Contacts of the helix formed by residues 194 - 206 (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 ASP 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B GLY 4.7 3.8 + - - +
149B PRO* 4.0 26.7 - - + +
192B ARG* 3.6 25.6 - - - +
193B ASN* 1.3 68.2 + - - +
195B THR* 1.3 64.4 + - - +
196B ILE 3.1 1.7 + - - -
197B PRO* 3.5 16.2 - - + +
198B ILE* 3.8 16.6 - - - +
239B TYR* 4.4 1.4 + - - -
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Residues in contact with THR 195 (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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143B ILE* 4.3 0.7 - - + +
144B VAL* 4.0 15.2 - - + +
147B GLY* 3.7 1.8 - - - -
148B SER 3.5 40.2 - - - +
149B PRO* 4.2 3.3 - - + -
152B LEU* 3.9 19.3 - - + -
184B ALA* 3.6 13.0 - - - +
193B ASN* 2.6 26.0 + - - +
194B ASP* 1.3 78.5 - - - +
196B ILE* 1.3 64.3 + - - +
198B ILE* 3.3 5.2 + - - +
199B LEU* 2.9 31.6 + - - +
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Residues in contact with ILE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 4.1 18.3 - - + +
184B ALA* 3.5 26.0 - - + -
185B LEU* 3.5 36.1 - - + +
188B LEU* 4.4 0.7 - - + -
193B ASN* 3.0 26.1 + - + +
195B THR* 1.3 78.1 - - - +
197B PRO* 1.3 72.4 - - + +
199B LEU* 3.3 6.7 + - - +
200B LEU* 3.2 27.1 + - + +
239B TYR* 3.9 29.2 - - + -
242B LEU* 4.1 10.1 - - + -
243B LEU* 5.3 3.8 - - + -
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Residues in contact with PRO 197 (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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193B ASN 4.0 2.9 - - - +
194B ASP* 3.5 20.0 - - - +
196B ILE* 1.3 98.5 - - + +
198B ILE* 1.3 63.6 + - + +
200B LEU* 3.5 5.5 + - + +
201B ASP* 3.2 23.0 + - - +
238B HIS* 5.6 4.3 - - + -
239B TYR* 4.6 6.3 - - + +
242B LEU* 4.2 24.2 - - + -
246B LYS* 6.1 0.6 - - - -
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Residues in contact with ILE 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B PRO* 3.5 43.5 - - + +
152B LEU* 3.6 22.9 - - + +
194B ASP 3.8 9.6 - - - +
195B THR 3.3 7.4 + - - +
196B ILE 3.2 0.6 - - - -
197B PRO* 1.3 76.1 - - + +
199B LEU* 1.3 63.4 + - - +
201B ASP* 3.3 7.9 + - - +
202B ILE* 3.0 35.8 + - + +
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 4.5 0.4 - - + -
144B VAL* 4.1 10.5 - - + -
152B LEU* 3.7 26.9 - - + -
155B LEU* 4.4 8.1 - - + -
166B LEU* 4.1 11.7 - - + +
180B CYS* 3.7 42.2 - - - +
181B LEU* 4.6 7.0 - - + -
184B ALA* 4.4 6.3 - - + -
195B THR* 2.9 37.0 + - - +
196B ILE* 3.7 6.1 - - - +
198B ILE* 1.3 75.1 - - - +
200B LEU* 1.3 56.6 - - - +
202B ILE* 3.3 7.5 + - - +
203B ALA* 2.9 29.3 + - - +
212B PHE* 4.0 15.2 - - + -
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Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 4.4 5.8 - - + -
196B ILE* 3.2 16.3 + - + +
197B PRO* 3.7 7.6 - - + +
198B ILE 3.3 0.2 - - - -
199B LEU* 1.3 75.5 - - - +
201B ASP* 1.3 57.2 + - - +
203B ALA* 3.5 4.4 + - - +
204B GLU* 3.0 22.2 + - - +
209B MET* 3.1 24.4 - - + +
212B PHE* 4.1 15.0 - - + -
213B ILE* 3.6 33.4 - - + -
242B LEU* 3.9 27.8 - - + +
243B LEU* 4.1 20.2 - - + -
246B LYS* 3.9 23.8 - - + -
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Residues in contact with ASP 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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156B LEU* 5.2 2.1 - - - +
197B PRO 3.2 14.8 + - - +
198B ILE* 3.7 7.2 - - - +
199B LEU 3.3 0.2 - - - -
200B LEU* 1.3 76.2 - - - +
202B ILE* 1.3 64.5 + - - +
204B GLU* 3.2 16.0 + - - +
205B LYS* 2.5 68.1 + - - +
246B LYS* 6.1 1.1 - - - +
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Residues in contact with ILE 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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152B LEU* 4.6 6.1 - - + +
155B LEU* 3.9 32.5 - - + -
156B LEU* 3.8 32.5 - - + +
159B LEU* 3.4 32.1 - - + -
166B LEU* 3.9 11.0 - - + -
198B ILE* 3.0 37.4 + - + +
199B LEU* 3.5 10.3 - - - +
201B ASP* 1.3 80.6 - - - +
203B ALA* 1.3 52.8 + - - +
205B LYS* 3.5 0.6 + - - -
206B THR* 2.7 35.0 + - - +
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Residues in contact with ALA 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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166B LEU* 4.9 4.3 - - + -
199B LEU 2.9 11.0 + - - +
200B LEU 3.7 4.9 - - - +
202B ILE* 1.3 74.1 - - - +
204B GLU* 1.3 65.1 + - - +
206B THR* 3.2 12.5 + - - -
207B GLY 3.3 0.2 + - - -
208B ASN* 2.8 33.3 + - - +
209B MET* 3.8 9.6 - - + -
212B PHE* 3.6 44.2 - - + -
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Residues in contact with GLU 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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200B LEU 3.0 13.3 + - - +
201B ASP* 3.3 19.4 - - - +
203B ALA* 1.3 77.3 - - - +
205B LYS* 1.3 63.7 + - + +
206B THR 3.1 0.2 - - - -
207B GLY* 3.1 18.5 + - - -
208B ASN 4.4 0.2 + - - -
209B MET* 3.8 33.1 - - + +
246B LYS* 4.1 14.4 + - - -
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Residues in contact with LYS 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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156B LEU* 3.6 37.0 - - + -
160B LEU* 3.8 14.9 - - + +
201B ASP* 2.5 47.6 + - - +
202B ILE 3.5 0.2 + - - -
203B ALA 3.3 0.2 - - - -
204B GLU* 1.3 80.6 + - + +
206B THR* 1.3 58.8 + - - +
207B GLY 3.6 0.8 + - - -
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Residues in contact with THR 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 3.8 10.3 - - + -
159B LEU* 4.2 23.8 - - + +
160B LEU* 3.5 26.9 - - + -
164B LYS 4.5 10.3 - - - +
165B ARG* 4.2 14.4 - - - +
166B LEU* 5.4 1.0 + - - +
202B ILE* 2.7 23.9 + - - +
203B ALA* 3.2 12.3 + - - -
204B GLU 3.1 0.2 - - - -
205B LYS* 1.3 77.3 - - - +
207B GLY* 1.3 60.3 + - - +
208B ASN* 3.4 12.2 + - - +
387C HIS* 4.7 4.2 + - - -
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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