Contacts of the helix formed by residues 154 - 163 (chain C) in PDB entry 3V9G
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 THR 154 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C MET* 4.2 3.6 - - - -
152C GLY 4.0 2.9 + - - +
153C LYS* 1.3 76.5 - - - +
155C VAL* 1.3 68.2 + - - +
156C ILE* 3.9 9.8 - - - +
157C GLN* 3.1 25.8 + - + +
158C ALA* 2.9 20.8 + - - +
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Residues in contact with VAL 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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40C PHE* 3.7 39.3 - - + -
50C LEU* 3.8 20.9 - - + -
54C LEU* 5.8 0.9 - - + -
144C LEU* 4.9 1.9 - - - +
148C MET* 3.6 28.6 - - + +
154C THR* 1.3 74.6 - - - +
156C ILE* 1.3 60.4 + - + +
158C ALA* 3.3 2.9 + - - +
159C GLU* 2.9 26.5 + - - +
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Residues in contact with ILE 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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37C VAL* 4.1 26.2 - - + -
38C LEU 4.5 7.4 - - - +
39C ALA 6.1 1.1 - - - +
40C PHE* 5.6 2.2 - - + -
154C THR* 3.9 12.1 - - - +
155C VAL* 1.3 81.7 - - + +
157C GLN* 1.3 73.8 + - - +
159C GLU* 4.1 8.5 - - + -
160C ILE* 3.1 35.8 + - + +
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Residues in contact with GLN 157 (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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153C LYS* 3.5 33.0 + - + +
154C THR* 3.1 20.9 + - - +
156C ILE* 1.3 88.6 - - - +
158C ALA* 1.3 65.2 + - - +
160C ILE* 3.5 26.7 - - - +
161C ASP* 3.2 25.8 + - - +
212C PHE* 5.5 3.3 - - - -
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Residues in contact with ALA 158 (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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144C LEU* 3.2 27.9 - - + +
147C THR* 4.2 14.6 - - + -
148C MET* 3.7 23.6 - - + -
153C LYS* 4.1 10.9 - - + +
154C THR 2.9 15.9 + - - +
155C VAL 3.7 4.0 - - - +
157C GLN* 1.3 76.1 - - - +
159C GLU* 1.3 59.1 + - - +
162C ALA* 2.8 27.3 + - - +
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Residues in contact with GLU 159 (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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37C VAL* 3.4 23.0 - - + +
38C LEU* 2.7 27.5 + - - +
40C PHE* 3.5 28.9 - - + -
140C ARG* 2.8 38.4 + - - -
144C LEU* 3.7 11.8 - - + +
155C VAL 2.9 16.7 + - - +
156C ILE* 3.6 12.1 - - + +
158C ALA* 1.3 78.4 - - - +
160C ILE* 1.3 57.9 + - - +
161C ASP 3.4 0.2 + - - -
163C ALA* 3.4 6.2 - - - +
164C ALA* 3.0 25.6 + - - +
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Residues in contact with ILE 160 (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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37C VAL* 4.3 13.9 - - + -
156C ILE* 3.1 31.3 + - + +
157C GLN* 3.5 39.3 - - - +
159C GLU* 1.3 76.9 - - - +
161C ASP* 1.3 62.8 + - + +
164C ALA* 3.8 9.2 - - + +
165C GLU* 3.2 26.8 + - - +
212C PHE* 5.5 7.2 - - + -
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Residues in contact with ASP 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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147C THR* 4.0 1.4 - - - +
153C LYS* 3.3 29.3 - - - +
157C GLN 3.2 16.2 + - - +
158C ALA 4.1 0.2 - - - +
159C GLU 3.2 0.4 - - - -
160C ILE* 1.3 78.2 - - - +
162C ALA* 1.3 68.1 + - - +
163C ALA 3.1 3.1 + - - -
165C GLU* 3.4 8.4 + - - -
166C LEU 3.2 23.2 + - - -
212C PHE* 3.4 21.7 - - + -
213C THR* 3.1 22.5 + - - -
214C ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 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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135C LEU* 4.5 3.6 - - - +
143C ILE* 3.6 34.4 - - + +
144C LEU* 4.3 1.6 - - + -
147C THR* 3.3 29.4 - - + +
158C ALA 2.8 15.5 + - - +
161C ASP* 1.3 78.5 - - - +
163C ALA* 1.3 57.6 + - - +
166C LEU* 3.7 21.8 - - - +
213C THR* 3.9 12.1 - - - -
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Residues in contact with ALA 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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135C LEU* 5.1 1.1 - - - +
140C ARG* 3.9 24.2 - - + +
143C ILE* 4.9 1.8 - - + -
144C LEU* 3.9 11.2 - - + -
158C ALA 3.6 3.0 + - - -
159C GLU* 3.4 24.9 - - - +
161C ASP 3.1 0.2 - - - -
162C ALA* 1.3 79.6 - - - +
164C ALA* 1.3 62.4 + - - +
165C GLU 3.4 1.1 + - - -
166C LEU 3.5 1.0 + - - -
167C ILE* 2.9 46.5 + - + +
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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