Contacts of the strand formed by residues 201 - 212 (chain D) in PDB entry 6BCH
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 TYR 201 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191D ILE* 4.7 21.3 - - + -
192D ALA 3.1 9.4 - - - +
193D LYS* 3.5 33.4 - - + +
194D ASN 3.7 1.3 + - - +
197D LEU* 3.7 13.7 - - - +
199D THR* 3.1 22.4 + - - -
200D GLY* 1.3 84.6 - - - +
202D GLN* 1.3 66.4 + - - +
203D VAL* 3.9 5.6 + - + +
293D HIS 5.3 0.3 - - - +
299D LEU* 3.5 38.6 - - + -
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Residues in contact with GLN 202 (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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190D ARG 3.6 0.9 - - - +
191D ILE* 3.4 6.1 - - - +
192D ALA* 2.9 41.2 + - + +
194D ASN* 4.5 5.2 + - + -
197D LEU* 3.4 20.4 - - + +
201D TYR* 1.3 73.4 - - - +
203D VAL* 1.3 70.9 + - - +
204D GLN* 3.5 17.0 - - + +
5E T 3.5 30.7 + - + +
6E A 2.7 53.6 + - - +
7E A 3.5 9.8 + - - -
21F T 3.5 8.1 - - - +
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Residues in contact with VAL 203 (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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189D ILE* 4.1 17.0 - - + -
190D ARG 3.6 2.5 - - - +
191D ILE* 4.5 6.1 - - + -
201D TYR* 3.9 6.4 + - + +
202D GLN* 1.3 80.2 - - - +
204D GLN* 1.3 68.5 + - - +
288D ILE* 3.7 29.0 - - + +
293D HIS* 4.1 33.6 - - + +
299D LEU* 3.8 28.9 - - + -
302D ILE* 4.1 17.0 - - + -
5E T 4.6 7.3 + - - -
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Residues in contact with GLN 204 (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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189D ILE* 3.5 4.9 - - - +
190D ARG* 2.9 61.2 + - + +
202D GLN* 3.5 19.9 + - + +
203D VAL* 1.3 79.4 - - - +
205D SER* 1.3 62.5 + - - +
206D VAL* 4.4 5.8 - - + -
252D THR* 4.2 16.8 + - + +
288D ILE* 4.4 4.9 - - - -
5E T 5.7 2.0 - - + -
6E A 3.1 26.7 + - + +
7E A 2.8 46.8 + - - +
20F T 5.0 0.2 - - - +
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Residues in contact with SER 205 (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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189D ILE* 3.7 16.2 - - - -
204D GLN* 1.3 74.2 - - - +
206D VAL* 1.3 62.4 + - - +
251D VAL 3.9 2.4 - - - +
252D THR* 3.9 11.4 + - - +
254D LEU* 4.1 14.6 - - - +
257D ILE* 3.2 30.2 - - - +
281D TRP* 4.1 3.1 - - - -
285D VAL* 3.6 29.4 - - - +
288D ILE* 4.1 11.6 - - - +
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Residues in contact with VAL 206 (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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186D SER 3.7 0.7 - - - +
187D PHE* 3.5 1.2 - - - -
188D TYR* 2.9 84.3 + - + +
190D ARG* 4.1 19.5 - - + +
204D GLN* 4.1 11.7 - - + +
205D SER* 1.3 80.3 - - - +
207D PHE* 1.3 70.8 + - - +
208D GLN* 4.6 0.7 - - + -
250D VAL* 4.0 17.9 - - + -
251D VAL 3.6 3.1 - - - +
252D THR* 4.2 12.1 - - + -
281D TRP* 3.1 11.3 + - - +
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Residues in contact with PHE 207 (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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181D THR* 4.0 5.8 - - + -
185D GLY* 4.8 0.4 - - - -
186D SER 3.4 7.6 - - - -
187D PHE* 3.3 40.2 - + - -
206D VAL* 1.3 75.1 - - - +
208D GLN* 1.3 75.4 + - - +
209D ILE* 3.8 31.6 - - + -
226D LEU* 4.4 7.2 - - + -
249D LEU* 3.8 10.9 - - + +
250D VAL* 3.5 2.1 - - - -
251D VAL* 2.9 58.1 + - + +
257D ILE* 5.1 0.2 - - + -
261D ILE* 4.1 22.4 - - + -
265D PHE* 3.8 20.0 - + - -
281D TRP* 3.9 18.3 - - + -
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Residues in contact with GLN 208 (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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184D GLU 4.1 0.6 - - - +
185D GLY* 3.3 4.7 - - - -
186D SER* 2.9 42.5 + - - +
188D TYR* 3.1 37.4 + - + +
206D VAL* 4.6 1.6 - - + -
207D PHE* 1.3 80.2 - - - +
209D ILE* 1.3 70.1 + - - +
210D THR* 3.7 14.1 + - - +
232D ARG* 5.1 2.6 - - - +
248D ASP* 2.7 36.0 + - + +
249D LEU 3.2 10.3 - - - +
250D VAL* 4.6 7.5 - - + +
16F G 4.8 0.5 - - - -
17F A 3.1 27.8 + - - +
18F C 4.9 1.4 - - - +
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Residues in contact with ILE 209 (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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180D PHE* 3.8 31.9 - - + -
181D THR* 3.7 25.8 - - + -
184D GLU* 4.0 15.9 - - + -
185D GLY* 4.3 8.1 - - - -
207D PHE* 3.8 19.1 - - + -
208D GLN* 1.3 79.8 - - - +
210D THR* 1.3 68.6 + - - +
219D MET* 3.6 14.1 - - + +
222D LEU* 5.1 10.1 - - + -
226D LEU* 5.4 4.0 - - + -
248D ASP* 3.3 3.5 - - - -
249D LEU* 2.9 53.6 + - + -
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Residues in contact with THR 210 (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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184D GLU* 3.8 22.0 + - - +
208D GLN* 3.7 7.6 + - - +
209D ILE* 1.3 77.7 - - - +
211D GLN* 1.3 78.3 + - - +
219D MET* 5.0 0.2 - - - -
246D CYS* 4.2 23.6 - - + -
247D VAL 3.5 6.1 - - - +
248D ASP* 2.6 23.8 + - - +
15F C 4.5 18.8 - - + +
16F G 3.6 33.9 - - + +
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Residues in contact with GLN 211 (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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27D ASP 4.8 3.4 + - - -
28D ALA 5.7 0.2 + - - -
106D THR* 4.5 15.8 - - - +
180D PHE* 4.3 19.6 - - + -
184D GLU* 3.3 25.1 + - - +
209D ILE* 5.6 0.2 - - + -
210D THR* 1.3 86.7 - - - +
212D ASP* 1.3 73.8 + - + +
215D ASP* 4.6 19.5 + - + +
219D MET* 4.4 20.9 - - + -
246D CYS* 4.3 4.7 - - - -
247D VAL* 2.8 35.2 + - - +
15F C 3.9 17.0 + - - +
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Residues in contact with ASP 212 (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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211D GLN* 1.3 86.3 - - + +
213D THR* 1.3 75.2 + - - +
214D ARG* 2.7 27.3 + - + +
215D ASP 3.8 5.9 + - - -
216D ILE* 5.0 0.2 - - - +
245D THR* 3.1 21.0 - - - +
246D CYS* 4.1 9.0 - - - -
247D VAL* 5.0 0.9 - - - +
14F A 4.6 18.0 + - - +
15F C 3.4 21.8 + - - +
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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