Contacts of the helix formed by residues 160 - 174 (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 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A VAL* 4.0 2.1 - - - +
159A ASN* 1.3 79.5 - - + +
161A VAL* 1.3 58.9 + - - +
162A GLU* 3.1 30.4 + - - +
163A GLU* 2.8 41.4 + - - +
164A ALA* 2.9 27.2 + - - +
187A ALA* 3.2 14.4 - - - +
188A GLY 5.2 0.9 - - - +
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Residues in contact with VAL 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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160A ASN* 1.3 71.8 - - - +
162A GLU* 1.3 69.0 + - - +
164A ALA* 2.9 17.9 + - - +
165A VAL* 2.9 19.8 + - + +
184A LEU* 3.9 16.6 - - + -
187A ALA 3.2 12.0 + - - +
188A GLY 4.1 0.2 - - - -
189A TYR* 3.5 69.3 - - + +
197A LEU* 4.4 8.3 - - + -
206A HIS* 4.6 0.4 - - + -
287A LEU* 3.8 21.8 - - + -
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Residues in contact with GLU 162 (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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160A ASN* 3.1 39.5 + - - +
161A VAL* 1.3 87.6 + - - +
163A GLU* 1.3 55.8 + - - +
165A VAL* 3.7 7.1 + - - +
166A LEU* 3.2 31.9 + - + +
189A TYR* 4.3 18.1 + - - -
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Residues in contact with GLU 163 (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 HIS* 5.4 4.2 - - + -
157A ALA 4.0 6.3 - - - +
158A VAL* 3.4 12.7 - - + +
159A ASN* 2.5 55.5 + - - +
160A ASN* 2.8 30.7 + - - +
162A GLU* 1.3 71.5 - - - +
164A ALA* 1.3 61.7 + - - +
165A VAL 3.3 0.2 - - - -
166A LEU* 3.7 16.3 - - + +
167A ALA* 3.0 27.5 + - - +
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Residues in contact with ALA 164 (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* 4.0 12.2 - - + +
158A VAL* 3.7 17.0 - - + -
160A ASN 2.9 13.5 + - - +
161A VAL* 2.9 9.3 + - - +
163A GLU* 1.3 74.8 - - - +
165A VAL* 1.3 60.6 + - - +
167A ALA* 3.3 3.8 + - - +
168A ALA* 2.9 29.3 + - - +
181A VAL* 4.8 1.3 - - + +
184A LEU* 3.9 19.7 - - + -
187A ALA* 5.1 0.2 - - + -
197A LEU* 3.8 18.2 - - + -
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Residues in contact with VAL 165 (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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161A VAL 2.9 22.5 + - - +
162A GLU* 3.8 7.4 - - - +
164A ALA* 1.3 76.2 - - - +
166A LEU* 1.3 65.5 + - + +
168A ALA* 3.0 9.7 + - - +
169A ARG* 3.0 54.1 + - - +
197A LEU* 3.5 20.6 - - + -
199A VAL* 4.3 4.7 - - + -
204A ALA* 4.0 24.7 - - + -
287A LEU* 4.4 11.0 - - + -
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Residues in contact with LEU 166 (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 HIS* 6.4 0.4 - - + -
162A GLU* 3.2 19.7 + - + +
163A GLU* 3.9 17.3 - - + +
164A ALA 3.3 0.4 - - - -
165A VAL* 1.3 80.0 - - + +
167A ALA* 1.3 62.3 + - - +
169A ARG* 3.0 22.3 + - + +
170A GLU* 3.2 23.0 + - - +
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Residues in contact with ALA 167 (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* 3.9 14.8 - - + -
154A CYS* 4.0 13.2 - - - +
156A HIS* 4.6 3.3 - - + -
158A VAL* 3.6 22.0 - - + -
163A GLU 3.0 19.8 + - - +
164A ALA 3.6 4.0 - - - +
166A LEU* 1.3 75.8 - - - +
168A ALA* 1.3 63.4 + - - +
