Contacts of the helix formed by residues 186 - 204 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A GLN* 1.3 71.3 - - - +
187A LYS* 1.3 53.2 + - - +
189A ILE* 2.9 10.8 + - - +
190A GLU* 2.7 52.4 + - - +
222A ARG* 2.8 51.4 + - - +
226A ILE* 3.7 8.1 - - + +
175C GLY* 5.9 1.6 - - - -
176C GLY 3.0 29.5 + - - +
177C GLY* 3.2 11.8 - - - -
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Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A GLN* 3.2 12.4 - - + +
186A ASP* 1.3 77.5 - - - +
188A SER* 1.3 58.1 + - - +
190A GLU* 3.2 19.8 + - + +
191A ASP* 2.8 60.6 + - - +
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Residues in contact with SER 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A HIS* 2.9 29.3 + - - -
184A ASN* 3.5 6.7 + - - -
185A GLN* 3.1 17.7 + - - +
187A LYS* 1.3 76.4 - - - +
189A ILE* 1.3 64.7 + - - +
191A ASP* 3.5 9.4 + - - +
192A PHE* 3.1 22.9 + - - +
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A HIS* 4.6 1.6 - - - -
184A ASN* 4.2 14.1 - - + +
185A GLN 3.2 14.3 + - - +
186A ASP* 2.9 11.5 + - - +
188A SER* 1.3 77.9 - - - +
190A GLU* 1.3 62.4 + - - +
192A PHE* 3.2 8.2 + - - +
193A ALA* 3.0 20.6 + - - +
222A ARG* 4.0 24.7 - - + -
223A PHE* 3.8 55.4 - - + +
226A ILE* 3.8 28.7 - - + -
227A PHE* 4.2 3.2 - - + -
178C VAL* 4.5 5.8 - - + -
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Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ASP* 2.7 35.2 + - - +
187A LYS* 3.5 23.2 - - + +
189A ILE* 1.3 72.8 - - - +
191A ASP* 1.3 65.5 + - - +
193A ALA* 3.1 3.5 + - - +
194A HIS* 2.9 32.9 + - + -
226A ILE* 3.8 21.4 - - + +
230A ILE* 3.9 20.2 - - + -
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Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLY* 5.6 4.9 - - - +
106A THR* 4.8 1.1 - - - -
187A LYS* 2.8 55.1 + - - +
188A SER* 3.8 8.4 - - - +
190A GLU* 1.3 72.7 - - - +
192A PHE* 1.3 62.9 + - - +
194A HIS* 3.3 2.9 + - - -
195A SER* 2.9 30.9 + - - -
298A PRO* 3.7 34.6 - - + +
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Residues in contact with PHE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A THR* 3.6 36.1 - - + +
108A PHE* 5.3 0.4 - + - -
131A GLY 4.3 2.5 - - - -
132A HIS 4.3 1.1 - - - -
133A HIS* 3.6 42.2 - - + +
188A SER 3.1 14.1 + - - +
189A ILE 3.2 8.0 + - - +
191A ASP* 1.3 76.0 - - - +
193A ALA* 1.3 60.5 + - - +
195A SER* 4.1 0.7 - - - -
196A SER* 2.8 43.7 + - - -
209A LEU* 4.3 7.0 - - + -
223A PHE* 3.9 17.7 - + - -
227A PHE* 3.7 21.3 - + - -
268A ALA* 3.8 20.4 - - + -
269A CYS 3.7 23.1 - - - -
270A LYS* 4.8 0.7 - - + -
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ILE 3.0 10.0 + - - +
190A GLU* 3.1 8.3 + - - +
192A PHE* 1.3 76.8 - - - +
194A HIS* 1.3 59.2 + - - +
196A SER* 3.0 3.1 + - - -
197A PHE* 2.8 50.0 + - + -
226A ILE* 4.7 0.9 - - + +
227A PHE* 3.5 35.1 - - + -
230A ILE* 3.9 15.7 - - + -
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Residues in contact with HIS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A GLU* 2.9 30.8 + - + +
191A ASP* 4.9 2.5 - - - -
193A ALA* 1.3 75.2 - - - +
195A SER* 1.3 55.2 + - - +
197A PHE* 3.2 4.8 + - - +
198A GLN* 2.7 41.2 + - - +
230A ILE* 3.7 30.7 - - + +
234A GLN* 3.2 32.2 + - - -
235A TYR* 2.5 30.0 + + - +
298A PRO* 3.7 27.9 + - + +
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Residues in contact with SER 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLY* 4.2 0.3 - - - -
106A THR* 3.7 21.7 + - - -
108A PHE* 3.9 3.9 - - - -
191A ASP 2.9 17.6 + - - -
192A PHE 4.1 0.2 - - - -
194A HIS* 1.3 76.6 - - - +
196A SER* 1.3 57.2 + - - +
198A GLN* 3.4 2.6 + - - +
199A MET* 2.8 31.0 + - - +
