Contacts of the helix formed by residues 183 - 200 (chain B) in PDB entry 1JQO
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 ARG 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A SER* 5.9 0.2 - - - -
368A ASN* 5.7 3.2 - - - +
369A GLU* 3.3 26.9 + - - -
372A ARG* 4.7 0.4 - - - +
182B ALA* 1.3 73.0 - - - +
184B ARG* 1.3 56.7 + - - +
185B SER* 3.7 25.0 + - - +
186B LEU* 2.8 37.1 + - + +
187B LEU* 3.0 13.1 + - - +
227B THR* 4.2 10.5 - - + +
228B ASP* 2.6 31.1 + - - +
229B GLU* 3.8 26.4 - - + +
230B ILE 4.7 1.5 + - - -
231B ARG* 4.1 30.4 - - - +
960B LYS* 3.8 7.1 - - - +
1071B SO4 2.7 40.7 + - - +
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Residues in contact with ARG 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 3.5 35.0 - - + -
360A GLU* 3.0 39.0 + - - -
180B GLN* 6.1 0.4 - - + -
182B ALA 3.4 6.2 + - - +
183B ARG* 1.3 71.6 - - - +
185B SER* 1.3 59.7 + - - +
186B LEU 3.2 0.4 + - - -
187B LEU* 3.6 18.4 + - - +
188B GLN 3.6 8.8 + - - -
231B ARG* 3.9 5.5 - - - +
239B ALA 5.6 0.6 + - - -
242B ARG* 4.6 7.3 + - - +
243B TYR* 3.2 51.6 - - + +
246B SER* 3.6 26.1 + - - -
247B TYR* 5.8 1.0 - - - -
1071B SO4 2.7 29.3 + - - +
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Residues in contact with SER 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 4.4 6.7 - - - -
331A SER* 4.6 9.0 - - - -
372A ARG* 2.8 32.1 + - - +
183B ARG* 3.0 22.0 + - - -
184B ARG* 1.3 77.3 - - - +
186B LEU* 1.3 59.3 + - - +
188B GLN* 2.8 28.1 + - - +
189B LYS* 3.6 6.8 + - - +
227B THR* 5.0 3.6 - - - -
1071B SO4 2.5 26.4 + - - -
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Residues in contact with LEU 186 (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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103B LEU* 6.5 1.1 - - + -
104B HIS* 3.7 33.4 - - + +
107B ASN* 4.3 16.6 - - + +
182B ALA* 4.9 10.3 - - + -
183B ARG* 2.8 30.3 + - + +
185B SER* 1.3 78.7 - - - +
187B LEU* 1.3 65.2 + - + +
188B GLN 3.2 0.4 - - - -
189B LYS* 3.1 8.1 + - - +
190B ASN* 3.1 36.8 + - - +
224B ALA* 4.0 17.7 - - + +
227B THR* 6.6 0.2 - - - -
229B GLU* 4.9 8.7 - - + -
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B GLN* 3.4 25.4 - - - +
182B ALA* 4.0 19.3 - - + +
183B ARG 3.0 16.1 + - - +
184B ARG* 3.9 15.5 - - + +
185B SER 3.5 0.2 - - - -
186B LEU* 1.3 79.6 - - + +
188B GLN* 1.3 64.7 + - - +
190B ASN* 3.0 24.9 + - - +
191B ALA* 3.1 14.4 + - - +
194B ARG* 4.5 2.1 + - - -
243B TYR* 3.8 10.8 - - + -
247B TYR* 3.6 9.9 - - + +
678B GLU* 3.4 38.8 - - + +
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Residues in contact with GLN 188 (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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325A GLU* 6.5 1.1 - - + -
328A PHE* 3.3 42.9 + - + -
329A GLU* 3.5 17.5 - - - +
184B ARG 3.6 3.2 + - - +
185B SER 2.8 15.3 + - - +
186B LEU 3.2 0.4 - - - -
187B LEU* 1.3 79.9 - - - +
189B LYS* 1.3 100.4 + - - +
191B ALA* 3.4 7.0 + - - +
192B ARG* 3.1 39.4 + - + +
220B GLU* 3.5 11.1 - - - +
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Residues in contact with LYS 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE 3.5 2.4 + - - -
329A GLU 3.1 19.7 + - - -
331A SER* 3.0 28.2 + - - -
185B SER 3.6 8.6 + - - +
186B LEU* 3.1 10.4 + - - +
188B GLN* 1.3 112.9 - - - +
190B ASN* 1.3 61.0 + - - +
192B ARG* 3.4 2.8 - - - +
193B ILE* 2.8 35.7 + - + +
220B GLU* 3.5 21.5 - - + +
223B ALA* 3.7 25.8 - - + -
224B ALA* 3.4 35.2 - - + +
227B THR* 4.0 2.0 - - - +
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Residues in contact with ASN 190 (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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107B ASN* 3.2 40.1 + - - +
111B LEU* 3.9 26.1 - - + +
186B LEU* 3.1 27.8 + - - +
187B LEU* 3.0 20.4 + - - +
189B LYS* 1.3 76.3 - - - +
191B ALA* 1.3 61.7 + - - +
193B ILE* 3.1 7.4 + - - +
194B ARG* 2.8 42.6 + - - +
678B GLU* 5.0 1.9 - - - +
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Residues in contact with ALA 191 (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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187B LEU 3.1 6.9 + - - +
188B GLN* 3.5 10.8 - - - +
190B ASN* 1.3 79.4 - - - +
192B ARG* 1.3 63.6 + - - +
194B ARG* 3.1 22.8 + - - +
195B ASN* 2.9 24.7 + - - +
682B GLY 5.5 3.4 - - - +
683B GLU* 3.7 9.4 - - - +
