Contacts of the strand formed by residues 153 - 161 (chain C) in PDB entry 3C6Q
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 GLU 153 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C GLY 3.0 12.3 + - - +
123C LYS* 3.5 39.3 - - + +
124C GLY* 3.7 10.8 + - - +
152C SER* 1.3 75.3 - - - +
154C ILE* 1.3 60.6 + - - +
155C GLU* 3.7 5.8 + - - +
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Residues in contact with ILE 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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116C MET* 4.8 1.3 - - + -
117C LYS* 3.8 30.1 - - + +
120C LEU* 3.6 22.2 - - + -
122C GLY 3.4 4.0 - - - -
123C LYS 3.4 26.0 - - - +
124C GLY 3.4 14.4 - - - +
126C VAL* 4.3 18.8 - - + -
145C PHE* 5.7 0.2 - - + -
149C ILE* 3.5 43.2 - - + +
150C LYS* 5.9 0.2 - - - -
152C SER* 3.1 16.6 - - - +
153C GLU* 1.3 78.1 - - - +
155C GLU* 1.3 63.1 + - - +
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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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124C GLY 2.9 15.8 + - - +
125C LYS* 3.5 23.5 - - + +
126C VAL* 3.1 24.8 + - - +
153C GLU 3.7 5.3 + - - +
154C ILE* 1.3 75.9 - - - +
156C ILE* 1.3 63.5 + - - +
157C VAL* 3.6 20.7 + - - +
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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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126C VAL* 3.5 12.1 - - + +
128C ILE* 3.7 24.5 - - + -
145C PHE* 4.0 19.7 - - + -
146C LYS* 3.6 35.2 - - + -
149C ILE* 3.7 27.6 - - + -
155C GLU* 1.3 73.9 - - - +
157C VAL* 1.3 62.3 + - - +
158C ASP 3.9 14.1 - - - +
159C ILE* 4.0 11.9 - - + -
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Residues in contact with VAL 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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125C LYS* 3.8 36.3 - - + -
126C VAL 3.0 15.8 + - - +
127C VAL* 3.9 18.2 - - + -
155C GLU* 3.8 19.1 - - - +
156C ILE* 1.3 74.1 - - - +
158C ASP* 1.3 72.7 + - - +
180C HIS* 3.8 29.6 + - + +
183C LEU* 4.3 6.5 - - + -
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Residues in contact with ASP 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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126C VAL 3.7 0.6 + - - -
127C VAL* 3.5 20.7 - - + -
128C ILE* 2.7 34.1 + - - +
156C ILE* 3.5 4.0 - - - +
157C VAL* 1.3 91.8 - - + +
159C ILE* 1.3 66.3 + - - +
160C LEU* 3.8 21.7 - - + +
176C ALA* 5.5 2.7 - - + +
180C HIS* 3.7 18.8 + - + +
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Residues in contact with ILE 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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128C ILE* 3.7 29.8 - - + -
130C THR* 4.4 10.3 - - + -
133C LEU* 4.6 13.5 - - + +
142C ILE* 4.2 24.7 - - + -
146C LYS* 4.3 25.6 - - - +
156C ILE* 4.0 8.3 - - + -
158C ASP* 1.3 82.5 + - - +
160C LEU* 1.3 63.0 + - - +
161C ASN* 3.8 2.6 + - - +
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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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127C VAL* 3.5 28.0 - - + -
128C ILE 2.9 13.1 + - - +
129C GLY* 3.6 4.9 - - - -
130C THR* 3.0 28.6 + - - +
158C ASP* 3.8 26.0 - - + +
159C ILE* 1.3 72.5 - - - +
161C ASN* 1.3 59.8 + - - +
162C ASP* 3.7 1.6 + - - +
172C LEU* 3.7 55.6 - - + +
173C ALA* 5.1 1.1 - - - -
176C ALA* 3.8 7.4 - - + -
186C PHE* 5.6 0.2 - - + -
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Residues in contact with ASN 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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130C THR* 3.4 8.3 - - + -
131C GLY 3.0 16.8 - - - +
132C SER* 3.9 14.7 - - - +
133C LEU* 4.0 33.7 - - + +
159C ILE 3.8 3.6 + - - +
160C LEU* 1.3 70.1 - - - +
162C ASP* 1.3 59.9 + - - +
163C CYS* 2.8 46.0 + - - -
168C ARG* 5.2 2.3 + - - +
172C LEU* 4.0 8.8 - - - +
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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