Contacts of the strand formed by residues 215 - 226 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D LEU* 5.4 3.1 - - - +
158D PHE* 3.7 38.6 - - + +
159D ILE 3.6 3.8 - - - +
160D THR* 5.1 5.4 + - - +
204D LYS* 4.9 14.2 - - - +
205D GLU 5.0 6.3 + - - +
207D LYS* 2.8 43.7 + - + +
213D SER* 3.3 6.4 + - - -
214D ASP* 1.3 76.9 + - - +
216D ALA* 1.3 65.5 + - - +
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Residues in contact with ALA 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D PHE 4.3 4.0 - - - -
159D ILE* 3.0 38.0 + - - +
162D GLY 4.4 2.9 - - - -
163D SER* 4.1 25.8 - - - +
201D VAL* 4.1 20.4 - - + -
202D GLY* 4.5 3.4 - - - +
204D LYS* 5.7 8.1 - - + +
214D ASP* 4.3 0.6 - - - +
215D THR* 1.3 79.8 - - - +
217D GLN* 1.3 62.7 + - - +
218D LEU* 3.9 1.8 + - - +
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Residues in contact with GLN 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D PRO* 4.0 4.4 - - - +
155D THR* 3.5 22.0 - - + +
156D LYS 3.1 17.5 - - - +
157D GLN* 3.3 39.3 - - + +
158D PHE 4.6 0.4 - - - +
201D VAL 3.4 0.2 - - - -
202D GLY* 2.3 47.4 + - - -
203D ARG* 4.6 7.2 + - - +
205D GLU* 5.3 2.4 + - - +
216D ALA* 1.3 76.0 - - - +
218D LEU* 1.3 62.7 + - - +
219D ILE* 3.9 19.4 - - - +
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Residues in contact with LEU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D GLY* 5.0 5.2 - - - +
154D GLY 3.8 0.7 - - - +
155D THR* 3.2 8.3 - - - +
156D LYS* 2.6 49.2 + - + +
159D ILE* 3.9 34.1 - - + -
162D GLY* 3.6 32.1 - - - +
168D TYR* 4.1 24.0 - - + -
170D VAL* 5.1 7.2 - - + -
199D LEU* 4.6 13.7 - - + -
200D LYS 3.8 1.8 - - - +
201D VAL* 5.0 4.9 - - - -
216D ALA 4.4 0.9 - - - +
217D GLN* 1.3 81.3 - - - +
219D ILE* 1.3 61.7 + - - +
220D LEU* 4.0 10.8 - - + +
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Residues in contact with ILE 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D GLY 3.9 2.7 - - - +
155D THR* 4.6 11.2 - - - +
198D GLY 3.6 0.9 - - - +
199D LEU* 3.4 3.3 - - - -
200D LYS* 2.7 66.2 + - + +
201D VAL 4.7 7.0 - - - +
202D GLY* 5.0 2.9 - - - -
203D ARG* 5.0 18.6 - - + +
217D GLN* 3.9 22.9 - - + +
218D LEU* 1.3 75.0 - - - +
220D LEU* 1.3 62.8 + - - +
221D GLU* 3.7 26.9 + - + +
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Residues in contact with LEU 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D THR* 4.2 15.9 - - + +
152D LEU* 4.0 19.7 - - + +
153D ASN* 3.3 8.1 - - - +
154D GLY 2.8 39.8 + - - +
156D LYS* 5.1 5.2 - - + -
170D VAL* 3.8 33.9 - - + -
192D PHE* 5.1 2.0 - - + -
198D GLY 3.3 3.6 - - - +
199D LEU* 3.9 24.9 - - + -
218D LEU* 4.8 12.1 - - + +
219D ILE* 1.3 72.0 - - - +
221D GLU* 1.3 66.4 + - - +
222D ASP 3.9 0.7 - - - -
223D LEU* 3.5 26.5 - - + -
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Residues in contact with GLU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ASN* 3.6 3.3 - - - +
198D GLY* 2.8 27.0 + - - +
200D LYS* 4.6 22.7 - - + +
219D ILE* 3.7 23.7 + - + +
220D LEU* 1.3 76.5 - - - +
222D ASP* 1.3 76.7 + - - +
223D LEU 2.9 2.1 + - - -
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Residues in contact with ASP 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D GLU* 4.9 2.4 - - - +
151D ARG* 3.3 36.2 + - - +
152D LEU 3.3 4.0 + - - -
153D ASN* 2.5 41.3 + - - +
198D GLY* 4.6 1.6 - - - -
221D GLU* 1.3 75.9 - - - +
223D LEU* 1.3 60.4 + - - +
224D PHE 3.6 0.2 + - - -
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Residues in contact with LEU 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D TRP 3.4 1.4 - - - +
151D ARG* 3.2 4.5 - - - -
152D LEU* 2.7 50.5 + - + +
192D PHE* 3.5 36.3 - - + -
195D PRO* 3.5 22.0 - - + -
197D ARG 3.4 22.9 - - - +
198D GLY* 3.5 16.8 - - - +
199D LEU* 4.5 2.5 - - + -
220D LEU* 3.5 24.7 - - + -
221D GLU 2.9 2.6 + - - -
222D ASP* 1.3 74.3 - - - +
224D PHE* 1.3 71.2 + - - +
225D VAL* 4.4 4.3 - - + -
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Residues in contact with PHE 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D VAL* 3.5 28.0 - - + -
147D GLU 4.0 7.2 - - - -
148D GLY 3.4 21.5 - - - -
149D GLY* 3.8 8.5 - - - -
150D TRP 3.3 14.6 - - - -
151D ARG* 3.1 33.2 - - - +
195D PRO* 5.3 2.6 - - - +
197D ARG 5.2 1.0 + - - -
222D ASP 3.6 2.4 + - - -
223D LEU* 1.3 84.1 - - - +
225D VAL* 1.3 77.0 + - - +
226D PRO* 4.0 9.5 - - + +
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Residues in contact with VAL 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLY* 3.1 2.6 - - - -
150D TRP* 2.8 55.1 + - + +
152D LEU* 4.4 15.5 - - + -
190D PHE* 4.2 11.2 - - + -
192D PHE* 3.5 39.7 - - + -
223D LEU* 4.4 6.3 - - + -
224D PHE* 1.3 85.8 - - - +
226D PRO* 1.3 69.0 - - + +
229D ALA* 3.5 21.5 - - + -
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Residues in contact with PRO 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D GLY 3.8 9.9 - - - +
149D GLY* 3.8 1.6 - - - -
150D TRP* 4.1 5.2 - - - -
192D PHE* 5.3 6.7 - - + -
224D PHE* 4.0 12.5 - - + +
225D VAL* 1.3 94.7 - - + +
227D GLU* 1.3 67.7 + - - +
228D GLU* 3.1 22.9 - - + +
229D ALA* 3.1 25.2 + - + +
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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