Contacts of the helix formed by residues 184 - 202 (chain B) in PDB entry 1OJ7
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 PRO 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B THR 3.4 4.9 - - - +
183B LEU* 1.3 90.1 - - + +
185B PRO* 1.3 73.6 - - + +
186B ARG* 4.4 4.3 - - + +
187B GLN* 3.0 34.0 + - + +
188B VAL* 3.2 8.8 + - - +
1388B NZQ 3.6 23.1 - - + +
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Residues in contact with PRO 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU 3.4 5.6 - - - +
184B PRO* 1.3 83.1 - - + +
186B ARG* 1.3 59.5 + - + +
188B VAL* 3.3 4.7 + - + -
189B ALA* 3.0 24.4 + - - +
232B LEU* 3.3 31.3 - - + +
337B LEU 5.1 0.4 - - - +
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Residues in contact with ARG 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PRO* 3.2 4.7 - - + +
185B PRO* 1.3 81.7 - - + +
187B GLN* 1.3 60.9 + - + +
189B ALA* 3.6 7.6 + - + +
190B ASN* 3.0 36.6 + - - +
280B ASP* 5.9 1.3 - - - +
283B GLN* 5.6 12.0 - - - +
337B LEU 6.0 0.9 - - - +
338B GLY* 4.9 16.7 + - - +
339B VAL* 5.3 0.2 - - - +
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Residues in contact with GLN 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PRO* 6.1 0.2 - - - +
139B LEU* 4.0 18.1 - - + +
183B LEU* 4.0 17.3 - - + -
184B PRO* 3.0 27.7 + - + +
186B ARG* 1.3 78.9 - - + +
188B VAL* 1.3 65.2 + - - +
190B ASN* 3.3 19.7 + - - +
191B GLY* 3.0 18.5 + - - -
280B ASP* 3.8 20.2 + - - -
1388B NZQ 3.6 44.4 + - - +
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Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 5.7 0.4 - - - -
140B PRO* 5.2 1.3 - - - +
183B LEU* 3.6 28.5 - - + +
184B PRO 3.2 7.7 + - - +
185B PRO* 3.5 9.9 - - + +
187B GLN* 1.3 75.2 - - - +
189B ALA* 1.3 63.3 + - - +
191B GLY* 3.1 3.9 + - - -
192B VAL* 3.0 28.2 + - + +
228B GLY 4.9 0.2 - - - +
231B ALA* 3.9 28.7 - - + +
232B LEU* 3.7 17.3 - - + -
241B ARG* 3.6 27.6 - - - +
244B VAL* 5.6 4.2 - - + +
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PRO 3.0 16.4 + - - +
186B ARG* 3.6 8.5 - - - +
188B VAL* 1.3 76.7 - - - +
190B ASN* 1.3 62.4 + - - +
192B VAL* 3.2 9.2 + - - +
193B VAL* 3.0 26.9 + - - +
232B LEU* 4.0 5.8 - - + +
337B LEU* 3.3 34.3 - - + +
338B GLY 5.2 0.9 - - - -
339B VAL* 3.9 14.6 - - + -
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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
----------------------------------------------------------
141B ALA* 4.9 0.9 - - - -
186B ARG* 3.0 24.6 + - - +
187B GLN* 3.3 27.2 + - - +
189B ALA* 1.3 75.4 - - - +
191B GLY* 1.3 58.0 + - - +
193B VAL* 3.4 1.0 + - - -
194B ASP* 2.9 26.7 + - - +
280B ASP* 3.0 34.6 + - - +
282B ALA* 3.1 31.6 - - + +
283B GLN* 4.3 11.7 + - - +
339B VAL* 4.1 12.5 - - - +
1388B NZQ 5.3 5.6 - - - +
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Residues in contact with GLY 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 4.5 0.6 - - - +
140B PRO 3.4 13.6 - - - +
141B ALA* 3.3 30.0 - - - -
187B GLN 3.0 13.6 + - - -
188B VAL 3.1 3.7 + - - -
190B ASN* 1.3 72.7 - - - +
192B VAL* 1.3 65.6 + - - +
194B ASP 3.3 0.2 + - - -
195B ALA* 3.0 26.7 + - - +
244B VAL* 5.9 1.8 - - - -
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL* 3.0 20.0 + - + +
189B ALA* 3.2 8.3 + - - +
191B GLY* 1.3 74.8 - - - +
193B VAL* 1.3 63.4 + - - +
195B ALA* 3.8 2.0 - - - +
196B PHE* 3.0 22.7 + - - +
224B LEU* 3.9 25.7 - - + +
228B GLY* 3.8 25.4 - - - +
244B VAL* 4.3 18.8 - - + -
333B PHE* 3.9 19.1 - - + -
337B LEU* 3.6 24.5 - - + -
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ALA 3.0 19.4 + - - +
190B ASN 3.7 3.8 - - - +
192B VAL* 1.3 75.8 - - - +
194B ASP* 1.3 57.7 + - - +
196B PHE* 3.2 7.0 + - - +
197B VAL* 2.8 42.1 + - + +
282B ALA* 3.6 30.1 - - + +
285B LEU* 4.5 0.7 - - + -
286B ALA* 4.5 7.0 - - + +
333B PHE* 5.9 0.2 - - - -
334B PHE* 3.8 31.2 - - + -
337B LEU* 3.9 12.3 - - + -
339B VAL* 4.0 20.0 - - + -
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Residues in contact with ASP 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ALA* 3.8 13.2 - - + +
