Contacts of the helix formed by residues 56 - 63 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52Q LEU* 3.9 18.5 - - + +
53Q MET 3.4 6.2 + - - +
54Q GLN 3.2 2.9 - - - +
55Q GLN* 1.3 86.5 - - + +
57Q GLU* 1.3 66.4 - - - +
58Q ILE* 3.0 15.3 - - + -
59Q TRP* 2.8 22.7 + - - +
60Q ARG* 4.1 1.4 + - - +
192Q PHE* 3.8 3.6 - - - -
197Q LEU 3.4 14.5 + - - -
198Q THR 3.8 2.7 - - - -
199Q GLY* 3.8 18.4 - - - -
202Q TYR* 3.3 41.7 - + + -
52R LEU* 5.6 0.6 - - + +
55R GLN* 2.8 64.8 + - + +
56R TYR* 4.8 8.5 - + - -
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Residues in contact with GLU 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Q GLN 4.2 0.4 + - - -
56Q TYR* 1.3 73.5 - - + +
58Q ILE* 1.3 64.5 + - + +
59Q TRP 3.2 1.0 + - - -
60Q ARG* 3.3 27.0 + - - +
61Q GLU* 3.4 15.0 + - - +
57R GLU* 3.8 37.8 - - + +
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Residues in contact with ILE 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53Q MET* 5.9 1.3 - - + -
56Q TYR* 4.2 16.6 - - + -
57Q GLU* 1.3 74.9 - - + +
59Q TRP* 1.3 64.2 + - - +
61Q GLU* 3.8 17.4 - - - +
62Q LEU* 3.1 41.9 + - + +
63Q PHE* 4.8 1.0 - - + -
199Q GLY* 4.5 16.6 - - - +
202Q TYR* 4.8 6.7 - - + -
203Q ALA* 4.1 19.3 - - + +
206Q CYS* 3.3 40.6 - - + -
207Q LYS 4.7 1.6 - - - +
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Residues in contact with TRP 59 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Q PHE* 4.1 24.0 - + - -
53Q MET* 3.4 40.9 + - + +
54Q GLN* 3.6 40.3 - - + +
56Q TYR 2.8 15.8 + - - +
58Q ILE* 1.3 79.0 - - - +
60Q ARG* 1.3 60.4 + - + +
61Q GLU 3.1 0.2 - - - -
63Q PHE* 3.1 44.6 + + + -
64Q SER* 3.0 42.6 + - - +
68Q ALA* 4.1 26.7 + - + -
69Q LEU 4.8 0.4 - - - -
70Q ASN* 3.6 37.9 - - + -
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Residues in contact with ARG 60 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Q TYR 4.1 1.4 + - - +
57Q GLU* 3.3 20.6 + - - +
59Q TRP* 1.3 80.9 - - + +
61Q GLU* 1.3 59.9 + - + +
64Q SER* 2.8 28.8 - - - +
65Q PRO* 4.0 6.4 - - - +
360S LYS* 4.7 11.7 - - - +
380S GLU* 2.9 37.9 + - - +
381S HIS* 5.0 14.4 - - + +
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Residues in contact with GLU 61 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57Q GLU* 3.4 14.4 + - - +
58Q ILE* 3.8 19.7 + - - +
59Q TRP 3.1 0.8 - - - -
60Q ARG* 1.3 82.2 - - + +
62Q LEU* 1.3 73.3 + - + +
65Q PRO* 4.5 8.3 - - - +
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Residues in contact with LEU 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58Q ILE* 3.1 39.1 + - + +
60Q ARG 3.6 0.2 - - - -
61Q GLU* 1.3 100.0 - - + +
63Q PHE* 1.3 70.7 + - + +
64Q SER 3.7 0.4 - - - -
65Q PRO* 3.9 7.2 - - - +
66Q LEU* 3.6 19.2 - - - +
206Q CYS* 4.1 12.6 - - + +
207Q LYS* 4.4 4.5 - - - +
210Q HIS* 3.4 58.2 + - + +
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Residues in contact with PHE 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42Q VAL* 6.2 0.4 - - + -
44Q PHE* 4.2 9.0 - + - -
53Q MET* 3.9 20.9 - - - -
58Q ILE* 5.1 1.1 - - + -
59Q TRP* 3.1 50.5 + + + +
62Q LEU* 1.3 82.1 - - + +
64Q SER* 1.3 69.0 + - - +
65Q PRO 3.3 1.8 - - - -
66Q LEU* 2.9 36.0 + - + +
68Q ALA* 3.4 17.3 - - + +
206Q CYS* 4.1 15.5 - - + -
209Q LEU* 3.6 21.5 - - + -
210Q HIS* 3.7 38.8 - + + -
213Q ILE* 3.7 15.0 - - + -
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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