Contacts of the strand formed by residues 201 - 212 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ILE* 4.6 21.1 - - + -
192A ALA 3.1 9.9 - - - +
193A LYS* 3.5 34.6 - - + +
194A ASN 3.7 1.9 + - - +
197A LEU* 3.7 13.6 - - - +
199A THR* 3.1 23.2 + - - -
200A GLY* 1.3 85.7 - - - +
202A GLN* 1.3 66.5 + - - +
203A VAL* 3.9 4.3 + - - +
293A HIS 5.3 0.3 - - - +
299A LEU* 3.5 37.7 - - + -
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Residues in contact with GLN 202 (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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190A ARG 3.6 1.1 - - - +
191A ILE* 3.3 6.2 - - - +
192A ALA* 2.9 41.0 + - + +
194A ASN* 4.6 4.9 + - + -
197A LEU* 3.4 20.4 - - + +
201A TYR* 1.3 73.6 - - - +
203A VAL* 1.3 72.5 + - - +
204A GLN* 3.5 18.6 - - + +
5B T 3.5 29.1 - - + +
6B A 2.7 53.2 + - - +
7B A 3.4 9.7 + - - -
21C T 3.6 7.6 - - - +
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Residues in contact with VAL 203 (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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189A ILE* 4.1 17.0 - - + -
190A ARG 3.5 2.7 - - - +
191A ILE* 4.5 5.6 - - + -
201A TYR 3.9 6.4 + - - +
202A GLN* 1.3 82.0 - - - +
204A GLN* 1.3 69.6 + - - +
288A ILE* 3.6 29.3 - - + +
293A HIS* 4.1 33.3 - - + +
299A LEU* 3.8 28.9 - - + -
302A ILE* 4.1 16.8 - - + -
5B T 4.6 6.9 + - - -
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Residues in contact with GLN 204 (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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189A ILE* 3.5 5.4 - - - +
190A ARG* 2.9 64.6 + - + +
202A GLN* 3.5 23.1 + - + +
203A VAL* 1.3 80.0 - - - +
205A SER* 1.3 62.2 + - - +
206A VAL* 3.8 6.0 + - + -
252A THR* 4.2 16.3 + - - +
288A ILE* 4.5 4.5 - - - -
5B T 5.7 1.1 - - + -
6B A 3.2 25.9 + - + +
7B A 2.9 43.8 + - - +
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Residues in contact with SER 205 (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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189A ILE* 3.8 16.4 - - - -
204A GLN* 1.3 74.0 - - - +
206A VAL* 1.3 62.3 + - - +
251A VAL 3.9 2.6 - - - +
252A THR* 3.9 11.0 + - - +
254A LEU* 4.0 14.9 - - - +
257A ILE* 3.2 29.9 - - - +
281A TRP* 4.1 2.0 - - - -
285A VAL* 3.6 30.0 - - - +
288A ILE* 4.2 11.4 - - - +
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Residues in contact with VAL 206 (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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186A SER 3.7 0.9 - - - +
187A PHE* 3.5 1.6 - - - -
188A TYR* 2.9 85.8 + - + +
190A ARG* 4.2 18.8 - - + +
204A GLN* 4.1 10.8 - - + +
205A SER* 1.3 80.1 - - - +
207A PHE* 1.3 70.2 + - - +
208A GLN* 4.5 0.9 - - + -
250A VAL* 4.0 18.8 - - + -
251A VAL 3.6 2.5 - - - +
252A THR* 4.3 12.1 - - + -
281A TRP* 3.1 11.3 + - - +
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Residues in contact with PHE 207 (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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181A THR* 3.9 4.0 - - + -
185A GLY* 4.8 1.8 - - - -
186A SER 3.4 6.7 - - - -
187A PHE* 3.3 40.8 - + - -
206A VAL* 1.3 75.1 - - - +
208A GLN* 1.3 75.9 + - - +
209A ILE* 3.8 32.5 - - + -
226A LEU* 4.4 7.0 - - + -
249A LEU* 3.8 10.9 - - + +
250A VAL* 3.5 1.9 - - - -
251A VAL* 2.9 58.2 + - + +
257A ILE* 5.0 0.2 - - + -
261A ILE* 4.1 23.3 - - + -
265A PHE* 3.8 20.0 - + - -
281A TRP* 3.9 17.4 - - + -
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Residues in contact with GLN 208 (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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184A GLU 4.1 0.2 - - - +
185A GLY* 3.3 0.3 - - - -
186A SER* 2.9 41.8 + - - +
188A TYR* 3.1 35.9 + - + -
206A VAL* 4.5 2.9 - - + -
207A PHE* 1.3 80.5 - - - +
209A ILE* 1.3 72.3 + - - +
210A THR* 3.8 13.0 + - - +
232A ARG* 5.1 3.2 - - - +
248A ASP* 2.8 35.7 + - + +
249A LEU 3.2 11.2 - - - +
250A VAL* 4.4 7.0 - - + +
16C G 4.9 0.3 - - - -
17C A 3.2 27.6 + - - +
18C C 4.8 1.6 - - - +
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Residues in contact with ILE 209 (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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180A PHE* 3.9 31.2 - - + +
181A THR* 3.7 25.6 - - + -
184A GLU* 4.0 16.2 - - + -
185A GLY* 4.2 7.6 - - - +
207A PHE* 3.8 20.0 - - + -
208A GLN* 1.3 80.6 - - - +
210A THR* 1.3 68.6 + - - +
211A GLN* 5.5 0.2 - - + -
219A MET* 3.8 13.7 - - + +
222A LEU* 5.1 11.0 - - + -
226A LEU* 5.4 3.8 - - + -
248A ASP* 3.3 3.8 - - - -
249A LEU* 2.9 54.7 + - + -
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Residues in contact with THR 210 (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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184A GLU* 3.7 22.8 + - - +
208A GLN* 3.8 7.6 - - - +
209A ILE* 1.3 77.9 - - - +
211A GLN* 1.3 78.8 + - - +
246A CYS* 4.3 22.7 - - + -
247A VAL 3.5 5.8 - - - +
248A ASP* 2.6 24.8 + - - +
15C C 4.5 17.1 - - + +
16C G 3.5 34.5 - - + +
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Residues in contact with GLN 211 (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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27A ASP 4.8 3.6 + - - -
28A ALA 5.5 0.4 + - - -
106A THR* 4.5 9.3 - - - +
180A PHE* 4.2 21.9 - - + -
184A GLU* 3.0 24.5 + - - +
209A ILE* 5.5 0.4 - - + -
210A THR* 1.3 87.3 - - - +
212A ASP* 1.3 74.5 + - - +
214A ARG* 5.2 11.6 - - + +
215A ASP* 4.4 24.9 + - + +
219A MET* 4.5 20.8 - - + +
246A CYS* 4.3 4.7 - - - -
247A VAL* 2.8 35.5 + - - +
15C C 4.0 17.1 + - - +
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Residues in contact with ASP 212 (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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211A GLN* 1.3 83.6 - - - +
213A THR* 1.3 54.1 + - - +
214A ARG* 2.7 39.3 + - - +
215A ASP 3.9 3.6 + - - -
216A ILE* 5.0 0.3 - - - +
245A THR 3.8 9.4 - - - +
246A CYS* 4.1 8.3 - - - -
247A VAL* 5.0 0.9 - - - +
14C A 4.5 12.3 - - - -
15C C 3.3 22.6 + - - +
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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