Contacts of the helix formed by residues 184 - 202 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182D THR 3.4 7.4 - - - +
183D LEU* 1.3 91.3 - - + +
185D PRO* 1.3 76.3 - - + +
186D ARG* 4.4 9.9 - - + +
187D GLN* 2.9 34.1 + - + +
188D VAL 3.0 8.1 + - - -
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Residues in contact with PRO 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D LEU 3.6 2.9 - - - +
184D PRO* 1.3 86.2 - - + +
186D ARG* 1.3 62.3 + - - +
188D VAL* 3.2 5.5 + - + +
189D ALA* 2.9 26.4 + - - +
232D LEU* 3.5 22.6 - - + +
337D LEU 5.7 0.9 - - - -
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Residues in contact with ARG 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D PRO* 4.7 8.7 - - + +
185D PRO* 1.3 79.0 - - - +
187D GLN* 1.3 68.9 + - - +
189D ALA* 3.5 5.3 + - - +
190D ASN* 2.9 33.7 + - - +
278D GLY 5.7 1.0 + - - -
280D ASP* 2.9 43.6 + - - +
283D GLN* 3.9 17.9 + - - +
338D GLY 6.1 1.1 - - - -
339D VAL* 5.3 0.5 - - - +
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Residues in contact with GLN 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D PRO* 6.1 2.6 - - - +
139D LEU* 3.9 37.1 - - + +
183D LEU* 4.1 12.7 - - + +
184D PRO* 2.9 27.3 + - + +
186D ARG* 1.3 89.4 - - + +
188D VAL* 1.3 65.7 + - - +
190D ASN* 3.1 18.8 + - - +
191D GLY* 3.1 19.8 + - - -
280D ASP* 3.6 21.1 + - - -
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Residues in contact with VAL 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D LEU* 3.8 21.5 - - + +
184D PRO 3.0 15.0 + - - +
185D PRO* 3.5 11.0 - - + +
187D GLN* 1.3 78.6 - - - +
189D ALA* 1.3 61.4 + - - +
191D GLY* 3.3 1.6 + - - -
192D VAL* 3.2 27.6 + - + +
228D GLY 4.8 0.7 - - - +
231D ALA* 3.7 32.5 - - + +
232D LEU* 3.7 17.3 - - + -
235D PRO* 6.4 0.4 - - + -
241D ARG* 3.6 27.4 - - - +
244D VAL* 5.6 3.4 - - + +
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Residues in contact with ALA 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D PRO 2.9 15.5 + - - +
186D ARG* 3.6 6.3 - - - +
188D VAL* 1.3 74.9 - - - +
190D ASN* 1.3 64.8 + - - +
192D VAL* 3.2 8.6 + - - +
193D VAL* 3.0 27.5 + - - +
232D LEU* 4.3 3.5 - - + +
337D LEU* 3.3 34.9 - - + +
338D GLY 5.1 0.7 - - - -
339D VAL* 3.6 19.7 - - + -
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Residues in contact with ASN 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LEU* 5.9 0.9 - - + -
141D ALA* 4.8 1.8 - - + -
186D ARG* 2.9 23.6 + - - +
187D GLN* 3.1 27.5 + - - +
188D VAL 3.4 0.2 - - - -
189D ALA* 1.3 75.6 - - - +
191D GLY* 1.3 58.6 + - - +
193D VAL* 3.4 0.6 + - - -
194D ASP* 2.9 27.6 + - - +
280D ASP* 2.9 35.4 + - - +
282D ALA* 3.2 31.0 - - + +
283D GLN* 4.0 17.0 + - - +
339D VAL* 4.4 7.5 - - - +
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Residues in contact with GLY 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LEU* 4.9 0.2 - - - +
140D PRO 3.3 24.8 - - - +
141D ALA* 3.4 18.1 - - - -
187D GLN 3.1 14.0 + - - -
188D VAL 3.7 4.3 - - - -
189D ALA 3.2 0.2 - - - -
190D ASN* 1.3 73.2 - - - +
192D VAL* 1.3 63.4 + - - +
195D ALA* 3.0 26.5 + - - +
244D VAL* 5.6 2.2 - - - -
248D ALA* 5.1 0.6 - - - +
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Residues in contact with VAL 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D VAL* 3.2 20.4 + - + +
189D ALA* 3.6 8.1 - - - +
191D GLY* 1.3 75.5 - - - +
193D VAL* 1.3 59.3 + - - +
195D ALA* 3.5 1.9 + - - +
196D PHE* 3.0 27.2 + - - +
224D LEU* 4.0 27.1 - - + +
228D GLY* 3.9 25.4 - - - +
244D VAL* 4.2 19.3 - - + +
333D PHE* 3.9 17.3 - - + -
337D LEU* 3.6 23.8 - - + -
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Residues in contact with VAL 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D ALA 3.0 20.2 + - - +
190D ASN 3.8 3.6 - - - +
192D VAL* 1.3 75.4 - - - +
194D ASP* 1.3 60.6 + - - +
196D PHE* 3.2 6.7 + - - +
197D VAL* 2.9 47.1 + - + +
282D ALA* 3.7 29.4 - - + +
285D LEU* 4.6 0.7 - - + -
286D ALA* 4.5 7.6 - - + +
334D PHE* 3.8 31.9 - - + -
337D LEU* 4.0 13.5 - - + -
339D VAL* 4.1 17.7 - - + -
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Residues in contact with ASP 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ALA* 3.8 13.1 - - + +
142D THR* 3.7 19.6 - - - +
190D ASN 2.9 18.3 + - - +
