Contacts of the helix formed by residues 142 - 153 (chain W) in PDB entry 1VQ7
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 142 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56W GLU 4.6 0.9 - - - -
132W VAL* 6.1 0.7 - - - +
141W HIS* 1.3 77.5 - - - +
143W THR* 1.3 61.3 + - - +
144W GLU* 3.8 7.9 - - + +
145W GLY* 2.7 29.6 + - - +
146W ILE* 2.8 13.0 + - - +
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Residues in contact with THR 143 (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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56W GLU* 2.9 38.8 + - - +
57W PRO 3.9 1.1 - - - +
58W SER* 3.7 24.0 - - - +
142W ASP* 1.3 72.2 - - - +
144W GLU* 1.3 62.5 + - - +
147W ASP* 2.7 43.1 + - - +
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Residues in contact with GLU 144 (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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142W ASP* 3.1 7.9 - - + +
143W THR* 1.3 80.2 - - - +
145W GLY* 1.3 56.3 + - - +
147W ASP* 3.6 6.1 - - - +
148W ASP* 2.7 50.0 + - - +
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Residues in contact with GLY 145 (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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137W GLN* 5.1 1.6 + - - -
141W HIS* 3.9 16.9 + - - -
142W ASP* 2.7 19.9 + - - +
144W GLU* 1.3 76.8 - - - +
146W ILE* 1.3 65.7 + - - +
148W ASP* 3.2 18.2 + - - +
149W LEU* 3.3 10.4 + - - +
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Residues in contact with ILE 146 (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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3W ALA* 4.1 7.2 - - + +
5W VAL* 5.3 1.1 - - + -
53W ALA 4.2 4.9 - - - +
54W PHE* 3.4 31.2 - - - +
55W GLY* 3.3 34.8 - - - +
56W GLU 4.4 1.3 - - - +
57W PRO* 3.9 16.6 - - + -
141W HIS* 3.5 13.6 - - + +
142W ASP 2.8 13.3 + - - +
143W THR 4.2 1.8 - - - +
145W GLY* 1.3 70.3 - - - -
147W ASP* 1.3 56.2 + - - +
149W LEU* 2.9 17.1 + - + +
150W LEU* 2.7 64.4 + - + -
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Residues in contact with ASP 147 (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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57W PRO* 3.4 8.8 - - - +
58W SER* 2.5 44.6 + - - -
61W THR* 2.7 23.8 + - - +
143W THR* 2.7 29.7 + - - +
144W GLU* 3.6 8.2 - - - +
146W ILE* 1.3 75.9 - - - +
148W ASP* 1.3 65.2 + - - +
150W LEU* 3.9 0.2 - - - +
151W GLU* 2.8 36.7 + - - +
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Residues in contact with ASP 148 (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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144W GLU* 2.7 34.7 + - - +
145W GLY* 3.2 9.3 + - - +
147W ASP* 1.3 77.0 - - - +
149W LEU* 1.3 65.0 + - - +
151W GLU* 3.3 9.6 + - - +
152W ALA* 2.9 26.2 + - - +
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Residues in contact with LEU 149 (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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5W VAL* 4.7 4.5 - - + -
7W LEU* 4.2 7.4 - - + -
53W ALA* 3.6 31.6 - - + -
121W PRO* 4.5 4.9 - - + -
125W HIS* 4.3 14.8 - - + -
137W GLN* 4.0 32.5 - - + +
141W HIS* 4.5 2.5 - - + -
145W GLY 3.3 7.0 + - - +
146W ILE* 2.9 17.6 + - + +
148W ASP* 1.3 79.0 - - - +
150W LEU* 1.3 63.6 + - - +
152W ALA* 3.0 15.7 + - + +
153W MET* 3.0 52.3 + - + +
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Residues in contact with LEU 150 (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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3W ALA* 4.1 11.9 - - + -
5W VAL* 3.7 30.3 - - + -
32W CYS* 4.3 7.4 - - - -
34W LEU* 6.3 0.4 - - + -
57W PRO* 4.0 9.6 - - + -
61W THR* 3.9 25.6 - - + -
62W LEU* 6.0 3.1 - - + -
65W VAL* 3.8 21.5 - - + +
118W LEU* 3.8 15.8 - - + +
146W ILE* 2.7 47.0 + - + +
147W ASP 3.9 0.2 - - - +
149W LEU* 1.3 74.5 - - + +
151W GLU* 1.3 56.4 + - - +
153W MET* 3.3 8.2 + - + +
154W ARG* 3.0 24.9 + - - -
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Residues in contact with GLU 151 (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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60W GLU* 5.8 0.7 - - - +
61W THR* 2.3 41.4 + - + +
64W THR* 5.2 13.5 - - + +
65W VAL* 5.4 1.6 - - + -
147W ASP* 2.8 28.3 + - - +
148W ASP* 3.8 8.2 - - - +
150W LEU* 1.3 75.3 - - - +
152W ALA* 1.3 57.7 + - - +
154W ARG* 3.0 40.3 + - + +
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Residues in contact with ALA 152 (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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121W PRO* 4.2 9.2 - - + -
122W ARG* 2.4 68.4 + - + +
124W GLY 5.7 0.9 - - - +
148W ASP 2.9 17.5 + - - +
149W LEU* 3.0 6.7 + - - +
151W GLU* 1.3 76.9 - - - +
153W MET* 1.3 54.0 + - - +
154W ARG* 3.2 3.1 - - - +
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Residues in contact with MET 153 (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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5W VAL* 3.5 34.3 - - + -
7W LEU* 4.5 4.7 - - + -
30W ASN* 4.4 10.3 - - - +
118W LEU* 3.6 27.2 - - + +
119W HIS 2.9 39.2 + - - +
121W PRO* 3.6 28.7 - - + -
122W ARG* 3.7 2.5 - - - +
149W LEU* 3.0 48.2 + - + +
150W LEU* 3.4 6.5 - - + +
151W GLU 3.2 0.2 - - - -
152W ALA* 1.3 76.4 - - - +
154W ARG* 1.3 69.3 + - - +
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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