Contacts of the helix formed by residues 151 - 162 (chain C) in PDB entry 3GBA
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 ILE 151 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A ASN* 3.8 50.0 - - + +
149C SER* 3.1 13.8 + - - +
150C LYS* 1.3 83.3 - - + +
152C SER* 1.3 67.6 + - - +
153C THR 4.0 4.0 - - - +
154C TYR* 3.0 23.8 + - + -
155C GLU* 2.8 22.7 + - - +
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Residues in contact with SER 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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150C LYS 3.7 3.5 + - - -
151C ILE* 1.3 72.6 - - - +
153C THR* 1.3 63.6 + - - +
155C GLU* 3.3 15.9 + - - +
156C LYS* 3.0 24.3 + - - +
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Residues in contact with THR 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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254A ASN* 2.8 32.7 + - - +
124C ASP* 2.9 28.8 + - - +
127C ALA* 3.4 24.4 - - + +
151C ILE* 3.3 2.2 - - - +
152C SER* 1.3 78.5 - - - +
154C TYR* 1.3 62.5 + - + +
156C LYS* 3.3 8.2 + - - +
157C MET* 3.0 36.8 + - - +
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Residues in contact with TYR 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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254A ASN* 3.7 35.1 + - + +
255A GLY 4.9 4.5 + - - -
123C ALA* 4.2 15.2 - - + +
145C PHE* 3.7 23.3 - + + -
146C PHE* 3.8 30.3 - + + +
149C SER* 3.4 25.8 - - - +
151C ILE* 3.0 31.8 + - + +
153C THR* 1.3 77.5 - - + +
155C GLU* 1.3 61.3 + - - +
157C MET* 3.3 6.9 + - - +
158C TRP* 2.8 29.5 + - - +
211C ILE* 3.5 39.7 + - + +
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Residues in contact with GLU 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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146C PHE 5.0 1.3 - - - -
149C SER* 3.4 20.8 - - - +
150C LYS* 3.6 29.5 - - - +
151C ILE 2.8 10.7 + - - +
152C SER* 3.5 24.8 + - - +
154C TYR* 1.3 76.5 - - - +
156C LYS* 1.3 61.5 + - - +
158C TRP* 3.3 8.1 + - - +
159C ALA* 3.0 23.7 + - - +
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Residues in contact with LYS 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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127C ALA* 3.0 34.4 + - + +
128C LYS* 3.5 19.4 + - - +
134C TYR* 4.2 1.3 + - - +
152C SER 3.0 14.0 + - - +
153C THR* 3.5 10.1 - - - +
155C GLU* 1.3 77.2 - - - +
157C MET* 1.3 62.1 + - - +
159C ALA* 3.3 8.5 + - + +
160C PHE* 3.1 21.4 + - + +
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Residues in contact with MET 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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123C ALA* 3.9 34.5 - - + +
126C LEU* 4.5 9.0 - - + -
127C ALA* 3.7 14.4 - - + -
134C TYR* 3.4 31.5 - - + +
146C PHE* 3.8 34.3 - - + -
153C THR* 3.0 23.5 + - - +
154C TYR* 3.6 10.1 - - - +
156C LYS* 1.3 76.4 - - - +
158C TRP* 1.3 57.4 + - - +
160C PHE* 3.2 3.3 + - - +
161C MET* 2.8 35.2 + - + +
188C LEU* 4.1 20.9 - - + -
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Residues in contact with TRP 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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143C MET* 3.6 39.9 - - + -
146C PHE* 3.4 29.8 - - + +
147C LYS* 3.6 53.3 - - + +
154C TYR 2.8 15.3 + - - +
155C GLU* 3.3 6.5 + - - +
157C MET* 1.3 72.6 - - - +
159C ALA* 1.3 54.8 + - - +
161C MET* 3.9 22.0 - - + -
162C SER* 2.7 63.5 + - - -
166C GLN* 4.3 8.7 - - - -
169C LEU* 4.3 10.3 - - + -
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Residues in contact with ALA 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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155C GLU 3.0 13.8 + - - +
156C LYS* 3.3 11.6 + - + +
158C TRP* 1.3 77.5 - - - +
160C PHE* 1.3 61.4 + - - +
162C SER* 3.8 5.2 + - - -
163C SER* 3.2 22.9 + - - -
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Residues in contact with PHE 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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129C GLN 4.8 11.0 - - - -
131C LYS 5.7 4.3 - - - -
132C ILE 4.3 5.4 - - - -
133C GLU* 3.9 24.9 - - + -
134C TYR* 3.4 67.8 - + - +
156C LYS* 3.1 10.6 + - + +
157C MET 3.5 2.5 - - - +
158C TRP 3.2 0.2 - - - -
159C ALA* 1.3 74.5 - - - +
161C MET* 1.3 68.1 + - - +
163C SER* 3.1 22.4 + - - +
168C ALA* 4.3 9.6 - - + +
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Residues in contact with MET 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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134C TYR* 3.8 23.3 - - + +
135C GLY* 3.9 16.6 - - - -
136C ALA* 4.3 5.2 - - + -
143C MET* 5.8 0.2 - - - -
146C PHE* 3.8 35.7 - - + -
157C MET* 2.8 22.1 + - + +
158C TRP* 3.2 27.1 + - + +
160C PHE* 1.3 77.6 - - - +
162C SER* 1.3 60.3 + - - +
163C SER 3.7 0.3 + - - +
166C GLN* 3.6 13.0 - - - -
167C SER 4.4 0.2 + - - -
168C ALA* 3.6 19.8 + - - +
169C LEU* 3.9 24.7 - - + +
188C LEU* 3.9 25.1 - - + -
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Residues in contact with SER 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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158C TRP* 2.7 58.3 + - - -
159C ALA* 3.8 5.4 + - - -
161C MET* 1.3 75.0 - - - +
163C SER* 1.3 69.0 + - - +
164C ARG* 3.1 4.9 + - - +
166C GLN* 3.5 26.9 + - - +
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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