Contacts of the helix formed by residues 160 - 175 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158C VAL* 3.8 1.7 - - - +
159C ASN* 1.3 79.7 - - - +
161C VAL* 1.3 64.3 + - - +
162C GLU* 3.9 14.5 + - - +
163C GLU* 2.9 38.9 + - - +
164C ALA* 3.0 17.0 + - - +
187C ALA* 3.2 13.5 - - - +
188C GLY 5.5 0.2 - - - -
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Residues in contact with VAL 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ASN* 1.3 73.1 - - - +
162C GLU* 1.3 60.8 + - - +
164C ALA* 2.7 27.6 + - - +
165C VAL* 3.0 12.7 + - + +
184C LEU* 4.1 13.9 - - + -
187C ALA 3.0 18.5 + - - +
188C GLY* 3.9 9.9 - - - -
189C TYR* 3.5 52.4 - - + +
197C LEU* 4.3 13.0 - - + -
206C HIS* 4.7 1.8 - - + -
287C LEU* 4.1 20.6 - - + -
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Residues in contact with GLU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ASN* 3.3 13.4 + - - +
161C VAL* 1.3 93.9 - - - +
163C GLU* 1.3 59.4 + - - +
165C VAL* 3.7 10.7 + - + +
166C LEU* 3.3 26.9 + - + +
189C TYR* 4.2 10.9 + - - -
287C LEU* 4.6 8.1 - - - +
288C GLU 3.0 25.5 - - - +
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Residues in contact with GLU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C HIS* 5.2 5.9 - - + -
157C ALA 3.5 9.7 - - - +
158C VAL* 3.6 12.2 - - + +
159C ASN* 3.0 49.3 + - - +
160C ASN* 2.9 31.1 + - - +
162C GLU* 1.3 74.0 - - - +
164C ALA* 1.3 60.2 + - - +
165C VAL 3.3 0.2 - - - -
166C LEU* 3.8 13.3 - - + +
167C ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LEU* 4.2 13.2 - - + +
158C VAL* 3.6 15.5 - - + -
160C ASN 3.0 11.0 + - - +
161C VAL 2.7 15.0 + - - +
163C GLU* 1.3 75.9 - - - +
165C VAL* 1.3 56.7 + - - -
167C ALA* 3.7 0.9 - - - +
168C ALA* 2.8 32.2 + - - +
181C VAL* 4.7 0.6 - - + +
184C LEU* 3.9 17.0 - - + -
197C LEU* 3.6 20.6 - - + -
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Residues in contact with VAL 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C VAL* 3.0 16.5 + - + +
162C GLU* 4.0 12.8 - - + +
164C ALA* 1.3 76.1 - - - +
166C LEU* 1.3 66.8 + - + +
168C ALA* 3.2 7.6 + - - +
169C ARG* 2.9 56.1 + - - +
197C LEU* 3.9 20.2 - - + -
199C VAL* 4.4 8.4 - - + +
204C ALA* 4.2 23.6 - - + -
287C LEU* 4.4 9.9 - - + -
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Residues in contact with LEU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C HIS* 6.4 0.7 - - + -
162C GLU 3.3 18.6 + - - +
163C GLU* 3.9 11.2 - - + +
164C ALA 3.3 0.2 - - - -
165C VAL* 1.3 84.3 - - + +
167C ALA* 1.3 55.7 + - - +
169C ARG* 3.1 17.0 + - + +
170C GLU* 3.0 35.1 + - - +
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Residues in contact with ALA 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LEU* 4.0 14.4 - - + -
154C CYS* 4.1 11.3 - - - +
156C HIS* 4.4 4.9 - - + -
158C VAL* 3.7 23.3 - - + -
163C GLU 2.9 20.0 + - - +
164C ALA 3.7 3.1 - - - +
166C LEU* 1.3 71.8 - - - +
168C ALA* 1.3 67.1 + - - +
170C GLU* 2.8 26.0 + - - +
171C LEU* 3.0 14.9 + - - +
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Residues in contact with ALA 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LEU* 4.1 4.4 - - + +