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Residues in contact with ARG 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLU* 3.4 30.9 + - - +
329A GLU* 2.9 41.3 + - - +
435A SER* 4.2 3.7 + - - -
188B GLN* 3.1 27.5 + - + +
189B LYS* 3.4 9.6 - - - +
191B ALA* 1.3 79.1 - - - +
193B ILE* 1.3 63.2 + - - +
195B ASN* 3.2 7.7 + - - +
196B CYS* 3.0 27.9 + - - +
220B GLU* 2.6 62.0 + - + +
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Residues in contact with ILE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 4.5 24.0 - - + -
107B ASN* 5.8 0.7 - - - +
108B LEU* 4.3 7.0 - - + -
111B LEU* 3.9 26.0 - - + -
189B LYS* 2.8 23.7 + - + +
190B ASN* 3.1 10.1 + - - +
192B ARG* 1.3 76.5 - - - +
194B ARG* 1.3 57.0 + - - +
196B CYS* 2.9 9.0 + - - +
197B LEU* 2.7 35.9 + - + +
217B LEU* 4.7 11.0 - - + +
220B GLU* 4.1 17.9 - - + +
221B ILE* 3.9 30.1 - - + -
224B ALA* 5.8 3.4 - - + -
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Residues in contact with ARG 194 (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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111B LEU* 3.5 36.1 - - + +
114B GLU* 2.7 45.9 + - - -
115B VAL* 4.7 9.2 - - + +
187B LEU 4.5 2.0 + - - -
190B ASN* 2.8 21.4 + - - +
191B ALA* 3.1 25.5 + - - +
193B ILE* 1.3 72.1 - - - +
195B ASN* 1.3 63.6 + - - +
197B LEU* 3.1 8.5 + - - +
198B THR* 2.9 29.6 + - - +
678B GLU* 3.4 33.1 + - - -
682B GLY 4.6 3.2 + - - -
683B GLU* 2.7 43.5 + - - +
685B HIS* 5.6 1.1 - - - +
686B LEU* 4.2 6.1 - - - +
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Residues in contact with ASN 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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191B ALA 2.9 12.2 + - - +
192B ARG* 3.3 12.3 + - - +
194B ARG* 1.3 77.9 - - - +
196B CYS* 1.3 61.5 + - - +
198B THR* 3.7 5.0 - - - -
199B GLN* 3.0 62.3 + - - +
683B GLU* 5.3 3.3 + - - +
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Residues in contact with CYS 196 (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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192B ARG* 3.0 15.8 + - - +
193B ILE* 2.9 8.7 + - - +
195B ASN* 1.3 81.9 - - - +
197B LEU* 1.3 58.1 + - - +
199B GLN* 4.6 5.2 - - - +
200B LEU* 2.9 32.4 + - - +
213B LEU* 4.3 17.7 - - - +
216B ALA* 4.2 25.4 - - - -
217B LEU* 4.0 27.8 - - + +
220B GLU* 6.2 2.0 - - - -
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Residues in contact with LEU 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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37B TYR* 3.7 32.6 - - + -
40B LEU* 3.8 22.7 - - + -
41B LEU* 3.8 33.9 - - + -
111B LEU* 5.1 1.1 - - + -
112B ALA* 4.3 2.7 - - - +
115B VAL* 3.7 27.4 - - + -
193B ILE* 2.7 17.8 + - + +
194B ARG* 3.1 11.4 + - - +
196B CYS* 1.3 72.5 - - - +
198B THR* 1.3 62.9 + - - +
200B LEU* 3.6 1.9 + - + +
201B ASN* 2.7 34.4 + - - +
217B LEU* 4.0 13.2 - - + +
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Residues in contact with THR 198 (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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115B VAL* 4.4 9.9 - - - +
119B HIS* 3.8 28.0 + - + -
194B ARG* 2.9 16.8 + - - +
195B ASN* 3.7 6.7 - - - -
197B LEU* 1.3 75.4 - - - +
199B GLN* 1.3 70.6 + - + +
201B ASN* 3.0 20.6 + - - +
202B ALA* 3.6 1.9 + - - +
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Residues in contact with GLN 199 (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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195B ASN* 3.0 43.9 + - - +
196B CYS* 4.3 4.0 - - - +
198B THR* 1.3 79.8 - - + +
200B LEU* 1.3 54.7 + - - +
201B ASN 2.7 14.9 + - - -
202B ALA* 2.9 25.3 + - - +
205B ILE* 3.8 10.2 - - + +
213B LEU* 4.1 27.5 - - + +
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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
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40B LEU* 5.2 11.0 - - + -
44B ARG* 5.4 1.8 - - - +
196B CYS 2.9 20.0 + - - +
197B LEU* 3.9 5.6 - - - +
198B THR 3.3 0.4 - - - -
199B GLN* 1.3 75.6 - - - +
201B ASN* 1.3 62.8 + - - +
202B ALA 3.6 0.8 - - - +
205B ILE* 3.9 8.8 - - - +
210B LYS* 3.4 51.1 - - + +
213B LEU* 3.8 15.9 - - + +
214B ASP* 3.6 35.4 - - + +
217B LEU* 4.2 16.6 - - + -
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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
------------------------------------------------------------
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