191D GLY 3.9 2.0 - - - +
192D VAL 3.4 0.2 - - - -
193D VAL* 1.3 75.5 - - - +
195D ALA* 1.3 57.1 + - - +
197D VAL* 3.3 0.7 + - - -
198D HIS* 2.9 66.9 + - - -
281D HIS* 3.2 33.8 + - - -
282D ALA* 4.5 4.0 - - + -
285D LEU* 3.3 13.7 - - - +
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Residues in contact with ALA 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ALA 3.7 5.8 + - - +
191D GLY 3.0 17.9 + - - +
192D VAL 3.8 1.1 - - - +
194D ASP* 1.3 77.2 - - - +
196D PHE* 1.3 62.6 + - - +
198D HIS* 3.4 3.7 + - - +
199D THR* 3.0 26.7 + - - -
224D LEU* 3.8 22.7 - - + -
244D VAL* 6.5 0.2 - - + -
247D ALA 4.8 0.2 - - - +
248D ALA* 3.8 31.0 - - + +
251D ALA* 3.6 9.6 - - + +
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Residues in contact with PHE 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D VAL 3.0 18.4 + - - +
193D VAL* 3.3 8.7 - - - +
195D ALA* 1.3 76.7 - - - +
197D VAL* 1.3 63.0 + - + +
199D THR* 3.3 6.1 + - - -
200D VAL* 3.2 33.3 + - + +
221D LEU* 3.5 21.7 - - + +
224D LEU* 3.5 18.6 - - + +
225D ILE* 3.9 31.6 - - + -
289D LEU* 5.0 0.7 - - + -
293D TRP* 4.9 1.3 - + - -
307D TYR* 3.3 30.1 - + - -
312D TRP* 4.6 2.5 - + - -
330D THR* 4.0 16.2 - - + -
333D PHE* 3.7 21.3 - + + -
334D PHE* 3.8 19.3 - + + -
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Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D VAL* 2.9 28.6 + - + +
194D ASP 4.0 0.2 - - - +
196D PHE* 1.3 72.4 - - - +
198D HIS* 1.3 67.6 + - - +
199D THR 3.1 0.2 - - - -
200D VAL* 3.1 11.8 + - + +
201D GLU* 2.9 39.7 + - + +
266D THR* 4.3 13.5 - - + -
267D HIS* 3.7 21.1 - - + +
285D LEU* 3.9 28.3 - - + -
289D LEU* 4.3 11.2 - - + -
334D PHE* 4.2 15.7 - - + -
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Residues in contact with HIS 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ALA 3.7 6.2 + - - -
142D THR* 3.3 30.5 + - - -
194D ASP* 2.9 47.2 + - - +
195D ALA* 3.5 7.6 - - - +
197D VAL* 1.3 76.5 - - - +
199D THR* 1.3 61.7 + - - +
201D GLU* 3.5 5.7 + - - +
202D GLN* 2.9 28.7 + - - +
248D ALA 5.4 0.2 + - - -
251D ALA* 4.0 16.4 - - + +
252D LEU* 3.5 21.3 - - + +
264D TRP* 3.8 15.2 - + + -
267D HIS* 3.2 29.0 + + - -
281D HIS* 4.6 0.6 + - - -
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Residues in contact with THR 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D ALA 3.0 12.7 + - - -
196D PHE 3.4 9.0 - - - -
197D VAL 3.1 0.4 - - - -
198D HIS* 1.3 79.4 - - - +
200D VAL* 1.3 57.5 + - - +
202D GLN* 3.0 17.3 + - - +
203D TYR* 3.2 16.3 + - - +
217D ALA* 3.3 44.0 - - + +
220D ILE* 3.3 18.8 - - + +
221D LEU* 3.7 16.2 - - + -
251D ALA* 3.6 8.8 - - - +
256D ILE* 4.0 12.1 - - + +
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Residues in contact with VAL 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D PHE* 3.2 21.3 + - + +
197D VAL* 3.1 26.0 + - + +
199D THR* 1.3 71.9 - - - +
201D GLU* 1.3 63.3 + - + +
202D GLN 3.0 2.0 - - - -
203D TYR* 4.3 1.3 - - - -
204D VAL* 2.8 43.5 + - + +
221D LEU* 3.9 25.1 - - + -
263D ASP* 5.3 0.2 - - - +
289D LEU* 4.0 19.3 - - + -
293D TRP* 3.7 34.4 + - + +
307D TYR* 4.3 0.9 - - + -
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Residues in contact with GLU 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D VAL* 2.9 34.8 + - + +
198D HIS 3.5 7.4 - - - +
199D THR 3.2 0.2 - - - -
200D VAL* 1.3 76.2 - - + +
202D GLN* 1.3 58.1 + - - +
203D TYR 3.5 0.2 - - - -
205D THR* 3.6 4.6 - - - +
262D GLN* 3.5 4.2 - - - +
263D ASP* 2.9 42.9 + - - +
264D TRP* 2.8 55.8 + - + -
265D ALA 3.9 0.3 + - - -
266D THR* 3.4 13.2 + - - -
267D HIS* 2.8 37.9 + - - -
289D LEU* 5.7 2.3 - - - +
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Residues in contact with GLN 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D HIS 2.9 19.9 + - - +
199D THR 3.0 7.3 + - - +
201D GLU* 1.3 81.6 - - - +
203D TYR* 1.3 55.9 + - - +
205D THR* 4.2 7.0 + - - -
217D ALA* 5.9 0.2 - - - -
251D ALA 2.8 28.9 + - - +
252D LEU* 3.7 20.6 - - - +
254D GLY* 5.2 6.2 - - - +
256D ILE* 3.7 19.9 + - + +
257D GLY* 3.4 28.7 + - - -
260D VAL* 3.8 20.4 - - - +
261D PRO 3.9 7.1 - - - +
262D GLN* 4.0 17.6 + - + +
264D TRP* 4.0 11.9 - - + -
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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