Contacts of the strand formed by residues 215 - 226 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A LEU* 5.6 1.7 - - - +
158A PHE* 3.7 39.0 - - + +
159A ILE 3.4 4.3 - - - +
160A THR* 5.0 3.8 + - - +
204A LYS* 3.6 23.1 - - - +
205A GLU* 3.7 11.7 + - + +
207A LYS* 3.4 40.7 + - + -
213A SER* 3.3 6.7 + - - -
214A ASP* 1.3 78.7 + - - +
216A ALA* 1.3 68.6 + - - +
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A PHE 3.7 5.3 + - - -
159A ILE* 3.0 36.8 + - - +
162A GLY 4.4 2.0 - - - -
163A SER* 4.2 18.2 - - - +
201A VAL* 3.8 27.6 - - + -
202A GLY 3.8 7.2 - - - +
203A ARG 4.6 5.6 - - - +
204A LYS* 4.9 1.8 - - - -
205A GLU* 5.2 4.0 - - - +
215A THR* 1.3 80.0 - - - +
217A GLN* 1.3 64.5 + - - +
218A LEU* 3.8 1.2 + - - +
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Residues in contact with GLN 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PRO* 4.0 5.7 - - - +
155A THR* 3.5 22.6 - - + +
156A LYS 3.3 17.5 - - - +
157A GLN* 2.9 29.9 + - - +
158A PHE 4.7 1.8 - - - +
201A VAL* 3.6 3.8 - - - +
202A GLY* 2.7 40.9 + - - +
203A ARG 4.8 2.1 + - - +
205A GLU* 4.7 9.4 + - - +
216A ALA* 1.3 74.0 - - - +
218A LEU* 1.3 63.6 + - - +
219A ILE* 3.9 18.3 + - + +
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLY* 5.2 4.3 - - - +
155A THR* 3.1 6.3 - - - +
156A LYS* 2.7 52.6 + - + +
159A ILE* 4.0 33.2 - - + -
162A GLY* 3.3 30.1 - - - +
168A TYR* 3.8 28.9 - - + -
170A VAL* 5.3 5.2 - - + -
199A LEU* 4.0 13.0 - - + -
200A LYS 3.7 0.9 - - - -
201A VAL* 3.9 16.2 - - + -
216A ALA 4.4 0.9 - - - +
217A GLN* 1.3 79.4 - - - +
219A ILE* 1.3 62.7 + - - +
220A LEU* 3.9 4.6 + - + +
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Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLY 3.7 3.6 - - - +
155A THR* 4.0 16.6 - - + +
199A LEU* 3.7 0.7 - - - +
200A LYS* 2.7 54.6 + - + +
201A VAL 6.1 0.2 - - - -
202A GLY* 5.5 5.4 - - - +
217A GLN* 3.9 24.7 - - + +
218A LEU* 1.3 77.2 - - - +
220A LEU* 1.3 63.5 + - - +
221A GLU* 3.6 28.0 + - + +
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Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A THR* 4.2 16.6 - - + -
152A LEU* 3.8 27.8 - - + +
153A ASN* 3.3 5.2 - - - +
154A GLY 2.7 40.0 + - - +
156A LYS* 5.0 6.3 - - + -
170A VAL* 3.8 34.1 - - + -
192A PHE* 5.1 3.4 - - + -
198A GLY 3.5 3.4 - - - +
199A LEU* 3.2 33.7 - - + -
218A LEU* 4.8 9.2 - - + +
219A ILE* 1.3 72.0 - - - +
221A GLU* 1.3 61.6 + - - +
223A LEU* 4.2 16.8 - - + -
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Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LEU 4.1 0.2 + - - -
153A ASN* 3.7 2.5 - - - -
198A GLY* 2.9 24.7 + - - +
200A LYS* 2.7 48.1 + - + +
219A ILE* 3.8 21.9 - - + +
220A LEU* 1.3 75.2 - - - +
222A ASP* 1.3 74.8 - - - +
223A LEU 3.1 1.1 + - - -
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Residues in contact with ASP 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG* 2.6 47.8 + - - +
152A LEU 3.0 3.9 + - - -
153A ASN* 2.5 40.3 + - - +
198A GLY* 4.9 1.2 - - - -
221A GLU* 1.3 75.3 - - - +
223A LEU* 1.3 59.3 + - - +
224A PHE 3.4 0.3 + - - -
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A TRP 3.4 1.6 - - - +
151A ARG* 3.3 4.0 - - - -
152A LEU* 2.7 53.6 + - + +
192A PHE* 3.4 38.4 - - + -
195A PRO* 3.5 24.2 - - + -
197A ARG 3.5 22.2 - - - +
198A GLY* 3.6 18.6 - - - +
199A LEU* 5.0 0.2 - - + -
220A LEU* 4.2 14.6 - - + -
221A GLU 3.1 3.0 - - - -
222A ASP* 1.3 75.0 - - - +
224A PHE* 1.3 70.7 + - - +
225A VAL* 3.8 9.2 + - + -
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Residues in contact with PHE 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A VAL* 3.7 26.0 - - + -
147A GLU 4.4 4.9 - - - -
148A GLY* 3.6 22.4 - - - -
149A GLY 4.0 4.7 - - - -
150A TRP 3.4 11.7 - - - -
151A ARG* 3.7 30.0 - - - +
195A PRO* 5.6 1.0 - - - +
197A ARG* 5.2 10.6 + - - +
222A ASP 3.4 2.6 + - - -
223A LEU* 1.3 82.9 - - - +
225A VAL* 1.3 77.4 + - - +
226A PRO* 4.2 10.4 - - + +
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Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A GLY* 3.3 1.2 - - - -
150A TRP* 2.8 50.9 + - + +
152A LEU* 3.9 19.7 - - + -
190A PHE* 4.1 11.2 - - + -
192A PHE* 3.6 36.6 - - + -
223A LEU* 3.9 8.3 - - + -
224A PHE* 1.3 84.3 - - - +
226A PRO* 1.3 70.3 - - + +
229A ALA* 3.7 20.0 - - + -
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Residues in contact with PRO 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLY 3.6 11.2 - - - +
149A GLY* 3.9 2.0 - - - -
150A TRP* 4.1 4.2 - - - -
192A PHE* 5.4 5.2 - - + -
224A PHE* 4.2 12.7 - - + +
225A VAL* 1.3 89.3 - - + +
227A GLU* 1.3 66.2 + - - +
228A GLU* 3.8 22.4 - - + +
229A ALA* 3.0 28.1 + - + +
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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