Contacts of the helix formed by residues 147 - 154 (chain D) in PDB entry 3VI4
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 THR 147 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144D SER 3.4 11.8 + - - -
145D LEU 3.3 0.2 - - - -
146D GLY* 1.3 73.5 - - - +
148D ASP* 1.3 66.4 + - - +
149D LEU 3.2 1.3 - - - -
150D MET* 3.2 7.2 + - + +
151D ASN* 2.9 31.4 + - - +
209D GLY* 3.8 19.5 - - - -
210D GLU* 3.9 12.6 - - + +
213D ASN* 3.3 21.6 + - - +
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Residues in contact with ASP 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D SER* 3.2 32.7 + - - +
145D LEU* 4.2 4.7 + - - -
147D THR* 1.3 80.9 + - - +
149D LEU* 1.3 56.6 + - - +
151D ASN* 3.4 6.8 + - - +
152D GLU* 3.0 28.1 + - - +
348D ILE* 3.2 21.9 - - + +
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Residues in contact with LEU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LEU* 4.2 22.0 - - + -
127D TYR* 5.5 3.6 - - + -
145D LEU* 3.7 23.3 - - + -
146D GLY* 3.9 8.7 - - - +
147D THR 3.2 0.4 - - - -
148D ASP* 1.3 76.4 - - - +
150D MET* 1.3 60.8 + - - +
152D GLU* 4.2 2.7 - - + +
153D MET* 2.8 51.6 + - + +
160D PHE* 4.2 2.5 - - + -
162D ILE* 3.6 25.1 - - + -
212D PHE* 6.4 0.2 - - + -
348D ILE* 3.5 32.9 - - + +
351D ILE* 4.4 23.8 - - + -
352D ILE* 5.3 0.7 - - + -
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Residues in contact with MET 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D GLY 3.2 21.4 + - - +
147D THR* 3.2 12.2 + - - +
149D LEU* 1.3 78.1 - - - +
151D ASN* 1.3 63.5 + - - +
153D MET* 3.8 0.7 - - - +
154D ARG* 3.0 70.4 + - - +
160D PHE* 3.9 45.3 - - + +
161D ARG* 5.5 0.7 - - - -
162D ILE* 4.8 3.8 - - + -
206D THR 5.6 0.2 - - - +
207D ASN* 3.4 28.9 - - + +
209D GLY* 3.6 20.2 - - - -
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Residues in contact with ASN 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D THR 2.9 16.4 + - - +
148D ASP* 3.6 7.2 - - - +
150D MET* 1.3 79.4 - - - +
152D GLU* 1.3 60.6 + - - +
154D ARG* 3.7 11.0 + - - +
155D ARG* 3.0 20.8 + - - +
54L PHE* 3.9 12.0 - - - -
58L ASN* 3.7 11.9 - - - +
59L LEU* 2.8 57.7 + - - +
60L ALA 5.2 0.2 + - - -
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Residues in contact with GLU 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ASP 3.0 18.0 + - - +
149D LEU* 4.0 3.8 - - + +
150D MET 3.2 0.4 - - - -
151D ASN* 1.3 77.7 + - - +
153D MET* 1.3 62.3 + - - +
154D ARG 3.4 0.2 - - - -
155D ARG* 2.9 61.7 + - - +
156D ILE* 4.4 2.8 - - - +
348D ILE* 3.6 29.3 - - + +
349D GLN* 6.0 3.8 - - - +
352D ILE* 3.9 27.7 - - + +
61L SER* 4.8 0.9 + - - -
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Residues in contact with MET 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ILE* 3.9 29.8 - - + -
125D LEU* 5.2 1.1 - - + -
149D LEU* 2.8 30.4 + - + +
152D GLU* 1.3 75.9 - - - +
154D ARG* 1.3 59.7 + - - +
155D ARG 3.2 2.5 - - - -
156D ILE* 2.9 30.2 + - + +
157D THR* 2.9 16.7 + - - +
160D PHE* 3.5 47.1 - - + -
253D LEU* 4.5 12.1 - - + -
351D ILE* 4.5 13.5 - - - -
352D ILE* 3.8 24.5 - - - -
355D TYR* 5.0 6.5 - - + -
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Residues in contact with ARG 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D MET* 3.0 60.9 + - - +
151D ASN* 3.7 2.6 + - - +
152D GLU 3.4 0.4 - - - -
153D MET* 1.3 74.4 - - - +
155D ARG* 1.3 63.1 + - - +
156D ILE 3.2 0.9 - - - -
157D THR* 3.1 15.0 - - - +
158D SER 5.8 1.6 - - - -
160D PHE* 4.5 13.8 - - + +
207D ASN* 4.3 6.3 + - - +
102H LEU* 3.4 0.5 - - - +
54L PHE* 3.8 12.8 - - + -
55L ARG* 2.7 41.9 + - - +
57L SER* 4.3 6.8 + - - -
58L ASN* 2.4 40.9 + - - +
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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