296A VAL* 2.8 38.7 + - - +
298A PRO* 3.2 19.3 - - - +
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Residues in contact with SER 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 3.7 14.8 - - - -
192A PHE* 2.8 39.9 + - - -
193A ALA 3.0 5.2 + - - -
195A SER* 1.3 76.5 - - - +
197A PHE* 1.3 62.9 + - - +
199A MET* 3.3 3.1 + - - +
200A ALA* 3.0 23.6 + - - +
207A LEU* 3.8 29.2 - - - +
227A PHE* 3.9 9.3 - - - -
266A ILE* 5.0 0.3 - - - +
268A ALA* 3.6 7.8 - - - +
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Residues in contact with PHE 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ALA* 2.8 44.9 + - + +
194A HIS 3.8 0.4 - - - +
196A SER* 1.3 69.5 - - - +
198A GLN* 1.3 66.0 + - - +
200A ALA* 3.2 2.6 + - - +
201A LEU* 3.0 29.5 + - - +
207A LEU* 3.6 22.9 - - + -
227A PHE* 3.3 39.9 - + + -
230A ILE* 3.8 3.4 - - + -
231A TYR* 3.5 34.8 - + + -
235A TYR* 3.5 38.8 - + + -
239A PHE* 3.7 17.0 - + + -
246A TYR* 3.9 10.8 - + - -
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Residues in contact with GLN 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A HIS 2.7 31.2 + - - +
195A SER* 3.8 6.3 - - - +
197A PHE* 1.3 71.6 - - - +
199A MET* 1.3 57.5 + - - +
201A LEU* 3.5 9.5 + - - +
202A SER* 2.9 31.4 + - - -
235A TYR* 3.4 27.9 + - - +
296A VAL* 4.7 7.2 - - + -
298A PRO 4.1 10.3 + - - +
299A ASP 4.2 4.9 + - - -
300A GLY* 3.7 34.5 - - - +
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Residues in contact with MET 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 3.5 40.8 - - + -
129A ILE* 4.5 8.3 - - + -
195A SER 2.8 18.5 + - - +
196A SER 3.6 4.7 - - - +
198A GLN* 1.3 78.1 - - - +
200A ALA* 1.3 62.2 + - - +
202A SER* 3.4 8.0 + - - -
203A LYS* 3.0 36.9 + - - +
266A ILE* 4.1 23.8 - - + -
294A VAL* 3.6 21.8 - - + -
296A VAL* 3.6 20.6 - - + +
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Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A SER 3.0 15.1 + - - +
197A PHE 3.7 0.2 - - - +
199A MET* 1.3 77.2 - - - +
201A LEU* 1.3 53.0 + - - +
203A LYS 3.4 0.2 + - - -
204A GLY* 2.7 31.7 + - - -
205A TRP 3.2 27.8 + - - +
207A LEU* 4.0 14.4 - - + -
239A PHE* 3.7 25.6 - - + -
244A ILE* 3.7 2.5 - - - +
266A ILE* 4.0 11.9 - - + +
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A PHE 3.0 17.0 + - - +
198A GLN* 4.0 9.4 - - - +
200A ALA* 1.3 72.3 - - - +
202A SER* 1.3 66.7 + - - +
204A GLY 3.5 5.2 + - - -
235A TYR* 3.5 34.5 - - + -
238A GLN* 3.5 49.1 - - + +
239A PHE* 3.5 21.1 - - + +
242A GLN* 3.1 34.3 + - - +
244A ILE* 3.9 7.9 - - + -
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Residues in contact with SER 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLN 2.9 18.8 + - - -
199A MET* 3.8 10.9 - - - -
200A ALA 3.3 0.2 - - - -
201A LEU* 1.3 78.8 - - - +
203A LYS* 1.3 60.6 + - - +
345A LYS* 3.2 31.6 + - - +
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Residues in contact with LYS 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLU* 3.4 32.8 + - - -
129A ILE* 3.7 21.5 - - + -
199A MET* 3.0 25.0 + - - +
200A ALA 4.1 1.8 - - - +
202A SER* 1.3 79.0 - - - +
204A GLY* 1.3 63.3 + - - +
205A TRP* 3.5 37.3 + - + +
266A ILE* 4.3 9.2 - - + -
338A ARG* 3.7 17.2 - - - +
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Residues in contact with GLY 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ALA 2.7 15.5 + - - -
201A LEU 3.5 1.8 + - - -
202A SER 3.4 3.0 + - - -
203A LYS* 1.3 74.7 - - - +
205A TRP* 1.3 63.9 + - - -
206A PRO* 4.7 0.5 - - - +
242A GLN* 3.4 25.0 - - - +
244A ILE* 3.4 17.8 - - - +
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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