Contacts of the helix formed by residues 47 - 54 (chain R) 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 ASP 47 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46R GLY* 1.3 72.3 - - - +
48R SER* 1.3 69.0 + - - +
49R MET* 3.1 23.7 + - - +
50R VAL* 2.8 14.4 + - - +
51R GLN* 3.0 9.9 + - - +
73R ILE 3.1 15.9 - - - +
76R ASP* 3.5 23.5 - - + +
101R TRP 3.2 14.3 + - - +
102R VAL* 4.3 9.8 - - + +
103R GLY 4.5 0.2 + - - -
104R THR* 3.1 24.5 + - - +
105R ASN* 2.9 23.8 + - - +
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Residues in contact with SER 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47R ASP* 1.3 74.1 + - - +
49R MET* 1.3 58.1 + - - -
51R GLN* 4.1 5.2 - - - -
52R LEU* 2.7 43.1 + - - +
73R ILE 3.3 4.8 + - - -
74R GLY* 3.8 17.5 - - - -
75R GLY 3.6 4.2 + - - -
105R ASN* 3.3 22.2 + - - -
196R HIS* 3.6 31.1 + - - -
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Residues in contact with MET 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R ASP* 3.1 20.4 + - - +
48R SER* 1.3 80.1 - - - +
50R VAL* 1.3 62.1 + - - +
53R MET* 3.6 2.6 + - - +
101R TRP* 3.5 39.2 - - + +
104R THR* 4.2 19.1 - - + -
140R LEU* 4.4 12.6 - - + -
195R LEU* 3.7 31.2 - - - +
196R HIS* 4.8 7.2 - - - -
197R LEU* 4.0 30.3 - - + +
202R TYR* 2.7 36.5 + - - +
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Residues in contact with VAL 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44R PHE* 3.5 45.8 - - + +
45R VAL 3.5 16.2 - - - +
46R GLY* 3.7 5.8 - - - -
47R ASP 2.8 7.4 + - - +
49R MET* 1.3 76.1 - - - +
51R GLN* 1.3 65.7 + - - +
53R MET* 3.3 16.8 + - - +
70R ASN* 3.3 27.6 + - - +
72R GLY* 4.2 3.8 - - - -
99R VAL* 5.4 1.3 - - + +
101R TRP* 3.4 44.2 - - + +
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Residues in contact with GLN 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192Q PHE* 3.9 37.5 + - + +
193Q ASP* 4.2 5.2 - - - +
27R GLN* 3.1 27.3 + - - +
30R ARG* 5.5 1.8 - - - +
31R PHE* 5.0 3.0 - - - -
47R ASP 3.0 8.1 + - - +
48R SER* 3.7 10.8 - - - +
50R VAL* 1.3 78.2 - - - +
52R LEU* 1.3 66.6 + - + +
53R MET 3.3 0.7 + - - -
54R GLN* 3.4 20.9 + - - +
55R GLN* 4.3 4.9 + - - +
70R ASN* 3.7 11.0 + - - +
72R GLY* 3.1 29.6 + - - +
73R ILE* 3.5 1.1 - - - +
74R GLY* 3.2 22.4 + - - +
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Residues in contact with LEU 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Q LEU* 5.0 17.7 - - + -
56Q TYR* 5.6 1.3 - - + +
192Q PHE* 4.9 11.4 - - + -
196Q HIS* 6.2 1.3 - - + +
48R SER* 2.7 22.3 + - - +
51R GLN* 1.3 78.6 - - + +
53R MET* 1.3 65.5 + - - +
55R GLN* 3.0 32.9 + - + +
56R TYR* 3.9 28.7 - - + +
192R PHE* 5.3 7.9 - - + -
196R HIS* 4.2 28.0 - - + +
197R LEU 5.3 0.4 - - - +
202R TYR* 3.2 21.5 - - + +
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Residues in contact with MET 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44R PHE* 4.4 15.0 - - + -
49R MET 3.6 8.0 + - - +
50R VAL* 3.3 15.0 + - - +
51R GLN 3.2 0.6 - - - -
52R LEU* 1.3 77.8 - - - +
54R GLN* 1.3 60.8 + - - +
55R GLN 3.3 0.5 + - - -
56R TYR* 3.4 14.3 + - - +
58R ILE* 5.7 1.8 - - + +
59R TRP* 3.4 26.6 + - + +
63R PHE* 3.9 22.7 - - + -
101R TRP* 4.1 20.0 - - + -
137R LEU* 5.8 0.2 - - + -
202R TYR* 3.7 38.3 + - + -
205R ILE* 4.2 9.2 - - + -
206R CYS* 3.8 19.3 - - - -
209R LEU* 4.4 11.2 - - + -
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Residues in contact with GLN 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192Q PHE* 5.7 2.6 - - - +
30R ARG* 4.7 14.5 + - - +
50R VAL 4.0 1.0 + - - -
51R GLN* 3.4 15.7 + - - +
52R LEU 3.1 0.6 - - - -
53R MET* 1.3 79.4 - - - +
55R GLN* 1.3 71.3 + - - +
56R TYR 3.4 2.3 + - - +
59R TRP* 3.4 53.3 - - + +
69R LEU* 5.7 4.6 - - - +
70R ASN* 3.6 34.3 + - + +
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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