142B THR* 3.6 15.9 - - - +
190B ASN 2.9 18.3 + - - +
191B GLY 3.8 1.8 - - - +
193B VAL* 1.3 78.0 - - - +
195B ALA* 1.3 57.1 + - - +
197B VAL* 3.3 0.9 + - - -
198B HIS* 2.9 39.1 + - - -
281B HIS* 3.3 19.1 + - + -
282B ALA* 4.6 1.8 - - + -
285B LEU* 3.3 11.7 - - + +
1388B NZQ 3.6 11.0 + - - +
1389B ZN 2.0 37.8 - - - -
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ALA 3.5 8.9 + - - +
191B GLY 3.0 18.4 + - - +
192B VAL 3.8 0.4 - - - +
194B ASP* 1.3 76.7 - - - +
196B PHE* 1.3 61.3 + - - +
198B HIS* 3.5 3.9 + - - +
199B THR* 3.0 28.6 + - - -
224B LEU* 3.8 21.3 - - + -
248B ALA* 3.9 30.5 - - + -
251B ALA* 3.5 9.2 - - + +
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Residues in contact with PHE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B VAL 3.0 19.5 + - - +
193B VAL* 3.4 8.1 - - - +
195B ALA* 1.3 76.0 - - - +
197B VAL* 1.3 64.2 + - + +
199B THR* 3.3 5.4 + - - -
200B VAL* 3.1 34.5 + - + +
221B LEU* 3.6 21.7 - - + +
224B LEU* 3.4 19.4 - - + +
225B ILE* 3.8 30.7 - - + -
289B LEU* 5.0 0.4 - - + -
293B TRP* 4.9 0.7 - + - -
307B TYR* 3.2 31.0 - + - -
312B TRP* 4.6 2.5 - + - -
330B THR* 4.0 17.7 - - + -
333B PHE* 3.7 21.3 - + + -
334B PHE* 3.9 17.3 - + + -
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B VAL* 2.8 25.3 + - + +
194B ASP 3.9 2.7 - - - +
196B PHE* 1.3 69.6 - - - +
198B HIS* 1.3 65.5 + - - +
200B VAL* 3.2 12.2 + - + +
201B GLU* 2.9 37.0 + - + +
266B THR* 4.3 9.0 - - + -
267B HIS* 3.6 24.5 - - + +
285B LEU* 3.9 31.2 - - + +
289B LEU* 4.1 11.0 - - + -
334B PHE* 4.0 23.8 - - + -
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Residues in contact with HIS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ALA 3.8 6.3 + - - -
142B THR* 3.3 32.7 + - - -
194B ASP* 2.9 21.5 + - - +
195B ALA* 3.5 6.8 - - - +
197B VAL* 1.3 75.7 - - - +
199B THR* 1.3 62.4 + - - +
201B GLU* 3.5 8.4 + - - +
202B GLN* 2.9 24.4 + - - +
251B ALA* 4.0 16.4 - - + +
252B LEU* 3.5 19.7 - - + +
264B TRP* 3.8 15.8 - + + -
267B HIS* 3.3 12.3 - + - -
1388B NZQ 2.6 37.3 + - - +
1389B ZN 2.6 15.3 - - - -
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Residues in contact with THR 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 ALA 3.0 12.8 + - - -
196B PHE 3.4 9.0 - - - -
197B VAL 3.2 0.2 - - - -
198B HIS* 1.3 79.4 - - - +
200B VAL* 1.3 62.0 + - - +
202B GLN* 3.1 14.6 + - - +
203B TYR* 3.2 15.1 + - - +
217B ALA* 3.4 42.8 - - + +
220B ILE* 3.5 13.4 - - + +
221B LEU* 3.7 16.4 - - + -
251B ALA* 3.5 15.8 - - - +
256B ILE* 3.9 13.3 - - + +
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PHE* 3.1 23.9 + - + +
197B VAL* 3.3 24.0 - - + +
199B THR* 1.3 69.8 - - - +
201B GLU* 1.3 60.8 + - + +
202B GLN 3.0 5.4 - - - -
203B TYR* 4.3 1.6 - - - -
204B VAL* 2.9 42.9 + - + +
221B LEU* 3.9 24.7 - - + -
263B ASP* 5.3 0.2 - - - +
289B LEU* 4.0 18.6 - - + -
293B TRP* 3.7 35.6 + - + +
307B TYR* 4.3 1.3 - - + -
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 2.9 29.5 + - + +
198B HIS 3.6 7.2 - - - +
199B THR 3.2 0.2 - - - -
200B VAL* 1.3 78.7 - - + +
202B GLN* 1.3 57.5 + - - +
203B TYR 3.5 0.2 - - - -
205B THR* 3.7 3.3 - - - +
262B GLN* 3.5 4.2 - - - +
263B ASP* 2.9 42.2 + - - +
264B TRP* 2.7 56.3 + - + -
265B ALA 3.9 0.5 + - - -
266B THR* 3.3 14.3 + - - -
267B HIS* 2.8 43.1 + - - +
289B LEU* 5.7 1.2 - - - +
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Residues in contact with GLN 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B HIS 2.9 18.1 + - - +
199B THR 3.1 6.3 + - - +
200B VAL 3.0 0.6 - - - -
201B GLU* 1.3 81.4 - - - +
203B TYR* 1.3 56.7 + - - +
205B THR* 4.1 6.8 + - - +
213B HIS* 6.1 0.3 - - - +
251B ALA 2.7 29.3 + - - -
252B LEU* 3.6 23.1 - - - +
254B GLY* 5.1 5.2 - - - +
256B ILE* 3.6 20.1 - - + +
257B GLY* 3.4 29.3 + - - -
260B VAL* 3.7 21.1 - - - +
261B PRO 3.8 2.4 - - - +
262B GLN* 4.0 26.5 + - + +
264B TRP* 4.0 5.6 - - + -
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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
------------------------------------------------------------
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