Contacts of the helix formed by residues 150 - 161 (chain A) in PDB entry 1VI7
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 GLN 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A CYS* 3.7 0.2 - - - +
147A GLU* 2.8 42.2 + - - +
149A HIS* 1.3 106.9 - - + +
151A LEU* 1.3 66.4 + - - +
152A THR 3.7 0.7 - - - -
153A GLY* 3.4 5.4 + - - +
154A ILE* 2.9 30.3 + - + +
195A PHE* 3.9 22.8 + - + -
196A SER* 3.9 17.0 - - - +
199A SER* 4.9 3.2 + - - -
200A LEU* 3.5 30.4 - - - +
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Residues in contact with LEU 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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146A CYS* 4.2 11.0 - - - -
147A GLU 3.5 5.2 + - - +
148A TYR* 3.5 22.1 + - + +
149A HIS 3.6 0.2 - - - -
150A GLN* 1.3 73.3 - - - +
152A THR* 1.3 70.9 + - + +
154A ILE* 2.7 17.7 + - - +
155A GLU* 3.0 31.1 + - + +
165A ILE* 5.1 2.2 - - + -
170A TYR* 3.9 30.7 - - + +
174A VAL* 4.0 27.6 - - + -
176A LEU* 4.1 20.2 - - + -
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Residues in contact with THR 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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148A TYR 5.1 0.2 + - - -
149A HIS 5.6 1.9 + - - -
150A GLN 3.7 0.6 - - - -
151A LEU* 1.3 79.9 - - + +
153A GLY* 1.3 65.8 + - - +
155A GLU* 3.2 17.4 + - - +
156A ALA* 3.1 23.7 + - - +
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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 HIS 5.6 0.4 + - - -
150A GLN* 3.4 7.7 + - - +
151A LEU 3.0 1.4 + - - -
152A THR* 1.3 83.0 + - - +
154A ILE* 1.3 60.3 + - - +
156A ALA* 3.5 6.3 + - - +
157A LEU* 3.1 27.8 + - - +
195A PHE* 3.7 24.7 - - - -
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Residues in contact with ILE 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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144A LEU* 4.0 23.3 - - + -
146A CYS* 3.5 42.0 - - + -
150A GLN* 2.9 19.6 + - + +
151A LEU* 2.7 12.4 + - + +
153A GLY* 1.3 68.5 - - - -
155A GLU* 1.3 69.5 + - + +
157A LEU* 3.1 6.1 + - - +
158A LEU* 2.9 26.1 + - + +
165A ILE* 6.5 0.2 - - + -
176A LEU* 4.3 13.5 - - + -
178A VAL* 5.5 0.2 - - + -
188A PHE* 4.6 7.4 - - + -
192A LEU* 4.5 11.4 - - + -
195A PHE* 3.9 15.0 - - + -
200A LEU* 4.1 14.8 - - + -
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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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151A LEU* 3.0 31.1 + - + +
152A THR* 3.6 23.4 - - - +
154A ILE* 1.3 76.7 - - - +
156A ALA* 1.3 66.0 + - - +
158A LEU* 3.0 11.9 - - - +
159A GLY* 3.0 19.8 + - - -
165A ILE* 4.1 31.6 - - + +
170A TYR* 5.4 2.3 + - - -
176A LEU* 6.3 0.2 - - + -
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Residues in contact with ALA 156 (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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152A THR 3.1 9.5 + - - +
153A GLY* 3.6 11.0 - - - +
155A GLU* 1.3 78.4 - - - +
157A LEU* 1.3 64.3 + - + +
159A GLY* 3.2 4.1 + - - -
160A GLN* 3.1 35.8 + - - +
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Residues in contact with LEU 157 (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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153A GLY 3.1 21.5 + - - +
154A ILE* 3.1 5.8 + - - +
156A ALA* 1.3 74.9 - - + +
158A LEU* 1.3 62.7 + - - +
160A GLN* 3.0 34.4 + - - +
161A CYS* 3.2 16.1 + - - -
188A PHE* 4.0 13.2 - - + -
191A LYS* 4.0 31.5 - - + +
192A LEU* 4.3 11.0 - - + +
195A PHE* 3.8 42.4 - - + -
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Residues in contact with LEU 158 (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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154A ILE* 2.9 15.7 + - + +
155A GLU* 3.0 15.3 - - - +
157A LEU* 1.3 75.3 - - - +
159A GLY* 1.3 52.8 + - - +
161A CYS* 3.1 12.3 + - - +
163A GLY* 2.6 47.5 + - - +
164A LYS* 4.1 1.1 - - - +
165A ILE* 3.3 42.2 - - + +
178A VAL* 3.6 32.3 - - + -
179A ALA 5.0 0.2 - - - +
180A LEU* 4.8 7.0 - - + -
188A PHE* 3.4 34.6 - - + -
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Residues in contact with GLY 159 (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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155A GLU 3.0 12.8 + - - -
156A ALA* 3.2 4.5 + - - -
158A LEU* 1.3 73.1 - - - +
160A GLN* 1.3 64.2 + - - +
162A ASP* 3.3 13.9 + - - +
163A GLY 3.8 11.2 + - - -
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Residues in contact with GLN 160 (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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156A ALA* 3.1 37.4 + - - +
157A LEU* 3.0 22.8 + - - +
159A GLY* 1.3 76.3 - - - +
161A CYS* 1.3 59.8 + - - +
162A ASP* 3.3 3.2 + - - +
184A LYS* 4.3 8.3 + - - -
187A GLU* 4.7 4.2 - - - +
191A LYS* 3.0 29.7 + - - +
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Residues in contact with CYS 161 (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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157A LEU 3.2 6.9 + - - +
158A LEU* 3.1 8.2 + - + +
160A GLN* 1.3 77.3 - - - +
162A ASP* 1.3 75.2 + - - +
163A GLY* 3.1 2.4 + - - +
180A LEU* 4.4 4.1 - - + +
181A PRO* 3.5 11.4 - - - +
184A LYS* 3.5 27.0 - - + +
187A GLU* 3.6 30.5 - - - -
188A PHE* 4.1 28.9 - - + -
191A LYS* 3.7 19.7 - - - -
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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