Contacts of the helix formed by residues 200 - 210 (chain B) in PDB entry 2JDQ
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 SER 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B SER* 4.7 10.1 - - - -
197B ALA 3.5 2.9 - - - +
198B GLY 3.7 0.6 - - - -
199B ASP* 1.3 80.0 - - - +
201B THR* 1.3 63.7 + - - +
202B MET* 3.2 22.9 + - - +
203B CYS* 3.0 31.2 + - - +
204B ARG* 3.1 23.7 + - - +
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Residues in contact with THR 201 (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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200B SER* 1.3 74.0 - - - +
202B MET* 1.3 72.0 + - + +
204B ARG* 3.2 41.8 + - - +
205B ASP* 3.2 27.7 + - - +
242B GLY* 4.6 5.5 - - - -
244B SER 3.7 10.4 + - - -
245B PRO* 3.3 35.4 + - + -
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Residues in contact with MET 202 (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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200B SER* 3.2 18.7 + - - +
201B THR* 1.3 87.8 - - + +
203B CYS* 1.3 61.7 + - - +
205B ASP* 3.7 4.7 + - - +
206B TYR* 3.3 21.7 + - - +
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Residues in contact with CYS 203 (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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159B SER 6.0 0.4 - - - -
163B ARG* 6.0 2.2 - - - -
166B ILE* 3.2 33.4 - - + -
196B ILE* 3.2 23.1 - - + +
199B ASP* 4.1 18.4 - - - -
200B SER* 3.0 24.8 + - - +
202B MET* 1.3 75.1 - - - +
204B ARG* 1.3 65.3 + - - +
206B TYR* 3.3 7.5 + - - +
207B VAL* 3.0 28.6 + - - +
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Residues in contact with ARG 204 (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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197B ALA* 3.4 23.3 + - - +
200B SER 3.1 13.9 + - - +
201B THR* 3.2 34.7 + - - +
203B CYS* 1.3 79.5 - - - +
205B ASP* 1.3 78.3 + - - +
207B VAL* 3.5 3.8 + - - +
208B LEU* 3.0 29.5 + - + +
238B ASN 3.6 17.7 - - - +
239B LEU* 3.6 24.8 - - + +
241B ARG 2.7 36.4 + - - -
242B GLY* 3.4 9.1 - - - -
245B PRO* 3.0 28.7 + - - +
246B PRO 3.5 1.6 + - - -
247B PRO* 3.4 21.4 - - - +
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Residues in contact with ASP 205 (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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201B THR* 3.2 15.7 + - - +
202B MET* 4.2 4.8 - - - +
203B CYS 3.3 0.2 - - - -
204B ARG* 1.3 109.2 + - - +
206B TYR* 1.3 56.5 + - - +
208B LEU* 3.6 9.7 - - - +
209B ASP* 2.8 47.6 + - - +
245B PRO* 4.9 3.6 - - - +
246B PRO 4.9 1.4 - - - +
247B PRO* 3.7 16.8 - - - +
248B GLU 4.4 3.6 + - - -
251B LYS* 5.2 4.6 - - + +
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Residues in contact with TYR 206 (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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166B ILE* 3.5 45.8 + - + -
169B GLY* 5.2 2.4 - - - -
171B VAL* 3.8 24.5 + - + +
172B PRO* 3.8 19.6 - - - +
202B MET 3.3 14.9 + - - +
203B CYS* 3.3 11.6 + - - +
204B ARG 3.3 0.4 - - - -
205B ASP* 1.3 75.3 - - - +
207B VAL* 1.3 66.3 + - + +
209B ASP* 3.2 8.7 + - + -
210B CYS* 3.0 46.7 + - - -
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Residues in contact with VAL 207 (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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171B VAL* 4.0 21.3 - - + -
175B ILE* 4.1 1.5 - - + +
193B LEU* 4.4 10.5 - - + +
196B ILE* 3.7 27.6 - - + -
197B ALA* 4.2 15.5 - - + +
203B CYS 3.0 14.4 + - - +
204B ARG 3.7 6.7 - - - +
206B TYR* 1.3 75.5 - - + +
208B LEU* 1.3 61.9 + - - +
210B CYS* 3.5 9.9 + - - +
212B ILE* 3.3 51.1 + - + +
239B LEU* 4.1 7.9 - - + -
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Residues in contact with LEU 208 (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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204B ARG* 3.0 17.8 + - + +
205B ASP* 3.6 27.1 - - - +
207B VAL* 1.3 77.2 - - - +
209B ASP* 1.3 58.1 + - - +
211B ASN* 2.9 25.6 + - - -
212B ILE* 4.1 7.9 + - + -
213B LEU* 5.1 5.6 + - + -
239B LEU* 3.6 42.8 - - + +
247B PRO* 4.0 18.6 - - + -
251B LYS* 4.3 43.4 + - + +
252B VAL* 4.5 7.0 - - + -
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Residues in contact with ASP 209 (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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205B ASP* 2.8 32.3 + - - +
206B TYR* 3.2 9.3 + - + +
208B LEU* 1.3 71.3 - - - +
210B CYS* 1.3 59.0 + - - +
211B ASN* 3.2 13.8 + - - +
251B LYS* 2.7 41.3 + - - +
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Residues in contact with CYS 210 (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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171B VAL* 3.7 16.8 - - - -
172B PRO* 4.6 13.5 - - + -
175B ILE* 3.4 30.5 - - + +
206B TYR* 3.0 47.4 + - - +
207B VAL 3.7 2.5 - - - +
208B LEU 3.1 0.4 - - - -
209B ASP* 1.3 74.3 - - - +
211B ASN* 1.3 73.3 + - - +
212B ILE 3.5 0.8 + - - -
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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