Contacts of the strand formed by residues 215 - 226 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B LEU* 5.6 1.7 - - - +
158B PHE* 3.6 40.8 - - + +
159B ILE 3.5 3.8 - - - +
160B THR* 4.9 3.6 + - - +
204B LYS* 3.9 7.6 - - - +
205B GLU* 3.6 26.2 + - + +
207B LYS* 3.2 40.9 + - + +
213B SER* 3.3 8.7 + - - -
214B ASP* 1.3 79.1 + - - +
216B ALA* 1.3 66.5 + - - +
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B PHE* 3.7 4.7 + - - -
159B ILE* 2.9 38.9 + - - +
162B GLY* 4.4 3.1 - - - -
163B SER* 4.1 18.2 - - - +
201B VAL* 3.5 29.6 - - + -
202B GLY 4.2 6.7 - - - +
203B ARG 4.9 4.7 - - - +
204B LYS* 5.2 2.5 - - + -
205B GLU* 5.1 5.4 - - - -
214B ASP* 4.3 0.4 - - - +
215B THR* 1.3 77.7 - - - +
217B GLN* 1.3 62.1 + - - +
218B LEU* 5.0 1.1 - - + -
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Residues in contact with GLN 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PRO* 4.5 1.9 - - - +
155B THR* 3.5 19.3 - - + +
156B LYS 3.2 15.3 - - - +
157B GLN* 3.1 29.2 + - - +
158B PHE 4.7 1.8 - - - +
201B VAL* 3.5 4.3 - - - +
202B GLY* 2.8 39.1 + - - +
203B ARG 5.1 1.0 + - - +
205B GLU* 4.6 9.5 + - - +
216B ALA* 1.3 74.7 - - - +
218B LEU* 1.3 66.2 + - - +
219B ILE* 3.5 28.9 + - + +
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLY* 5.2 4.3 - - - +
154B GLY 3.9 0.3 - - - +
155B THR* 3.2 7.1 - - - +
156B LYS* 2.8 50.2 + - + +
159B ILE* 3.9 31.0 - - + -
162B GLY* 3.4 30.7 - - - +
168B TYR* 3.8 26.0 - - + -
170B VAL* 5.3 6.3 - - + -
199B LEU* 3.9 16.6 - - + -
200B LYS 3.7 2.0 - - - -
201B VAL* 4.0 14.4 - - + -
216B ALA 4.8 0.7 - - - +
217B GLN* 1.3 82.4 - - - +
219B ILE* 1.3 61.0 + - - +
220B LEU* 3.9 6.8 + - + +
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Residues in contact with ILE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B GLY 3.7 5.8 - - - +
155B THR* 4.3 11.2 - - - +
198B GLY 3.5 3.3 - - - +
199B LEU* 3.6 0.3 - - - -
200B LYS* 2.8 56.1 + - + +
202B GLY* 5.6 4.5 - - - +
217B GLN* 3.5 30.3 - - + +
218B LEU* 1.3 74.3 - - - +
220B LEU* 1.3 61.7 + - - +
221B GLU* 3.7 27.4 + - + +
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Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B THR* 4.6 8.5 - - + -
152B LEU* 3.8 33.0 - - + +
153B ASN* 3.2 6.8 - - - +
154B GLY 2.9 37.2 + - - +
156B LYS* 5.1 5.2 - - + -
170B VAL* 3.8 37.2 - - + -
192B PHE* 5.2 2.7 - - + -
198B GLY 3.2 4.0 - - - +
199B LEU* 3.3 34.5 - - + -
218B LEU* 4.6 9.6 - - + +
219B ILE* 1.3 72.1 - - - +
221B GLU* 1.3 62.7 + - - +
223B LEU* 4.1 16.8 - - + -
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU 4.1 0.2 + - - -
153B ASN* 3.5 4.7 - - - +
198B GLY* 2.7 25.6 + - - +
200B LYS* 2.7 45.2 + - - +
219B ILE* 3.8 20.3 - - + +
220B LEU* 1.3 75.2 - - - +
222B ASP* 1.3 76.1 + - - +
223B LEU 3.1 0.9 + - - -
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Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ARG* 2.6 48.4 + - - +
152B LEU 3.1 5.2 + - - -
153B ASN* 2.7 32.5 + - - +
198B GLY* 4.8 1.6 - - - -
221B GLU* 1.3 74.7 - - - +
223B LEU* 1.3 59.8 + - - +
224B PHE 3.4 0.5 + - - -
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B TRP 3.4 1.2 - - - +
151B ARG* 3.3 5.3 - - - -
152B LEU* 2.8 49.3 + - + +
192B PHE* 3.6 36.6 - - + -
195B PRO* 3.4 24.5 - - + -
197B ARG 3.4 22.0 - - - +
198B GLY* 3.8 17.9 - - - +
199B LEU* 4.6 0.9 - - + -
220B LEU* 4.1 19.5 - - + -
221B GLU 3.1 1.0 - - - -
222B ASP* 1.3 76.3 - - - +
224B PHE* 1.3 73.6 + - - +
225B VAL* 3.9 9.4 + - + -
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Residues in contact with PHE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B VAL* 5.3 4.9 - - + -
147B GLU 4.5 7.9 - - - -
148B GLY* 3.5 23.6 - - - -
149B GLY* 3.7 23.8 - - - -
150B TRP 3.2 15.7 - - - -
151B ARG* 3.8 28.7 - - + +
195B PRO* 5.4 1.6 - - - +
197B ARG 5.2 0.4 + - - -
222B ASP 3.4 2.4 + - - -
223B LEU* 1.3 83.5 - - - +
225B VAL* 1.3 66.2 + - - +
226B PRO* 4.1 16.4 - - + +
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Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLY* 3.2 1.9 - - - -
150B TRP* 2.9 47.8 + - + +
152B LEU* 4.2 15.0 - - + -
190B PHE* 4.1 11.2 - - + -
192B PHE* 3.5 42.8 - - + -
223B LEU* 4.2 6.3 - - + -
224B PHE* 1.3 81.7 - - - +
226B PRO* 1.3 71.8 - - + +
229B ALA* 3.5 22.4 - - + -
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Residues in contact with PRO 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B GLY 3.7 10.5 - - - +
149B GLY* 3.7 0.9 - - - -
150B TRP* 4.3 2.1 - - - -
192B PHE* 5.2 6.1 - - + -
224B PHE* 4.1 13.1 - - + +
225B VAL* 1.3 94.3 - - + +
227B GLU* 1.3 66.3 + - - +
228B GLU* 3.1 24.7 - - + +
229B ALA* 3.1 26.8 + - + +
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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