Contacts of the helix formed by residues 151 - 162 (chain C) in PDB entry 5W69
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 ARG 151 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147C TRP 3.2 5.4 + - - -
148C GLU 3.5 16.4 + - - -
149C ALA* 3.1 19.1 - - - +
150C ALA* 1.4 81.8 - - - +
152C GLU* 1.4 63.0 + - - +
153C ALA* 3.4 4.0 - - - +
154C GLU* 3.6 45.2 + - + +
155C GLN* 4.4 6.1 + - - +
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Residues in contact with GLU 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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133C TRP* 4.2 6.7 - - + -
147C TRP* 3.0 54.6 + - + +
150C ALA* 4.0 19.7 - - + +
151C ARG* 1.4 73.0 - - - +
153C ALA* 1.3 65.4 + - - +
154C GLU 3.2 2.4 + - - -
155C GLN* 3.4 28.3 + - - +
156C TRP* 3.3 34.1 + - + -
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Residues in contact with ALA 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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126C LEU* 4.5 2.7 - - + -
130C LEU 4.0 14.9 - - - +
131C ARG* 4.2 21.3 - - - +
133C TRP* 4.0 25.3 - - + +
147C TRP 4.6 0.4 + - - -
151C ARG 3.4 0.8 - - - -
152C GLU* 1.3 75.9 - - - +
154C GLU* 1.4 55.0 + - + +
156C TRP* 3.0 6.0 + - - +
157C ARG* 2.7 37.6 + - - +
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Residues in contact with GLU 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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151C ARG* 3.6 46.5 + - + +
153C ALA* 1.4 77.0 - - + +
155C GLN* 1.4 64.0 + - + +
157C ARG* 3.1 36.4 + - - +
158C ALA* 3.1 25.1 + - - +
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Residues in contact with GLN 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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151C ARG 4.5 8.5 - - - +
152C GLU* 3.4 28.9 + - - +
153C ALA 3.3 0.4 - - - -
154C GLU* 1.4 75.1 - - + +
156C TRP* 1.4 62.5 + - + +
158C ALA* 3.4 7.0 + - - +
159C TYR* 2.9 28.6 + - - +
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Residues in contact with TRP 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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97C TRP* 6.5 0.4 - + - -
99C TYR* 3.6 56.1 - + + -
114C ASP* 4.0 25.9 + - - -
126C LEU* 4.1 15.9 - - + -
133C TRP* 4.5 10.9 - + + -
152C GLU* 3.3 36.1 + - + +
153C ALA* 3.0 8.4 + - - +
155C GLN* 1.4 81.6 - - + +
157C ARG* 1.3 56.5 + - - +
159C TYR* 3.0 21.4 + + + +
160C LEU* 2.8 52.1 + - + +
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Residues in contact with ARG 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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126C LEU* 5.0 0.4 - - - +
129C ASP 4.9 2.2 - - - -
130C LEU* 3.5 36.5 + - + +
131C ARG* 4.4 19.8 - - - +
153C ALA 2.7 20.1 + - - +
154C GLU* 3.1 32.1 + - - +
156C TRP* 1.3 70.4 - - - +
158C ALA* 1.3 57.1 + - - +
161C GLU* 3.0 66.1 + - - +
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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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154C GLU 3.1 17.6 + - - +
155C GLN* 3.6 7.0 - - - +
156C TRP 3.2 0.2 - - - -
157C ARG* 1.3 77.6 - - - +
159C TYR* 1.4 55.9 + - - +
161C GLU* 4.5 3.3 - - - +
162C GLY* 3.0 26.9 + - - +
163C THR* 3.8 3.4 + - - -
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Residues in contact with TYR 159 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C MET* 4.0 11.6 - - - +
7C TYR* 4.0 14.6 - - - -
99C TYR* 3.4 40.0 + + - -
155C GLN 2.9 18.6 + - - +
156C TRP* 3.0 17.4 + + + +
158C ALA* 1.4 74.0 - - - +
160C LEU* 1.3 74.8 + - + +
163C THR* 3.1 41.9 + - + -
164C CYS* 2.8 49.9 + - + -
167C TRP* 5.8 1.1 - + - -
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Residues in contact with LEU 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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100C GLY 3.4 28.9 - - - +
109C LEU* 3.3 11.4 - - + +
112C GLY* 4.4 6.3 - - - -
113C TYR 3.5 22.2 - - - +
126C LEU* 3.7 31.4 - - + -
130C LEU* 4.1 22.9 - - + -
156C TRP* 2.8 33.1 + - + +
159C TYR* 1.3 93.1 - - + +
161C GLU* 1.4 56.2 + - - +
164C CYS* 3.7 8.1 - - - +
165C VAL* 3.3 21.1 - - - +
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Residues in contact with GLU 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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109C LEU* 3.8 26.9 + - + +
129C ASP 5.3 2.3 - - - +
130C LEU* 4.2 10.4 - - + +
157C ARG* 3.0 49.5 + - - +
158C ALA* 4.5 3.4 - - - +
160C LEU* 1.4 76.0 - - - +
162C GLY* 1.3 59.7 + - - +
165C VAL* 3.5 15.8 - - - +
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Residues in contact with GLY 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 ALA 3.0 14.5 + - - -
161C GLU* 1.3 78.6 - - - +
163C THR* 1.3 65.1 + - - +
164C CYS 3.4 0.7 - - - -
165C VAL* 3.4 4.5 + - - +
166C GLU* 3.2 21.8 + - - +
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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