Contacts of the helix formed by residues 186 - 204 (chain D) in PDB entry 6B0Z
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 186 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175B GLY* 6.2 0.9 - - - -
176B GLY 3.1 27.0 + - - +
177B GLY* 3.2 6.8 - - - -
185D GLN* 1.3 71.8 - - - +
187D LYS* 1.3 52.2 + - - +
189D ILE* 3.0 5.7 + - - +
190D GLU* 2.7 54.7 + - - +
222D ARG* 2.8 48.2 + - - +
226D ILE* 3.6 15.5 - - + +
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Residues in contact with LYS 187 (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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185D GLN* 3.1 14.7 - - + +
186D ASP* 1.3 78.4 - - - +
188D SER* 1.3 57.5 + - - +
190D GLU* 3.3 18.1 + - + +
191D ASP* 2.8 61.9 + - - +
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Residues in contact with SER 188 (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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133D HIS* 3.4 26.2 - - - -
184D ASN* 4.3 3.8 - - - -
185D GLN* 3.2 23.8 + - - +
187D LYS* 1.3 77.3 - - - +
189D ILE* 1.3 52.4 + - - +
191D ASP* 3.4 10.3 + - - +
192D PHE* 2.7 35.2 + - - +
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Residues in contact with ILE 189 (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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178B VAL* 4.7 5.6 - - + -
133D HIS* 4.5 1.8 - - - -
184D ASN* 4.6 10.5 - - + +
185D GLN 3.4 15.9 - - - +
186D ASP* 3.0 10.2 + - - +
188D SER* 1.3 74.4 - - - +
190D GLU* 1.3 58.0 + - - +
192D PHE* 3.2 8.5 - - - +
193D ALA* 2.9 27.5 + - - +
222D ARG* 4.1 21.1 - - + -
223D PHE* 3.5 61.9 - - + +
226D ILE* 3.7 28.9 - - + -
227D PHE* 4.2 3.7 - - + -
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Residues in contact with GLU 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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186D ASP* 2.7 35.4 + - - +
187D LYS* 3.4 27.2 + - + +
189D ILE* 1.3 70.5 - - - +
191D ASP* 1.3 67.5 + - - +
193D ALA* 3.1 3.5 + - - +
194D HIS* 2.9 34.0 + - + +
226D ILE* 3.7 20.4 - - + +
230D ILE* 4.0 18.4 - - + -
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Residues in contact with ASP 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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105D GLY* 5.8 6.1 - - - +
106D THR* 4.9 0.9 - - - -
187D LYS* 2.8 58.2 + - - +
188D SER* 3.5 8.3 - - - +
190D GLU* 1.3 72.0 - - - +
192D PHE* 1.3 63.8 + - - +
194D HIS* 3.2 5.1 + - - +
195D SER* 3.0 28.7 + - - -
298D PRO* 3.7 31.6 - - + +
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Residues in contact with PHE 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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106D THR* 3.5 34.3 - - + -
108D PHE* 5.5 0.2 - + - -
131D GLY 4.2 4.5 - - - -
132D HIS 4.1 1.3 - - - -
133D HIS* 3.5 41.5 - + + +
188D SER 2.7 18.8 + - - +
189D ILE* 3.2 9.2 - - - +
191D ASP* 1.3 73.7 - - - +
193D ALA* 1.3 60.9 + - - +
195D SER* 3.5 1.7 + - - -
196D SER* 2.9 40.4 + - - -
209D LEU* 4.2 10.3 - - + -
223D PHE* 4.0 14.6 - + - -
227D PHE* 3.8 22.0 - + - -
268D ALA* 3.9 17.0 - - + -
269D CYS 3.7 23.8 - - - -
270D LYS 4.7 0.7 - - - -
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Residues in contact with ALA 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 ILE 2.9 11.4 + - - +
190D GLU* 3.6 7.0 - - - +
192D PHE* 1.3 75.7 - - - +
194D HIS* 1.3 57.8 + - - +
196D SER* 3.1 2.8 + - - -
197D PHE* 2.8 51.7 + - + -
226D ILE* 4.9 0.2 - - + -
227D PHE* 3.5 37.6 - - + +
230D ILE* 4.1 14.1 - - + -
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Residues in contact with HIS 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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190D GLU* 2.9 33.0 + - + +
191D ASP* 3.2 7.8 + - - +
193D ALA* 1.3 76.3 - - - +
195D SER* 1.3 57.4 + - - +
197D PHE* 3.3 2.1 + - - -
198D GLN* 2.8 37.4 + - - +
230D ILE* 3.5 32.8 - - + +
234D GLN* 3.5 25.4 + - - -
235D TYR* 2.9 25.3 + - - +
298D PRO* 3.7 26.6 + - + +
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Residues in contact with SER 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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105D GLY* 4.2 0.5 - - - -
106D THR* 3.9 22.5 + - - -
108D PHE* 3.9 3.8 - - - -
191D ASP 3.0 16.7 + - - -
192D PHE 4.0 0.9 - - - -
194D HIS* 1.3 76.7 - - - +
196D SER* 1.3 57.3 + - - +
