Contacts of the helix formed by residues 146 - 155 (chain A) in PDB entry 1VI9
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 ASN 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A GLY 2.8 24.4 + - - -
117A HIS* 4.4 5.5 - - - +
118A PRO* 4.6 7.3 - - + +
145A PRO* 1.3 78.6 - - - +
147A LEU* 1.3 63.3 + - - +
148A VAL* 3.1 10.5 - - - +
149A GLU* 2.7 50.5 + - - +
150A LEU* 3.0 17.5 + - - +
181A VAL* 4.5 2.2 - - - -
182A LYS* 3.7 21.8 - - + +
183A HIS* 3.5 24.7 + - + +
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Residues in contact with LEU 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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118A PRO* 6.3 0.4 - - + -
146A ASN* 1.3 73.4 - - - +
148A VAL* 1.3 66.9 + - + +
150A LEU* 3.4 8.2 + - + +
151A GLU* 3.2 27.2 + - + +
158A VAL* 3.4 37.9 - - + +
181A VAL* 4.8 1.6 - - - -
183A HIS 2.8 12.1 + - - +
184A LEU* 3.3 30.1 - - + +
185A ALA* 4.4 7.2 - - + -
186A ARG* 3.5 42.6 - - + +
187A ALA* 3.5 14.4 - - + +
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Residues in contact with VAL 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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116A GLY* 3.4 33.4 - - - +
117A HIS 4.2 3.8 - - - +
118A PRO* 4.0 28.9 - - + -
146A ASN* 3.1 15.0 + - - +
147A LEU* 1.3 79.3 - - + +
149A GLU* 1.3 65.8 + - + +
151A GLU* 3.3 15.7 + - - +
152A ILE* 3.1 32.8 + - + +
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Residues in contact with GLU 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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113A PRO* 3.1 24.0 - - + +
114A VAL* 3.5 5.4 - - - +
115A MSE 2.7 36.1 + - + +
116A GLY 3.2 16.2 + - - +
145A PRO* 3.4 17.4 - - + +
146A ASN* 2.7 45.0 + - - +
148A VAL* 1.3 74.8 - - + +
150A LEU* 1.3 60.9 + - - +
152A ILE* 3.3 7.7 + - - +
153A LEU* 2.9 35.0 + - + +
182A LYS* 2.9 19.3 + - - -
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Residues in contact with LEU 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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145A PRO* 3.6 14.3 - - + +
146A ASN 3.0 16.4 + - - +
147A LEU* 3.6 5.8 - - + +
148A VAL 3.3 0.2 - - - -
149A GLU* 1.3 74.8 - - - +
151A GLU* 1.3 59.4 + - - +
153A LEU* 3.3 2.5 + - - +
154A CYS* 2.9 33.0 + - - +
158A VAL* 4.1 16.4 - - + -
164A ALA* 4.0 16.4 - - - +
167A ALA* 3.9 35.4 - - + -
168A ALA* 4.2 4.0 - - - +
171A LEU* 3.6 30.3 - - + -
179A VAL* 5.0 0.4 - - + -
181A VAL* 4.1 25.1 - - + -
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Residues in contact with GLU 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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147A LEU* 3.2 18.8 + - - +
148A VAL* 3.5 17.6 - - - +
149A GLU 3.3 0.2 - - - -
150A LEU* 1.3 80.2 - - - +
152A ILE* 1.3 56.5 + - + +
154A CYS* 4.0 2.0 - - - -
155A GLU* 3.0 22.3 + - - -
156A HIS 3.2 29.0 + - - +
157A ALA* 3.7 9.6 - - - +
158A VAL* 3.3 33.2 + - + +
186A ARG* 3.3 24.9 + - - -
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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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115A MSE 4.0 35.7 - - + -
122A CYS* 5.9 6.7 - - - -
129A ALA* 4.8 9.0 - - + -
133A VAL* 3.7 24.8 - - + +
148A VAL* 3.1 25.4 + - + +
149A GLU 3.3 6.2 + - - +
151A GLU* 1.3 74.9 - - + +
153A LEU* 1.3 63.8 + - - +
155A GLU* 3.4 19.2 + - - +
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Residues in contact with LEU 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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113A PRO* 3.8 15.9 - - + -
115A MSE 4.2 15.5 - - + -
132A HIS* 3.8 28.7 - - + +
133A VAL* 4.1 17.4 - - + +
137A LEU* 4.2 16.5 - - + +
143A ILE* 4.1 9.9 - - + -
145A PRO* 3.8 22.9 - - + -
149A GLU* 2.9 21.4 + - + +
150A LEU 3.7 2.9 - - - +
152A ILE* 1.3 77.0 - - - +
154A CYS* 1.3 58.0 + - - +
155A GLU* 3.7 6.8 + - - +
171A LEU* 3.6 33.9 - - + +
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Residues in contact with CYS 154 (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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150A LEU* 2.9 23.9 + - + +
151A GLU* 3.8 2.0 - - - -
153A LEU* 1.3 75.1 - - - +
155A GLU* 1.3 69.0 + - - +
156A HIS* 3.2 61.2 - - - +
158A VAL* 4.2 2.2 - - - -
167A ALA* 4.0 22.2 - - + +
170A GLU* 4.1 12.8 - - + +
171A LEU* 4.2 11.4 - - + -
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Residues in contact with GLU 155 (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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133A VAL* 3.9 21.2 - - + +
134A ARG* 5.7 2.3 + - - -
151A GLU 3.0 10.1 + - - -
152A ILE* 3.6 14.6 - - - +
153A LEU 3.3 5.1 - - - +
154A CYS* 1.3 79.6 - - - +
156A HIS* 1.3 64.1 + - - +
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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