Contacts of the strand formed by residues 185 - 195 (chain C) in PDB entry 3VG9
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 LEU 185 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C ALA* 4.4 7.2 - - + -
126C LYS 4.4 1.8 - - - +
128C THR* 4.2 20.0 - - + +
155C GLY* 3.7 31.0 - - - +
156C TYR 3.5 6.5 - - - +
157C PHE* 3.5 25.1 - - + -
181C LEU* 3.3 7.2 - - - -
182C GLN* 2.7 40.1 + - - +
183C SER* 3.4 2.9 - - - +
184C ASP* 1.3 95.3 - - + +
186C TYR* 1.3 62.1 + - - +
187C THR* 5.3 0.2 - - - -
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Residues in contact with TYR 186 (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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121C THR* 4.5 16.3 - - + +
155C GLY* 3.0 23.6 + - - -
156C TYR* 2.7 52.5 + + + +
157C PHE* 3.8 24.7 - + - -
158C PRO* 5.2 0.2 - - + -
159C GLU* 3.5 47.7 + - + +
179C ALA* 3.9 16.4 - - + -
180C VAL 3.3 9.4 - - - -
181C LEU* 3.4 35.3 - - + +
185C LEU* 1.3 72.6 - - - +
187C THR* 1.3 60.0 + - - +
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Residues in contact with THR 187 (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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160B LEU* 6.0 0.7 - - - -
178B THR* 5.6 7.4 - - + +
152C LEU* 4.0 20.4 - - + -
153C VAL 3.4 10.3 - - - +
154C LYS* 3.5 22.9 - - - +
155C GLY* 3.4 13.3 + - - -
156C TYR* 4.1 0.7 - - - -
178C PRO 4.5 0.9 - - - +
179C ALA* 3.4 2.7 - - - -
180C VAL* 2.9 43.6 + - + +
182C GLN* 4.3 13.5 + - - +
185C LEU 4.9 1.4 + - - -
186C TYR* 1.3 77.1 + - - +
188C LEU* 1.3 66.7 + - - +
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Residues in contact with LEU 188 (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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152C LEU* 3.7 3.9 - - - +
153C VAL* 2.7 52.5 + - + +
156C TYR* 3.6 21.8 - - + +
159C GLU* 5.2 1.6 - - - +
161C VAL* 3.9 17.9 - - + +
163C LEU* 3.7 29.6 - - + -
176C THR* 4.3 10.5 - - + -
177C PHE* 3.6 20.9 - - - +
178C PRO 5.0 1.3 - - - -
179C ALA* 4.1 12.6 - - + +
187C THR* 1.3 78.3 - - - +
189C SER* 1.3 62.4 - - - +
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Residues in contact with SER 189 (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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133B VAL* 5.1 5.4 - - - -
135B PHE* 3.5 22.3 - - - -
176B SER* 3.5 22.5 + - - -
178B THR* 5.3 3.6 + - - -
135C LEU* 5.5 0.7 - - - -
151C CYS 3.1 12.3 - - - -
152C LEU* 4.3 13.2 - - - -
176C THR* 3.9 4.3 - - - +
177C PHE* 3.1 29.2 + - - +
188C LEU* 1.3 80.2 - - - +
190C SER* 1.3 62.1 + - - +
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Residues in contact with SER 190 (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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135B PHE* 3.7 4.9 - - - -
150C GLY* 3.1 3.8 - - - -
151C CYS 2.8 31.4 + - - -
163C LEU* 3.5 29.8 - - - -
165C TRP* 2.9 26.1 + - - -
174C VAL* 3.6 2.4 - - - +
175C HIS 3.3 13.0 + - - -
176C THR* 3.5 13.1 + - - -
177C PHE* 4.5 1.1 - - - -
189C SER* 1.3 76.6 - - - +
191C SER* 1.3 61.7 + - - +
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Residues in contact with SER 191 (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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135B PHE* 3.2 35.5 - - - -
137B ASN* 3.2 22.6 + - - -
148C THR* 4.2 7.9 - - - -
149C LEU 3.1 9.0 - - - -
165C TRP* 4.3 0.2 - - - -
173C GLY 3.6 1.3 - - - +
174C VAL* 3.3 4.3 - - - +
175C HIS* 2.9 35.6 + - - +
177C PHE* 4.0 8.5 - - - -
190C SER* 1.3 75.5 + - - +
192C VAL* 1.3 62.6 + - - +
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Residues in contact with VAL 192 (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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147C VAL 4.0 1.0 - - - +
148C THR* 3.5 1.3 - - - -
149C LEU* 2.9 45.5 + - + +
165C TRP* 3.6 38.1 - - + -
170C LEU* 3.9 25.6 - - + -
172C SER 4.2 5.8 - - - +
173C GLY 3.3 4.0 - - - -
174C VAL* 4.0 22.2 - - + -
191C SER* 1.3 75.0 - - - +
193C THR* 1.3 67.9 + - - +
194C VAL* 4.0 14.7 - - + +
204C ILE* 5.3 0.2 - - + -
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Residues in contact with THR 193 (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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114B THR* 5.9 3.4 - - + +
137B ASN* 4.6 9.2 + - - -
146C SER* 4.2 21.1 - - - +
147C VAL 3.4 9.0 - - - +
148C THR* 2.8 27.3 + - - +
172C SER 4.5 1.7 - - - +
173C GLY* 3.1 27.7 + - - -
192C VAL* 1.3 75.2 - - - +
194C VAL* 1.3 70.2 + - - +
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Residues in contact with VAL 194 (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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146C SER* 3.3 7.3 - - - -
147C VAL* 2.8 54.5 + - + +
149C LEU* 5.1 3.4 - - + -
170C LEU* 4.3 12.3 - - + -
172C SER 5.7 0.2 - - - +
192C VAL* 4.0 17.9 - - + +
193C THR* 1.3 80.0 - - - +
195C THR* 1.3 69.4 + - - +
198C THR* 3.9 16.2 - - + +
199C TRP* 3.9 15.7 - - + -
204C ILE* 4.1 17.7 - - + -
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Residues in contact with THR 195 (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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145C SER 3.5 11.7 - - - +
146C SER* 3.8 6.2 + - - +
194C VAL* 1.3 78.2 - - - +
196C SER* 1.3 58.0 + - - +
197C SER* 3.0 17.8 + - - -
198C THR* 2.7 51.3 + - - -
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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