198D GLN* 3.7 2.7 - - - +
199D MET* 3.0 30.8 + - - +
296D VAL* 2.9 38.2 + - - +
298D PRO* 3.3 19.3 - - - +
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Residues in contact with SER 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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108D PHE* 3.7 19.8 - - - -
192D PHE* 2.9 22.7 + - - -
193D ALA 3.1 5.2 + - - -
195D SER* 1.3 75.6 - - - +
197D PHE* 1.3 65.0 + - - +
199D MET* 3.9 1.7 - - - +
200D ALA* 3.1 19.8 + - - +
207D LEU* 3.5 35.2 - - - +
227D PHE* 4.1 8.3 - - - -
266D ILE* 4.6 0.5 - - - +
268D ALA* 3.7 16.1 - - - +
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Residues in contact with PHE 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 ALA* 2.8 40.1 + - + +
194D HIS 3.8 2.9 - - - +
196D SER* 1.3 71.6 - - - +
198D GLN* 1.3 65.0 + - - +
200D ALA 3.4 1.4 + - - -
201D LEU* 3.2 27.0 + - - +
207D LEU* 3.7 19.7 - - + -
227D PHE* 3.2 39.0 - + - -
230D ILE* 3.7 16.4 - - + -
231D TYR* 3.5 28.7 - + + -
235D TYR* 3.6 36.8 - + + -
239D PHE* 3.7 20.3 - + + -
246D TYR* 4.0 11.0 - + - -
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Residues in contact with GLN 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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194D HIS 2.8 29.5 + - - +
195D SER* 3.7 6.5 - - - +
197D PHE* 1.3 76.3 - - - +
199D MET* 1.3 64.1 + - - +
201D LEU* 3.0 15.3 + - - +
202D SER* 2.9 23.2 + - - -
235D TYR* 2.5 44.4 + - - -
238D GLN* 5.7 0.6 + - - -
296D VAL* 4.9 6.1 - - + -
297D CYS 5.3 0.4 - - - +
298D PRO 4.0 6.5 - - - +
299D ASP 4.9 2.8 + - - -
300D GLY* 3.4 34.7 - - - +
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Residues in contact with MET 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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108D PHE* 3.9 35.0 - - + -
129D ILE* 4.3 20.4 - - + -
195D SER 3.0 18.1 + - - +
196D SER 3.9 3.4 - - - +
198D GLN* 1.3 76.6 - - - +
200D ALA* 1.3 61.4 + - - +
202D SER* 3.4 10.9 + - - +
203D LYS* 3.2 28.3 + - - +
266D ILE* 3.9 15.9 - - + -
294D VAL* 5.2 9.9 - - + -
296D VAL* 3.5 31.6 - - + +
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Residues in contact with ALA 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 SER 3.1 17.7 + - - +
197D PHE 3.7 4.7 - - - +
198D GLN 3.1 0.2 - - - -
199D MET* 1.3 77.6 - - - +
201D LEU* 1.3 58.2 + - - +
204D GLY* 2.9 21.5 + - - -
205D TRP 2.9 30.9 + - - +
207D LEU* 3.8 15.3 - - + -
239D PHE* 3.9 10.1 - - + -
244D ILE* 3.7 2.9 - - - +
266D ILE* 3.7 19.0 - - + +
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Residues in contact with LEU 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 PHE 3.2 14.0 + - - +
198D GLN* 3.0 14.8 + - - +
200D ALA* 1.3 74.8 - - - +
202D SER* 1.3 65.9 + - - +
203D LYS 3.2 0.4 - - - -
204D GLY 3.2 8.5 + - - +
235D TYR* 3.9 23.8 - - + -
238D GLN* 3.8 36.1 - - + +
239D PHE* 3.6 25.8 - - + -
242D GLN* 3.5 34.3 + - - +
244D ILE* 4.0 10.8 - - + -
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Residues in contact with SER 202 (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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198D GLN 2.9 15.8 + - - -
199D MET* 3.8 13.6 + - - +
200D ALA 3.4 0.2 - - - -
201D LEU* 1.3 77.3 - - - +
203D LYS* 1.3 63.3 + - - +
342D HIS* 5.6 6.8 + - - -
345D LYS* 6.2 5.8 - - - -
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Residues in contact with LYS 203 (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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110D GLU* 2.9 37.8 + - - -
129D ILE* 3.8 15.9 - - + -
199D MET* 3.2 23.6 + - - +
202D SER* 1.3 79.3 - - - +
204D GLY* 1.3 64.2 + - - +
205D TRP* 3.4 52.8 + - + +
266D ILE* 4.3 1.6 - - + -
338D ARG* 4.1 14.8 - - - +
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Residues in contact with GLY 204 (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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200D ALA 2.9 7.7 + - - -
201D LEU 3.2 6.9 + - - -
202D SER 3.4 0.2 - - - -
203D LYS* 1.3 77.8 - - - +
205D TRP* 1.3 64.0 + - - +
206D PRO* 4.5 0.5 - - - +
242D GLN* 3.5 23.5 - - - +
244D ILE* 3.2 20.9 - - - +
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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
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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