Contacts of the helix formed by residues 92 - 102 (chain W) in PDB entry 1VQ4
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 92 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81W ASP* 2.8 27.4 - - + +
84W VAL* 3.8 14.2 - - - +
90W TYR* 3.7 1.1 - - - +
91W ASP* 1.3 90.1 - - - +
93W ILE* 1.3 55.7 + - - +
94W SER* 3.8 15.4 + - - -
95W GLY* 2.7 37.4 + - - -
96W LEU 3.0 9.2 + - - -
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Residues in contact with ILE 93 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63W GLU* 3.7 35.9 - - + +
66W LEU* 4.3 14.6 - - + -
67W ALA* 3.6 35.2 - - + -
79W VAL* 3.9 11.2 - - + +
80W ASP* 4.1 9.2 - - + -
81W ASP* 3.0 20.8 + - - +
84W VAL* 3.8 23.7 - - + +
92W ASP* 1.3 68.8 - - - +
94W SER* 1.3 66.5 + - - +
96W LEU* 2.8 7.3 + - + +
97W ALA* 2.7 22.9 + - - +
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Residues in contact with SER 94 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59W GLN* 3.3 5.2 + - - -
63W GLU* 2.9 38.1 + - - -
81W ASP* 4.7 0.4 + - - -
92W ASP* 3.1 16.9 + - - -
93W ILE* 1.3 78.7 - - - +
95W GLY* 1.3 62.2 + - - +
98W PHE* 3.0 24.4 + - - +
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Residues in contact with GLY 95 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90W TYR* 3.5 23.7 - - - -
91W ASP 5.1 0.7 - - - -
92W ASP* 2.7 25.0 + - - -
94W SER* 1.3 76.7 - - - +
96W LEU* 1.3 63.2 + - - +
98W PHE* 3.5 5.4 + - - +
99W ALA 3.2 13.7 + - - -
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Residues in contact with LEU 96 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66W LEU* 4.4 16.2 - - + -
79W VAL* 5.2 2.7 - - + -
84W VAL* 4.2 25.1 - - + -
88W THR* 4.2 4.3 - - + +
90W TYR* 3.9 27.6 - - + +
92W ASP 3.0 8.0 + - - +
93W ILE* 2.8 10.3 + - + +
95W GLY* 1.3 75.0 - - - +
97W ALA* 1.3 63.0 + - - +
99W ALA* 2.9 16.3 + - - +
100W LEU* 3.0 28.1 + - + +
105W THR* 4.6 3.1 - - + -
106W THR 5.4 0.2 - - - +
107W LEU* 4.7 2.7 - - + -
110W GLN* 4.0 21.1 - - + -
112W LEU* 3.6 29.4 - - + -
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Residues in contact with ALA 97 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59W GLN* 3.1 22.0 - - - +
62W LEU* 3.7 30.3 - - + +
63W GLU* 3.7 14.1 - - + -
66W LEU* 4.0 9.1 - - + +
93W ILE 2.7 17.0 + - - +
96W LEU* 1.3 73.2 - - - +
98W PHE* 1.3 64.5 + - - +
100W LEU* 2.9 14.6 + - - +
101W LEU* 3.0 13.4 + - - +
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Residues in contact with PHE 98 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59W GLN* 3.4 22.1 - - - +
94W SER 3.0 18.6 + - - +
95W GLY* 3.8 6.5 - - - +
97W ALA* 1.3 76.1 - - - +
99W ALA* 1.3 52.3 + - - +
101W LEU* 3.6 4.5 + - + +
102W SER* 2.6 53.4 + - - -
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Residues in contact with ALA 99 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90W TYR* 3.4 43.3 - - + +
95W GLY 3.2 2.2 + - - +
96W LEU 2.9 10.4 + - - +
98W PHE* 1.3 82.6 - - + +
100W LEU* 1.3 58.9 + - - +
102W SER* 2.9 10.7 + - - -
104W GLU* 2.9 35.2 + - + -
105W THR* 3.7 10.7 + - + -
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Residues in contact with LEU 100 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1W MET* 3.3 26.4 - - + +
34W LEU* 3.5 27.6 - - + -
62W LEU* 4.1 2.9 - - + -
66W LEU* 3.7 27.8 - - + -
96W LEU* 3.0 22.3 + - + +
97W ALA 2.9 6.8 + - - +
99W ALA* 1.3 73.6 - - - +
101W LEU* 1.3 61.3 + - - +
103W GLU* 2.8 20.8 + - - +
105W THR* 3.7 24.4 - - + +
106W THR* 3.9 22.2 - - - -
107W LEU* 3.9 19.1 - - + +
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Residues in contact with LEU 101 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1W MET* 3.6 35.7 + - + +
56W GLU* 4.5 14.7 - - - +
57W PRO* 3.6 26.9 - - + +
58W SER 4.4 0.2 - - - -
59W GLN* 3.7 47.6 - - + +
62W LEU* 4.0 11.0 - - + -
97W ALA 3.0 13.5 + - - +
98W PHE* 4.0 4.5 - - + +
100W LEU* 1.3 71.8 - - - +
102W SER* 1.3 60.2 + - - +
103W GLU* 2.9 19.4 + - - +
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Residues in contact with SER 102 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98W PHE* 2.6 42.4 + - - -
99W ALA* 2.9 18.5 + - - -
101W LEU* 1.3 74.5 - - - +
103W GLU* 1.3 68.9 + - - +
104W GLU* 3.3 12.2 + - - +
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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