Contacts of the helix formed by residues 141 - 153 (chain A) in PDB entry 2VR1
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 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A GLY* 3.4 3.7 - - - -
140A ASP* 1.3 75.6 - - - +
142A MET* 1.3 60.1 + - - +
143A ASP* 3.2 22.6 + - - +
144A LYS* 3.3 44.7 + - + +
145A ASN* 3.0 29.6 + - - +
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Residues in contact with MET 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ASP 3.5 9.2 + - - +
141A ASP* 1.3 70.8 + - - +
143A ASP* 1.3 60.7 + - - +
145A ASN* 3.5 21.7 - - + +
146A ARG* 2.9 54.5 + - - +
178A LEU* 3.7 26.2 - - + -
179A ALA* 3.4 46.4 - - + +
182A ILE* 4.1 10.3 - - + -
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Residues in contact with ASP 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ASP* 3.2 11.0 + - - +
142A MET* 1.3 79.8 - - - +
144A LYS* 1.3 57.5 + - + +
146A ARG* 3.0 25.5 + - - +
147A ALA* 3.0 27.1 + - - +
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Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ASP* 3.3 38.7 + - + +
143A ASP* 1.3 79.1 - - + +
145A ASN* 1.3 58.3 + - - +
147A ALA* 3.2 9.1 + - - +
148A ILE* 3.0 37.8 + - + +
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Residues in contact with ASN 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 3.6 31.4 - - - +
139A GLY 3.2 24.4 + - - +
140A ASP* 4.5 0.8 - - - +
141A ASP 3.0 21.5 + - - +
142A MET* 3.5 31.0 - - + +
143A ASP 3.4 0.2 - - - -
144A LYS* 1.3 77.9 - - - +
146A ARG* 1.3 62.7 + - - +
148A ILE* 3.4 10.2 + - - +
149A ALA* 3.1 17.7 + - - +
178A LEU* 3.8 2.6 - - - +
182A ILE* 3.9 20.4 - - + +
200A MET* 3.7 11.7 - - + +
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Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A MET* 2.9 44.9 + - - +
143A ASP* 3.0 32.3 + - - +
145A ASN* 1.3 74.5 - - - +
147A ALA* 1.3 63.8 + - - +
149A ALA* 3.1 4.9 + - - +
150A LYS* 3.0 23.8 + - - +
175A ASP* 3.6 41.1 + - + +
178A LEU* 3.6 21.3 - - + +
179A ALA* 5.7 2.2 - - - +
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ASP 3.0 15.1 + - - +
144A LYS* 3.2 13.4 + - - +
146A ARG* 1.3 74.8 - - - +
148A ILE* 1.3 58.2 + - + +
150A LYS* 3.5 8.5 + - - +
151A ARG* 3.1 28.6 + - - +
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Residues in contact with ILE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A SER* 4.2 23.6 - - - +
137A PRO 5.9 1.3 - - - +
138A LEU* 4.0 20.4 - - + -
144A LYS* 3.0 25.3 + - + +
145A ASN* 3.6 9.4 - - - +
146A ARG 3.2 0.4 - - - -
147A ALA* 1.3 76.4 - - + +
149A ALA* 1.3 59.6 + - - +
151A ARG* 3.5 20.9 + - - +
152A ILE* 3.1 46.0 + - + +
200A MET* 3.8 11.4 - - + -
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ASN 3.1 12.4 + - - +
146A ARG* 3.1 11.6 + - - +
148A ILE* 1.3 75.8 - - - +
150A LYS* 1.3 55.2 + - - +
152A ILE* 3.8 1.0 - - - +
153A GLY* 2.8 35.5 + - - -
154A TYR* 3.4 39.0 + - + +
156A VAL* 4.2 4.2 - - + +
178A LEU* 4.5 6.1 - - + -
200A MET* 3.8 17.9 - - + -
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Residues in contact with LYS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ARG 3.0 15.0 + - - +
147A ALA* 3.8 8.1 - - - +
149A ALA* 1.3 73.8 - - - +
151A ARG* 1.3 66.0 + - - +
153A GLY* 3.2 12.9 + - - -
154A TYR* 5.0 6.4 - - + -
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Residues in contact with ARG 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PRO* 5.4 2.6 - - - +
133A GLY 2.9 32.8 + - - +
134A SER* 4.1 15.6 + - - +
135A ASP* 4.6 5.8 + - - +
147A ALA 3.1 18.4 + - - +
148A ILE* 3.8 20.0 - - - +
150A LYS* 1.3 79.9 - - - +
152A ILE* 1.3 73.2 + - - +
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Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PRO* 4.2 10.1 - - + +
133A GLY* 3.9 27.6 - - - +
148A ILE* 3.1 27.0 + - + +
149A ALA 4.0 3.1 - - - +
151A ARG* 1.3 88.9 - - - +
153A GLY* 1.3 66.9 + - - +
156A VAL* 3.9 4.9 - - + -
200A MET* 3.5 34.8 - - + +
201A GLU 4.6 0.2 - - - -
202A LYS* 3.6 46.2 - - + +
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Residues in contact with GLY 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ALA 2.8 19.3 + - - -
150A LYS* 3.2 12.5 + - - -
152A ILE* 1.3 79.9 - - - +
154A TYR* 1.3 67.4 + - - -
155A PRO 3.6 3.5 - - - +
156A VAL* 3.7 1.2 - - - +
202A LYS* 3.2 19.5 + - - +
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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