Contacts of the strand formed by residues 206 - 216 (chain s) in PDB entry 3J7Y
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 VAL 206 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205s PRO* 1.3 81.2 - - - +
207s HIS* 1.3 64.1 + - - +
233s ILE 3.8 1.4 - - - +
234s ASP* 3.4 1.7 - - - -
235s ASP* 2.8 50.2 + - + +
237s PRO* 3.8 14.4 - - + -
240s GLN* 3.5 30.7 - - - +
283s PHE 3.5 9.2 - - - +
284s VAL 4.5 2.7 - - - -
298s GLN* 3.9 4.3 - - - +
331s SER 4.5 3.6 - - - +
334s ALA* 4.3 11.2 - - + -
335s TRP* 4.1 37.2 - - + +
338s ALA* 5.4 0.2 - - + -
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Residues in contact with HIS 207 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1675 THR* 3.3 40.6 + - + +
205s PRO* 3.6 21.6 - - + +
206s VAL* 1.3 82.5 + - - +
208s PHE* 1.3 63.0 + - - +
233s ILE 3.4 3.4 - - - -
234s ASP* 2.7 36.5 + - + +
235s ASP 4.6 2.0 - - - -
281s HIS* 3.2 32.7 + + + +
283s PHE* 2.8 47.6 + + + +
338s ALA* 4.4 3.1 - - - +
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Residues in contact with PHE 208 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207s HIS* 1.3 74.2 - - - +
209s TYR* 1.3 74.0 + - - +
210s TRP* 3.7 37.7 - + + -
232s GLN* 3.4 5.5 - - - +
233s ILE* 2.8 36.2 + - - -
281s HIS 3.3 5.6 + - - -
282s ILE* 4.0 12.8 - - + +
333s PHE* 3.9 18.6 - + - -
334s ALA* 3.4 36.3 - - + +
337s GLY* 3.5 24.5 - - - -
338s ALA* 3.7 13.0 - - - -
341s MET* 3.8 18.8 - - + -
377s LEU* 4.0 14.8 - - + -
379s LEU* 5.6 0.2 - - + -
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Residues in contact with TYR 209 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83s LEU* 4.3 16.8 + - + -
84s THR* 5.1 0.6 + - - -
86s MET 4.5 3.6 + - - -
88s PHE* 5.5 0.9 - - - -
90s LYS* 4.0 19.3 - - + -
208s PHE* 1.3 88.7 - - - +
210s TRP* 1.3 59.2 + - - +
211s VAL* 4.5 13.9 - - + +
230s ARG* 3.5 46.3 + - + +
231s TYR 3.3 20.0 - - - -
232s GLN* 4.6 3.6 - - + -
280s ASN* 3.2 38.8 + - + -
281s HIS 3.9 13.6 + - - +
282s ILE* 3.9 26.1 - - + +
341s MET* 4.9 2.9 - - - +
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Residues in contact with TRP 210 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93s VAL* 4.0 8.5 - - + -
109s PHE* 3.1 40.2 + - + -
110s THR* 4.6 1.1 - - - -
208s PHE* 3.7 28.5 - + + -
209s TYR* 1.3 74.8 - - - +
211s VAL* 1.3 79.5 + - - +
212s ARG* 3.8 2.6 - - + +
230s ARG* 3.7 1.6 - - - +
231s TYR* 2.8 72.2 + + + +
233s ILE* 3.4 51.1 - - + -
333s PHE* 3.5 27.4 - + - -
379s LEU* 4.3 18.4 - - + -
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Residues in contact with VAL 211 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209s TYR* 4.5 14.6 - - + +
210s TRP* 1.3 80.8 - - - +
212s ARG* 1.3 63.1 + - - +
213s GLY 4.5 3.4 - - - +
228s ASP* 3.7 38.8 - - + +
229s LEU 3.7 14.1 - - - +
230s ARG* 4.3 14.8 - - + +
379s LEU* 3.4 8.0 - - - +
380s THR* 3.4 40.1 + - + +
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Residues in contact with ARG 212 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108s TYR* 2.9 56.0 + - + +
109s PHE* 3.3 26.9 - - - +
111s LYS* 3.6 33.0 - - - +
210s TRP* 3.8 9.5 - - + +
211s VAL* 1.3 73.4 - - - +
213s GLY* 1.3 62.4 + - - +
229s LEU* 3.4 15.9 + - - +
231s TYR* 3.6 20.8 + - + -
261s ILE* 5.4 4.9 - - - +
379s LEU* 3.5 28.0 + - - -
381s THR* 6.2 1.4 - - - +
384s ASP* 2.7 27.6 + - - -
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Residues in contact with GLY 213 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108s TYR* 5.9 3.8 - - - -
211s VAL* 4.1 2.8 + - - +
212s ARG* 1.3 77.0 - - - +
214s GLU* 1.3 64.6 + - - -
228s ASP* 3.5 8.7 - - - +
229s LEU* 3.1 28.4 + - - +
379s LEU 4.1 6.1 + - - -
380s THR* 4.8 1.0 - - - +
381s THR* 3.6 19.2 - - - +
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Residues in contact with GLU 214 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213s GLY* 1.3 75.5 - - - +
215s GLU* 1.3 62.3 + - - +
226s ILE* 3.5 36.1 - - + +
227s ASP 3.7 4.0 - - - -
228s ASP* 4.4 5.8 - - + +
229s LEU* 3.2 11.6 - - - +
381s THR* 2.7 38.3 + - + +
382s GLN* 5.7 1.2 - - - +
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Residues in contact with GLU 215 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91s TYR* 3.9 8.0 + - - -
214s GLU* 1.3 79.9 - - - +
216s ILE* 1.3 76.2 + - - +
217s ILE* 4.8 5.4 - - + +
218s PRO* 5.2 5.6 - - + -
225s ARG 3.4 0.2 - - - +
226s ILE* 4.7 1.1 - - - -
227s ASP* 2.8 52.3 + - + +
229s LEU* 3.7 23.5 - - + +
267s LYS* 3.1 35.4 - - - +
268s PRO* 5.5 1.4 - - - +
275s LYS* 3.8 20.5 + - - -
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Residues in contact with ILE 216 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215s GLU* 1.3 79.4 - - - +
217s ILE* 1.3 67.4 + - - +
218s PRO* 3.3 6.3 - - + +
224s GLY* 4.7 16.2 - - - +
225s ARG 3.5 9.2 - - - +
226s ILE* 5.1 13.5 - - + -
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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