170A GLU* 3.2 17.1 + - - +
171A LEU* 3.2 24.9 + - - +
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Residues in contact with ALA 168 (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* 4.2 5.6 - - - +
164A ALA 2.9 13.4 + - - +
165A VAL 3.4 7.9 - - - +
167A ALA* 1.3 75.3 - - - +
169A ARG* 1.3 58.6 + - - +
171A LEU* 3.2 5.7 + - - +
172A ILE* 3.0 31.4 + - - +
179A VAL* 3.6 32.2 - - + +
181A VAL* 4.7 4.5 - - + -
199A VAL* 3.9 22.9 - - + -
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Residues in contact with ARG 169 (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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165A VAL* 3.0 31.6 + - - +
166A LEU* 3.0 14.3 + - + +
168A ALA* 1.3 79.3 - - - +
170A GLU* 1.3 56.0 + - - +
172A ILE* 3.4 10.6 + - + +
173A ALA* 2.9 27.5 + - - +
199A VAL* 3.9 5.1 - - + +
200A THR 3.0 20.1 + - - +
201A ALA* 3.2 20.8 + - - +
202A ASP* 3.7 2.6 - - - -
203A GLU* 3.1 43.2 + - - +
204A ALA* 4.0 5.9 - - - +
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Residues in contact with GLU 170 (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 CYS* 4.1 11.8 - - + +
156A HIS* 3.2 33.5 + - - -
166A LEU* 3.2 23.8 + - - +
167A ALA* 3.5 10.0 + - - +
169A ARG* 1.3 73.8 - - - +
171A LEU* 1.3 68.4 + - + +
173A ALA* 3.3 19.3 + - - +
174A GLN* 3.4 13.0 + - - +
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Residues in contact with LEU 171 (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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137A LEU* 3.8 19.6 - - + +
143A ILE* 4.3 16.8 - - + -
145A PRO* 4.3 3.4 - - + -
150A LEU* 3.6 23.3 - - + -
153A LEU* 3.6 55.0 - - + +
154A CYS* 4.0 7.4 - - + +
167A ALA 3.2 15.4 + - - +
168A ALA 3.5 5.6 - - - +
170A GLU* 1.3 78.8 - - + +
172A ILE* 1.3 59.0 + - - +
174A GLN* 2.8 28.3 + - + +
175A GLY 3.4 3.6 + - - -
176A PRO* 3.5 8.2 - - + +
179A VAL* 4.3 11.2 - - + -
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Residues in contact with ILE 172 (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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168A ALA 3.0 18.5 + - - +
169A ARG* 3.6 13.0 - - + +
171A LEU* 1.3 75.8 - - - +
173A ALA* 1.3 61.0 + - - +
175A GLY 2.9 14.7 + - - +
176A PRO* 3.2 29.6 - - - +
177A GLN* 4.1 10.3 - - - +
179A VAL* 3.5 15.0 - - + -
199A VAL* 3.7 19.3 - - + +
200A THR* 3.6 29.8 - - - +
201A ALA* 4.5 19.1 - - + -
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Residues in contact with ALA 173 (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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169A ARG 2.9 13.8 + - - +
170A GLU* 3.4 13.5 - - - +
171A LEU 3.2 0.2 - - - -
172A ILE* 1.3 77.1 - - - +
174A GLN* 1.3 66.0 + - - +
175A GLY 3.7 0.2 + - - -
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Residues in contact with GLN 174 (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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137A LEU* 4.1 27.4 - - + -
138A PRO* 3.4 26.4 - - + +
170A GLU 3.7 13.0 - - - +
171A LEU* 2.8 11.6 + - + +
173A ALA* 1.3 82.9 + - - +
175A GLY* 1.3 55.1 + - - +
176A PRO* 4.0 1.1 - - - -
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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