164C ALA 2.8 21.6 + - - +
165C VAL 3.6 3.6 - - - +
167C ALA* 1.3 72.0 - - - +
169C ARG* 1.3 58.1 + - - +
171C LEU* 2.9 20.4 + - - -
172C ILE* 3.0 11.8 + - - +
179C VAL* 3.4 41.3 - - + +
181C VAL* 4.5 6.1 - - + -
199C VAL* 4.1 19.7 - - + -
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Residues in contact with ARG 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C VAL* 2.9 36.7 + - - +
166C LEU* 3.1 19.2 + - + +
168C ALA* 1.3 77.4 - - - +
170C GLU* 1.3 59.5 + - - +
171C LEU 3.2 0.2 - - - -
172C ILE* 3.7 15.8 - - + +
173C ALA* 3.2 20.8 + - - +
199C VAL* 3.8 4.6 - - + +
200C THR 3.1 18.9 + - - +
201C ALA* 3.4 17.9 + - - -
202C ASP 3.8 3.2 + - - -
203C GLU* 3.2 38.6 + - - +
204C ALA* 4.1 4.4 - - - +
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Residues in contact with GLU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C CYS* 3.5 16.6 - - + +
156C HIS* 2.7 41.7 + - - -
166C LEU* 3.0 19.9 + - - +
167C ALA* 2.8 16.1 + - - +
169C ARG* 1.3 75.3 - - - +
171C LEU* 1.3 64.8 + - + +
173C ALA* 3.4 14.3 + - - +
174C GLN* 3.5 16.8 + - - +
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Residues in contact with LEU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C LEU* 3.8 20.1 - - + +
143C ILE* 4.3 10.8 - - + -
145C PRO* 4.0 18.2 - - + -
150C LEU* 3.6 22.2 - - + -
153C LEU* 3.7 37.5 - - + +
154C CYS* 3.9 18.4 - - + +
167C ALA 3.0 13.6 + - - +
168C ALA* 2.9 7.3 + - - +
170C GLU* 1.3 77.6 - - - +
172C ILE* 1.3 60.4 + - - +
174C GLN* 2.8 22.7 + - + +
176C PRO* 3.3 18.0 - - + +
179C VAL* 4.3 10.3 - - + -
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Residues in contact with ILE 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ALA 3.0 16.4 + - - +
169C ARG* 3.7 17.9 - - + +
170C GLU 3.3 0.2 - - - -
171C LEU* 1.3 75.8 - - - +
173C ALA* 1.3 57.3 + - - +
175C GLY* 2.9 19.1 + - - +
176C PRO* 3.2 26.7 - - - +
177C GLN* 3.9 11.9 - - - +
179C VAL* 3.7 14.6 - - + -
199C VAL* 3.9 9.9 - - + +
200C THR* 3.6 36.8 - - - +
201C ALA* 3.7 19.7 - - + +
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Residues in contact with ALA 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C ARG 3.2 14.2 + - - +
170C GLU* 3.5 12.6 - - - +
171C LEU 3.1 0.6 - - - -
172C ILE* 1.3 77.6 - - - +
174C GLN* 1.3 70.8 + - - +
175C GLY 3.3 0.6 + - - -
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Residues in contact with GLN 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C LEU* 3.9 28.3 - - + -
138C PRO* 3.3 28.0 - - + +
170C GLU 3.5 14.0 + - - +
171C LEU* 2.8 11.3 + - + +
173C ALA* 1.3 90.4 + - - +
175C GLY* 1.3 55.3 + - - +
176C PRO* 3.8 2.0 - - - -
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Residues in contact with GLY 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C PRO 4.0 10.3 - - - -
140C SER 3.6 5.6 - - - -
172C ILE 2.9 10.1 + - - +
173C ALA 3.3 0.8 - - - -
174C GLN* 1.3 80.6 - - - +
176C PRO* 1.3 71.6 - - - +
177C GLN* 3.0 17.3 + - - +
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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