH
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 TYR 56 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52I LEU* 3.6 26.3 - - + +
53I MET 3.4 4.9 + - - +
54I GLN 3.2 2.6 - - - +
55I GLN* 1.3 84.4 - - + +
57I GLU* 1.3 57.9 + - - +
58I ILE* 3.0 19.1 - - + -
59I TRP* 2.8 32.9 + - - +
60I ARG* 4.2 1.2 + - - +
192I PHE* 4.2 3.6 - - - -
197I LEU 3.2 24.9 + - - -
198I THR* 3.7 2.7 - - - -
199I GLY* 3.5 28.0 - - - -
202I TYR* 3.5 28.3 - + + -
52J LEU* 5.3 1.6 - - - +
55J GLN* 3.2 51.8 - - + +
56J TYR* 5.3 5.6 - + - -
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Residues in contact with GLU 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I GLN 4.2 0.8 + - - -
56I TYR* 1.3 73.3 - - - +
58I ILE* 1.3 61.2 + - + +
59I TRP 3.3 1.2 + - - -
60I ARG* 3.1 55.7 + - - +
61I GLU* 3.4 14.0 + - - +
57J GLU* 4.7 19.5 - - + -
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Residues in contact with ILE 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I MET* 5.4 2.7 - - + +
56I TYR* 3.8 21.5 - - + -
57I GLU* 1.3 73.3 - - + +
59I TRP* 1.3 64.7 + - - +
61I GLU* 3.8 16.7 - - - +
62I LEU* 3.2 39.3 + - + +
63I PHE* 4.9 1.1 - - + -
199I GLY* 4.7 9.6 - - - +
202I TYR* 4.6 12.6 - - + -
203I ALA* 4.0 22.2 - - + +
206I CYS* 3.4 35.0 - - + -
207I LYS* 4.9 1.1 - - + +
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Residues in contact with TRP 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I PHE* 3.3 42.4 - + - -
53I MET* 3.4 40.5 + - + +
54I GLN* 3.3 49.5 - - + +
56I TYR 2.8 10.6 + - - +
58I ILE* 1.3 76.4 - - - +
60I ARG* 1.3 59.2 - - + +
61I GLU 3.0 5.2 - - - -
63I PHE* 3.1 36.4 + + + -
64I SER* 3.0 43.8 + - - +
68I ALA* 4.2 24.3 + - + -
69I LEU 4.5 0.4 - - - -
70I ASN* 3.9 23.3 - - + -
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Residues in contact with ARG 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I TYR 4.2 0.4 + - - -
57I GLU* 3.1 45.4 + - - +
59I TRP* 1.3 80.0 - - + +
61I GLU* 1.3 68.3 + - - +
64I SER* 3.1 25.9 - - - +
65I PRO* 4.3 5.0 - - - +
360K LYS* 5.4 6.7 - - - +
380K GLU* 4.6 18.6 + - - +
381K HIS* 6.5 1.1 - - + -
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Residues in contact with GLU 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I GLU* 3.4 14.6 + - - +
58I ILE* 3.8 18.3 - - - +
59I TRP 3.0 0.6 - - - -
60I ARG* 1.3 93.7 + - - +
62I LEU* 1.3 73.2 + - + +
65I PRO* 4.1 9.8 - - - +
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Residues in contact with LEU 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I ILE* 3.2 43.0 + - + +
59I TRP 3.4 0.2 + - - -
61I GLU* 1.3 97.9 - - + +
63I PHE* 1.3 70.9 + - + +
65I PRO* 3.5 11.8 - - - +
66I LEU* 3.3 8.7 - - - +
206I CYS* 3.9 16.4 - - + +
207I LYS* 4.6 3.8 - - + +
210I HIS* 3.3 57.5 + - + +
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Residues in contact with PHE 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I PHE* 3.9 9.2 - + - -
53I MET* 3.4 23.8 - - + -
58I ILE* 5.2 1.3 - - + -
59I TRP* 3.1 46.2 + + + +
62I LEU* 1.3 85.7 - - + +
64I SER* 1.3 68.6 + - - +
65I PRO* 3.1 2.9 - - - -
66I LEU* 2.9 31.1 + - + +
68I ALA* 3.4 19.2 - - + +
206I CYS* 3.8 23.3 - - + -
209I LEU* 3.9 20.2 - - + -
210I HIS* 3.6 31.6 - + + -
213I ILE* 4.0 11.2 - - + -
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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