Contacts of the strand formed by residues 146 - 156 (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 SER 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C SER 5.0 1.2 - - - -
144C GLY* 3.2 12.7 + - - -
145C SER* 1.3 91.8 + - - +
147C VAL* 1.3 62.5 + - - +
148C THR* 5.6 0.4 - - - -
193C THR* 4.2 15.9 - - - +
194C VAL 3.3 13.9 + - - -
195C THR* 3.8 8.0 + - - +
196C SER* 3.9 4.2 - - - +
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Residues in contact with VAL 147 (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 PRO* 3.6 28.9 - - + -
146C SER* 1.3 76.4 - - - +
148C THR* 1.3 67.0 + - - +
149C LEU* 4.3 2.4 + - + -
192C VAL 4.0 0.3 - - - +
193C THR* 3.4 2.5 - - - +
194C VAL* 2.8 57.7 + - + +
196C SER* 4.0 18.8 - - - -
199C TRP* 4.0 26.9 - - + +
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Residues in contact with THR 148 (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* 4.9 10.2 - - - +
116B SER* 3.3 30.7 + - - +
118B PHE* 3.1 27.0 - - + -
135B PHE* 4.4 1.6 - - + -
137B ASN* 4.7 6.8 + - - +
137C PRO* 4.0 8.1 - - - +
146C SER 5.6 0.3 - - - -
147C VAL* 1.3 76.8 - - - +
149C LEU* 1.3 73.6 + - - +
191C SER* 4.2 12.1 - - - -
192C VAL 3.5 4.3 - - - +
193C THR* 2.8 26.1 + - - +
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Residues in contact with LEU 149 (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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118B PHE* 3.9 4.7 - - - -
135C LEU 3.8 3.8 - - - +
137C PRO* 3.5 29.6 - - + -
147C VAL* 4.6 4.7 - - + +
148C THR* 1.3 78.0 - - - +
150C GLY* 1.3 59.7 + - - +
165C TRP* 4.4 0.9 - - - -
191C SER* 3.1 8.5 - - - -
192C VAL* 2.9 43.1 + - + +
194C VAL* 5.1 2.2 - - + -
199C TRP* 3.8 32.1 - - + +
204C ILE* 3.6 44.9 - - + -
221C ILE* 3.7 23.3 - - + -
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Residues in contact with GLY 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PHE* 3.9 1.8 - - - -
135B PHE* 4.0 12.6 - - - -
135C LEU* 2.8 41.6 + - - +
149C LEU* 1.3 75.5 - - - +
151C CYS* 1.3 61.8 + - - +
165C TRP* 3.6 4.9 - - - -
190C SER 3.1 11.7 - - - -
221C ILE* 3.8 10.6 - - - +
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Residues in contact with CYS 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL* 3.5 23.6 - - - -
133C TYR 3.7 8.1 - - - -
134C PRO* 5.0 2.2 - - - -
135C LEU* 4.2 3.7 - - - +
150C GLY* 1.3 75.8 - - - +
152C LEU* 1.3 60.6 + - - +
153C VAL* 3.9 4.1 + - - +
163C LEU* 4.5 5.8 - - + -
165C TRP* 3.7 10.3 - - + -
189C SER* 3.1 5.7 - - - -
190C SER 2.8 30.1 + - - +
206C CYS* 2.0 53.6 - - + -
208C VAL* 4.3 2.5 - - - -
219C LYS* 5.3 0.2 - - - -
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Residues in contact with LEU 152 (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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124B GLN* 4.6 2.5 - - - +
131B SER* 3.8 30.5 - - - +
133B VAL* 4.3 15.3 - - + -
178B THR* 5.2 5.4 - - + +
131C SER 3.3 4.7 - - - +
132C VAL* 3.5 0.7 - - - -
133C TYR* 2.8 63.2 + - + +
135C LEU* 3.9 20.1 - - + +
151C CYS* 1.3 73.0 - - - +
153C VAL* 1.3 63.0 + - - +
154C LYS* 4.5 10.8 - - + -
187C THR* 4.0 21.3 - - + -
188C LEU 3.8 8.3 - - - +
189C SER* 4.3 11.9 - - - +
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Residues in contact with VAL 153 (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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130C PRO* 3.4 33.2 - - + -
131C SER 3.6 3.6 - - - +
132C VAL* 4.6 5.4 - - + -
151C CYS* 4.6 2.0 - - - +
152C LEU* 1.3 74.6 - - - +
154C LYS* 1.3 58.9 + - - +
156C TYR* 3.8 13.3 - - + -
161C VAL* 4.6 6.1 - - + -
163C LEU* 3.8 8.3 - - + -
187C THR* 3.4 4.0 - - - +
188C LEU* 2.7 63.4 + - + +
208C VAL* 3.7 34.3 - - + -
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Residues in contact with LYS 154 (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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124B GLN* 4.2 12.3 - - - +
131B SER* 2.8 27.1 + - - -
178B THR* 4.9 2.9 - - - +
180B THR* 3.0 27.1 + - - +
130C PRO* 3.4 2.4 - - - +
131C SER* 2.9 41.8 + - - +
133C TYR* 4.4 14.4 - - + -
152C LEU* 4.5 11.2 - - + -
153C VAL* 1.3 76.4 - - - +
155C GLY* 1.3 70.5 + - - +
156C TYR* 3.6 2.7 - - - -
182C GLN* 3.8 11.3 + - - +
187C THR* 3.5 28.0 - - + +
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Residues in contact with GLY 155 (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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128C THR* 3.1 24.4 - - - +
129C ALA 3.7 3.8 - - - +
154C LYS* 1.3 83.9 - - - +
156C TYR* 1.3 58.0 + - - -
185C LEU* 3.7 23.3 - - - +
186C TYR 3.0 13.5 + - - -
187C THR* 3.4 2.5 + - - -
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Residues in contact with TYR 156 (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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128C THR 3.3 13.5 - - - +
130C PRO* 3.7 20.4 - - + -
153C VAL* 3.8 34.8 - - + -
155C GLY* 1.3 76.5 - - - +
157C PHE* 1.3 68.6 + - - +
158C PRO 3.9 15.5 - - - -
159C GLU* 3.3 16.9 + - - -
161C VAL* 3.6 24.7 - - + +
179C ALA* 3.3 24.9 - - - +
185C LEU* 3.5 4.7 - - - -
186C TYR* 2.7 71.6 + + + +
187C THR* 4.0 1.8 - - - -
188C LEU* 3.6 16.7 - - + +
210C HIS* 4.2 2.2 - - + -
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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