Contacts of the helix formed by residues 56 - 63 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52I LEU* 5.6 0.5 - - - +
55I GLN* 3.2 52.6 + - + +
56I TYR* 5.3 5.2 - + - -
52J LEU* 3.7 25.8 - - + +
53J MET 3.8 6.5 - - - +
54J GLN 3.2 2.5 - - - +
55J GLN* 1.3 86.6 - - + +
57J GLU* 1.3 56.9 + - - +
58J ILE* 3.0 13.2 - - + +
59J TRP* 2.8 33.3 + - - +
60J ARG* 4.1 1.4 + - - +
192J PHE* 3.6 4.0 - - - -
197J LEU 3.1 17.2 + - - -
198J THR 4.0 1.6 - - - -
199J GLY* 3.9 23.1 - - - -
202J TYR* 3.3 46.9 - + + -
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Residues in contact with GLU 57 (chain J).
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* 4.7 19.1 - - + -
55J GLN 4.2 0.8 + - - -
56J TYR* 1.3 72.9 - - - +
58J ILE* 1.3 62.5 + - + +
59J TRP 3.2 1.4 + - - -
60J ARG* 2.9 71.4 + - - +
61J GLU* 3.4 11.4 + - - +
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Residues in contact with ILE 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J MET* 5.7 2.2 - - + +
56J TYR* 2.9 10.5 + - + -
57J GLU* 1.3 76.9 - - + +
59J TRP* 1.3 63.9 + - - +
61J GLU* 3.8 19.0 - - - +
62J LEU* 3.3 39.2 + - + +
63J PHE* 4.4 0.7 - - + -
199J GLY* 4.6 17.9 - - - +
202J TYR* 5.1 5.6 - - + +
203J ALA* 5.0 13.0 - - + +
206J CYS* 3.2 45.5 - - + -
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Residues in contact with TRP 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44J PHE* 3.7 30.7 - + - -
53J MET* 3.4 53.3 + - + +
54J GLN* 3.6 38.1 - - + +
56J TYR 2.8 15.9 + - - +
58J ILE* 1.3 70.8 - - - +
60J ARG* 1.3 62.3 + - + +
61J GLU 3.0 4.5 - - - -
63J PHE* 3.1 33.4 + + + -
64J SER* 3.0 42.6 + - - +
68J ALA* 4.1 26.2 + - + -
69J LEU 4.6 0.2 - - - -
70J ASN* 3.8 27.6 - - + -
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Residues in contact with ARG 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J TYR 4.1 1.0 + - - +
57J GLU* 2.9 50.6 + - - +
59J TRP* 1.3 80.2 - - + +
61J GLU* 1.3 69.3 + - - +
64J SER* 3.4 29.1 - - - +
65J PRO* 4.2 5.9 - - - +
360L LYS* 4.7 17.3 - - - +
380L GLU* 4.4 22.8 + - - +
381L HIS* 5.7 5.6 - - + -
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Residues in contact with GLU 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J GLU* 3.4 12.0 + - - +
58J ILE* 3.8 21.9 + - - +
59J TRP 3.0 1.0 - - - -
60J ARG* 1.3 94.5 - - - +
62J LEU* 1.3 75.2 + - + +
65J PRO* 4.4 8.5 - - - +
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Residues in contact with LEU 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58J ILE* 3.3 36.5 + - + +
59J TRP 3.4 0.2 + - - -
61J GLU* 1.3 103.2 - - + +
63J PHE* 1.3 75.8 + - + +
65J PRO* 3.6 9.2 - - - +
66J LEU* 3.2 20.1 - - - +
206J CYS* 4.1 8.3 - - + +
207J LYS* 4.7 3.8 - - - +
210J HIS* 3.3 50.8 + - + +
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Residues in contact with PHE 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42J VAL* 6.1 0.7 - - + -
44J PHE* 3.8 20.2 - + - -
53J MET* 4.1 8.5 - - + -
58J ILE* 4.4 2.0 - - + -
59J TRP* 3.1 45.3 + + + +
62J LEU* 1.3 97.8 - - + +
64J SER* 1.3 68.9 + - - +
65J PRO* 3.2 2.5 - - - -
66J LEU* 2.9 28.1 + - + +
68J ALA* 3.5 17.8 - - + +
206J CYS* 3.9 29.8 - - + -
209J LEU* 4.4 6.7 - - + -
210J HIS* 4.0 20.9 - + + -
213J ILE* 3.7 27.4 - - + -
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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