Contacts of the strand formed by residues 215 - 226 (chain C) in PDB entry 2CX9
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 215 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C LEU* 5.2 3.8 - - - +
158C PHE* 3.4 47.1 - - + +
159C ILE 3.8 4.0 - - - -
160C THR* 4.7 5.7 + - - +
204C LYS* 4.4 4.0 - - - +
205C GLU* 3.8 27.1 + - + +
207C LYS* 3.6 35.0 + - + +
213C SER* 3.6 7.1 + - - -
214C ASP* 1.3 81.5 + - - +
216C ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 216 (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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157C GLN* 4.9 0.4 - - - -
158C PHE* 3.6 5.6 + - - -
159C ILE* 3.1 36.1 + - - +
162C GLY* 3.8 14.6 - - - -
163C SER* 4.1 4.5 - - - +
201C VAL* 3.6 28.5 - - + -
202C GLY 4.3 7.0 - - - +
203C ARG 5.2 4.0 - - - +
204C LYS* 5.5 4.3 - - + -
205C GLU* 5.4 2.0 - - - +
214C ASP* 4.5 3.4 - - - +
215C THR* 1.3 77.7 - - - +
217C GLN* 1.3 61.8 + - - +
218C LEU* 4.0 1.2 + - - +
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Residues in contact with GLN 217 (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* 4.3 4.6 - - - +
155C THR* 3.6 18.4 - - + +
156C LYS 3.2 17.7 - - - +
157C GLN* 3.2 35.4 + - - +
201C VAL* 3.4 5.4 - - - +
202C GLY* 2.7 43.0 + - - +
203C ARG 5.1 3.2 + - - +
216C ALA* 1.3 76.9 - - - +
218C LEU* 1.3 60.8 + - - +
219C ILE* 3.8 20.4 - - - +
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Residues in contact with LEU 218 (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 ALA* 5.0 0.2 - - + -
126C GLY* 5.2 2.7 - - - +
154C GLY 4.0 0.2 - - - +
155C THR* 2.9 10.2 - - - +
156C LYS* 2.6 53.9 + - + -
159C ILE* 3.9 33.4 - - + -
162C GLY* 3.5 31.2 - - - +
168C TYR* 3.9 28.3 - - + -
170C VAL* 5.4 5.2 - - + -
199C LEU* 4.7 6.1 - - + -
200C LYS 3.4 2.7 - - - +
201C VAL* 4.2 12.1 - - + -
217C GLN* 1.3 84.8 - - - +
219C ILE* 1.3 61.8 + - - +
220C LEU* 4.0 10.7 - - + +
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Residues in contact with ILE 219 (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 GLY 3.7 2.2 - - - +
155C THR* 3.8 15.9 - - + +
198C GLY 3.4 3.1 - - - +
199C LEU* 3.4 1.4 - - - -
200C LYS* 2.6 66.0 + - + +
202C GLY* 5.1 7.9 - - - +
217C GLN* 3.8 24.2 - - + +
218C LEU* 1.3 77.4 - - - +
220C LEU* 1.3 65.0 + - - +
221C GLU* 3.8 26.7 + - + +
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Residues in contact with LEU 220 (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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141C THR* 4.8 6.3 - - + -
152C LEU* 3.8 39.0 - - + +
153C ASN* 3.5 7.8 - - - +
154C GLY 2.6 42.4 + - - +
155C THR* 4.9 0.9 - - - -
156C LYS* 5.0 7.0 - - + +
170C VAL* 4.4 20.9 - - + -
198C GLY 3.0 5.6 - - - +
199C LEU* 3.4 30.1 - - + -
218C LEU* 4.0 16.8 - - + +
219C ILE* 1.3 74.8 - - - +
221C GLU* 1.3 66.7 + - - +
222C ASP 3.7 0.6 + - - -
223C LEU* 3.9 13.0 - - + -
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Residues in contact with GLU 221 (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 ASN* 4.7 0.2 - - - -
198C GLY* 2.8 25.7 + - - +
200C LYS* 4.4 25.7 + - + +
219C ILE* 3.8 20.8 + - + +
220C LEU* 1.3 75.0 - - - +
222C ASP* 1.3 77.2 + - - +
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Residues in contact with ASP 222 (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* 3.3 31.8 + - - +
153C ASN* 3.0 32.5 + - - +
197C ARG 4.9 0.7 - - - +
198C GLY* 4.2 2.6 - - - -
220C LEU 3.7 0.6 + - - -
221C GLU* 1.3 75.4 - - - +
223C LEU* 1.3 59.2 + - - +
224C PHE 3.9 0.3 + - - -
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Residues in contact with LEU 223 (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 TRP 3.3 3.0 - - - +
151C ARG* 3.5 1.5 - - - -
152C LEU* 2.8 46.0 + - + +
192C PHE* 3.8 29.4 - - + -
195C PRO* 3.7 19.5 - - + -
197C ARG 3.1 26.7 - - - +
198C GLY* 3.6 14.6 - - - +
199C LEU* 4.0 13.2 - - + -
220C LEU* 3.9 24.2 - - + -
221C GLU 4.0 0.2 - - - -
222C ASP* 1.3 73.8 - - - +
224C PHE* 1.3 73.9 + - - +
225C VAL* 3.9 6.7 + - + -
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Residues in contact with PHE 224 (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 VAL* 3.6 15.3 - - + -
147C GLU 3.8 6.7 - - - -
148C GLY* 3.4 14.4 - - - -
149C GLY* 3.1 39.7 - - - -
150C TRP 3.2 15.5 - - - -
151C ARG* 3.6 28.1 - - - +
195C PRO* 5.6 1.2 - - - +
197C ARG 5.1 0.2 + - - -
222C ASP 3.9 0.4 + - - -
223C LEU* 1.3 84.2 - - - +
225C VAL* 1.3 72.6 + - - +
226C PRO* 4.0 8.4 - - + +
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Residues in contact with VAL 225 (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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149C GLY* 3.0 2.9 - - - -
150C TRP* 2.9 28.2 + - + +
152C LEU* 3.5 42.2 - - + -
190C PHE* 5.2 0.7 - - + -
192C PHE* 3.4 36.6 - - + -
223C LEU* 4.0 7.0 - - + +
224C PHE* 1.3 84.3 - - - +
226C PRO* 1.3 78.1 - - + +
229C ALA* 3.2 31.0 - - + -
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Residues in contact with PRO 226 (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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148C GLY 3.8 7.4 - - - +
149C GLY* 3.8 0.2 - - - -
150C TRP* 3.9 4.0 - - - -
192C PHE* 5.3 3.6 - - + -
224C PHE* 4.0 12.7 - - + +
225C VAL* 1.3 105.4 - - + +
227C GLU* 1.3 66.3 + - - +
228C GLU* 3.0 25.6 - - + +
229C ALA* 3.0 23.7 + - + +
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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