Contacts of the strand formed by residues 201 - 212 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191H ILE* 4.6 21.1 - - + -
192H ALA 3.1 9.4 - - - +
193H LYS* 3.5 33.9 - - + +
194H ASN 3.7 1.3 + - - +
197H LEU* 3.7 13.5 - - - +
199H THR* 3.1 22.6 + - - -
200H GLY* 1.3 85.2 - - - +
202H GLN* 1.3 65.9 + - - +
203H VAL* 3.9 5.1 + - + +
293H HIS 5.3 0.3 - - - +
299H LEU* 3.5 37.5 - - + -
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Residues in contact with GLN 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H ARG 3.6 0.9 - - - +
191H ILE* 3.4 6.1 - - - +
192H ALA* 2.9 41.3 + - + +
194H ASN* 4.5 5.0 + - + -
197H LEU* 3.4 20.0 - - + +
201H TYR* 1.3 74.3 - - - +
203H VAL* 1.3 71.0 - - - +
204H GLN* 3.5 20.7 - - + +
5I T 3.4 32.0 + - + +
6I A 2.7 50.8 + - - +
7I A 3.5 7.3 + - - -
21J T 3.5 8.1 - - - +
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Residues in contact with VAL 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H ILE* 4.1 16.4 - - + -
190H ARG 3.5 2.2 - - - +
191H ILE* 4.4 6.3 - - + -
201H TYR* 3.9 6.7 + - + +
202H GLN* 1.3 81.7 - - - +
204H GLN* 1.3 68.1 + - - +
288H ILE* 3.7 29.1 - - + +
293H HIS* 4.1 33.8 - - + +
299H LEU* 3.8 28.7 - - + -
302H ILE* 3.8 17.3 - - + -
5I T 4.7 6.7 + - - -
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Residues in contact with GLN 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H ILE* 3.5 4.7 - - - +
190H ARG* 2.9 61.5 + - + +
202H GLN* 3.5 22.2 + - + +
203H VAL* 1.3 79.5 - - - +
205H SER* 1.3 61.7 + - - +
206H VAL* 3.9 5.8 + - + -
252H THR* 4.2 17.2 + - + +
288H ILE* 4.5 4.7 - - - -
5I T 5.7 1.6 - - + -
6I A 3.1 27.5 + - + +
7I A 2.9 45.1 + - - +
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Residues in contact with SER 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H ILE* 3.8 16.2 - - - -
204H GLN* 1.3 74.3 - - - +
206H VAL* 1.3 62.4 + - - +
251H VAL 3.8 2.6 - - - +
252H THR* 3.9 12.6 + - - +
254H LEU* 4.1 14.7 - - - +
257H ILE* 3.2 29.5 - - - +
281H TRP* 4.2 2.5 - - - -
285H VAL* 3.6 29.4 - - - +
288H ILE* 4.2 12.0 - - - +
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Residues in contact with VAL 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H SER 3.7 0.7 - - - +
187H PHE* 3.6 0.7 - - - -
188H TYR* 2.9 83.0 + - + +
190H ARG* 4.1 20.4 - - + +
204H GLN* 4.1 11.7 - - + +
205H SER* 1.3 80.3 - - - +
207H PHE* 1.3 71.5 + - - +
208H GLN* 4.6 0.4 - - + -
250H VAL* 4.0 17.9 - - + -
251H VAL 3.6 3.1 - - - +
252H THR* 4.2 12.6 - - + -
281H TRP* 3.1 11.5 + - - +
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Residues in contact with PHE 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181H THR* 4.0 5.8 - - + -
185H GLY* 4.8 0.2 - - - -
186H SER 3.4 7.9 - - - -
187H PHE* 3.3 39.3 - + - -
206H VAL* 1.3 75.9 - - - +
208H GLN* 1.3 75.6 + - - +
209H ILE* 3.8 33.0 - - + -
226H LEU* 4.5 6.7 - - + -
249H LEU* 3.8 10.5 - - + +
250H VAL* 3.5 2.3 - - - -
251H VAL* 2.9 56.7 + - + +
257H ILE* 5.0 1.1 - - + -
261H ILE* 4.2 22.9 - - + -
265H PHE* 3.9 18.8 - + - -
281H TRP* 3.9 18.3 - - + -
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Residues in contact with GLN 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184H GLU 4.2 0.4 - - - +
185H GLY* 3.3 0.7 - - - -
186H SER* 2.9 39.4 + - - +
188H TYR* 3.0 40.7 + - + +
206H VAL* 4.6 1.6 - - + -
207H PHE* 1.3 80.4 - - - +
209H ILE* 1.3 73.6 + - - +
210H THR* 3.8 13.9 + - - +
232H ARG* 5.2 2.8 - - - +
248H ASP* 2.8 35.4 + - + +
249H LEU 3.2 10.5 - - - +
250H VAL* 4.5 8.1 - - + +
16J G 4.9 0.5 - - - -
17J A 3.1 27.7 + - - +
18J C 4.8 1.4 - - - +
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Residues in contact with ILE 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180H PHE* 3.9 31.2 - - + +
181H THR* 3.7 25.6 - - + -
184H GLU* 4.0 15.7 - - + -
185H GLY* 4.2 8.1 - - - -
207H PHE* 3.8 20.0 - - + -
208H GLN* 1.3 80.4 - - - +
210H THR* 1.3 68.4 + - - +
211H GLN* 5.6 0.2 - - + -
219H MET* 3.6 13.6 - - + +
222H LEU* 5.1 10.3 - - + -
226H LEU* 5.5 4.0 - - + -
248H ASP* 3.3 3.8 - - - -
249H LEU* 2.9 52.9 + - + -
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Residues in contact with THR 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184H GLU* 3.8 21.3 + - - +
208H GLN* 3.8 7.8 + - - +
209H ILE* 1.3 78.3 - - - +
211H GLN* 1.3 77.7 + - - +
219H MET* 5.0 0.2 - - - -
246H CYS* 4.2 23.8 - - + -
247H VAL 3.5 6.1 - - - +
248H ASP* 2.5 24.1 + - - +
15J C 4.3 19.4 - - + +
16J G 3.7 33.3 - - + +
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Residues in contact with GLN 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ASP 4.8 3.4 + - - -
106H THR* 4.5 11.5 - - - +
180H PHE* 4.3 18.8 - - + -
184H GLU* 3.1 27.8 + - - +
209H ILE* 5.6 0.2 - - + -
210H THR* 1.3 84.3 - - - +
212H ASP* 1.3 74.2 + - + +
215H ASP* 4.5 24.1 + - + +
219H MET* 4.4 20.4 - - + -
246H CYS* 4.3 4.9 - - - -
247H VAL* 2.8 35.2 + - - +
15J C 3.9 12.9 - - - +
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Residues in contact with ASP 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211H GLN* 1.3 86.2 - - + +
213H THR* 1.3 56.4 + - - +
214H ARG* 2.6 24.0 + - + +
215H ASP 3.8 6.2 + - - -
216H ILE* 4.9 0.2 - - - +
245H THR 3.7 10.5 - - - +
246H CYS* 4.2 5.5 - - - -
247H VAL* 5.0 0.7 - - - +
14J A 4.8 7.6 - - - -
15J C 2.9 26.6 + - - +
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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