Contacts of the helix formed by residues 208 - 215 (chain B) in PDB entry 3JXI
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 ASN 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ARG* 3.6 23.6 - - + +
166B LEU* 3.6 16.5 + - - +
167B THR* 3.0 35.9 + - - +
203B ALA* 2.8 17.3 + - - +
204B GLU 4.4 0.2 + - - -
206B THR* 3.6 16.7 + - - +
207B GLY* 1.3 76.5 - - - +
209B MET* 1.3 66.0 + - - +
210B ARG 3.4 1.7 + - - -
211B GLU* 3.0 25.1 - - - +
212B PHE* 2.9 28.9 + - - +
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Residues in contact with MET 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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200B LEU* 3.1 39.5 - - + +
203B ALA* 3.3 10.5 + - + -
204B GLU* 3.8 38.1 - - + +
207B GLY 3.8 1.0 - - - -
208B ASN* 1.3 79.3 - - - +
210B ARG* 1.3 63.9 + - - +
211B GLU* 4.0 0.6 + - - -
212B PHE* 3.5 1.0 + - - +
213B ILE* 3.1 34.0 + - + +
246B LYS* 3.3 56.1 - - + +
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Residues in contact with ARG 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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207B GLY 4.0 10.1 + - - -
208B ASN 5.5 0.2 - - - -
209B MET* 1.3 78.3 - - - +
211B GLU* 1.3 115.2 + - - +
213B ILE* 3.4 3.6 + - - -
214B ASN* 3.0 40.3 + - - +
246B LYS 5.2 4.0 - - - +
247B GLY* 5.1 6.5 - - - +
387C HIS* 4.5 10.9 - - - +
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Residues in contact with GLU 211 (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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165B ARG* 3.7 5.9 + - - +
167B THR* 3.6 9.7 - - + +
207B GLY 3.5 9.9 - - - +
208B ASN* 3.0 38.3 + - - +
210B ARG* 1.3 118.2 + - - +
212B PHE* 1.3 56.6 + - - +
214B ASN* 3.7 2.2 - - - -
215B SER* 2.9 32.4 + - - -
386C HIS 5.1 0.3 - - - +
387C HIS* 3.7 12.6 - - - -
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Residues in contact with PHE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 3.6 33.0 - - + -
167B THR* 3.4 15.5 - - + +
179B THR* 3.4 28.1 + - - -
180B CYS* 3.8 16.4 - - - -
181B LEU* 3.6 34.3 - - + +
199B LEU* 4.0 24.2 - - + -
200B LEU* 4.1 16.8 - - + -
203B ALA* 3.6 21.5 - - + -
208B ASN* 2.9 23.3 + - - +
209B MET 3.6 3.1 - - - +
211B GLU* 1.3 78.4 - - - +
213B ILE* 1.3 63.6 + - + +
214B ASN 3.3 0.3 + - - -
215B SER* 3.4 11.8 + - - +
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Residues in contact with ILE 213 (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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181B LEU* 3.9 6.5 - - - -
200B LEU* 3.6 30.7 - - + -
209B MET* 3.1 19.5 + - + +
210B ARG* 4.0 3.6 - - - +
212B PHE* 1.3 81.7 - - + +
214B ASN* 1.3 60.5 + - - +
215B SER 3.8 0.9 + - - +
226B THR* 4.5 1.6 - - - -
227B ALA* 3.9 23.6 + - + +
228B LEU 5.1 1.3 + - - +
243B LEU* 4.0 17.7 - - + +
246B LYS* 3.4 46.0 - - + +
247B GLY 4.3 0.2 - - - -
248B ALA* 3.5 36.1 - - + +
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Residues in contact with ASN 214 (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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210B ARG* 3.0 25.8 + - - +
211B GLU* 3.7 2.7 - - - +
213B ILE* 1.3 80.4 - - - +
215B SER* 1.3 67.3 + - - +
216B PRO* 3.0 8.9 - - - +
226B THR* 3.6 21.7 - - + +
228B LEU* 6.1 0.3 - - - +
247B GLY 3.2 22.3 + - - -
248B ALA* 3.5 6.2 - - - +
249B ASP* 2.8 39.8 + - + +
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Residues in contact with SER 215 (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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167B THR* 4.6 7.0 - - - +
172B ARG* 2.9 37.1 + - - -
177B GLY 4.2 0.5 + - - +
179B THR* 3.5 26.0 - - - +
182B PRO* 5.3 3.8 - - - +
211B GLU 2.9 18.9 + - - -
212B PHE 3.4 7.6 + - - +
213B ILE 3.5 1.4 - - - +
214B ASN* 1.3 76.4 - - - +
216B PRO* 1.3 66.4 - - - +
217B PHE* 4.0 4.5 + - - -
225B GLN 4.0 4.0 - - - +
226B THR* 4.2 6.6 - - - -
227B ALA 4.9 1.6 + - - -
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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