Contacts of the helix formed by residues 184 - 206 (chain D) in PDB entry 6S6A
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 SER 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 GLY 4.1 1.0 + - - -
183D LEU* 1.3 74.3 - - - +
185D ASP* 1.3 58.5 + - - +
186D ASP* 3.5 12.5 - - - +
187D HIS* 3.0 24.1 + - - +
188D LYS* 3.0 27.1 + - - +
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Residues in contact with ASP 185 (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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184D SER* 1.3 69.1 - - - +
186D ASP* 1.3 64.9 - - - +
188D LYS* 4.1 23.1 - - + +
189D ILE* 2.9 56.1 + - + +
217D LEU* 5.6 1.2 - - - +
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Residues in contact with ASP 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D SER* 3.1 12.5 - - - +
185D ASP* 1.3 78.6 - - - +
187D HIS* 1.3 62.0 + - - +
189D ILE* 4.1 3.7 - - - +
190D GLU* 3.3 22.6 + - - +
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Residues in contact with HIS 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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146D ALA 5.3 4.0 + - - -
183D LEU* 3.5 38.0 - - + +
184D SER* 3.0 24.2 + - - +
186D ASP* 1.3 74.7 - - - +
188D LYS* 1.3 60.9 - - - +
190D GLU* 3.2 9.9 + - + +
191D THR* 2.6 39.1 + - + -
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Residues in contact with LYS 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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177D ILE* 6.4 0.2 - - - -
180D VAL* 3.3 45.4 + - + +
183D LEU* 3.5 25.5 + - + +
184D SER* 3.0 12.7 + - - +
185D ASP* 3.6 34.0 - - - +
187D HIS* 1.3 70.0 - - - +
189D ILE* 1.3 52.0 + - - +
191D THR* 2.7 29.0 + - - -
192D GLN* 2.8 18.9 + - - +
217D LEU* 4.0 30.4 - - + +
222D ASP* 5.9 1.3 - - - -
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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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185D ASP* 2.9 45.0 + - - +
186D ASP* 4.2 3.8 - - - +
188D LYS* 1.3 78.4 - - + +
190D GLU* 1.3 57.0 + - - +
192D GLN* 4.0 14.3 - - + +
193D ARG* 3.1 55.2 + - + +
217D LEU* 5.5 3.4 - - + -
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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* 3.3 13.0 + - - +
187D HIS* 3.2 11.9 + - + +
188D LYS 3.1 0.2 - - - -
189D ILE* 1.3 75.4 - - - +
191D THR* 1.3 58.5 + - - +
193D ARG* 3.9 14.9 - - - +
194D ASP* 2.9 38.4 + - + +
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Residues in contact with THR 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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146D ALA* 4.4 22.9 - - + +
150D TYR* 3.5 37.2 - - + +
177D ILE* 4.7 8.1 - - + -
183D LEU* 4.9 2.3 - - + +
187D HIS* 2.6 31.3 + - + -
188D LYS* 2.7 13.6 + - - -
190D GLU* 1.3 70.1 - - - +
192D GLN* 1.3 58.1 + - - -
194D ASP* 4.4 0.2 - - - -
195D ILE* 3.0 45.6 + - + +
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Residues in contact with GLN 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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177D ILE* 4.7 13.3 - - + +
188D LYS 2.8 17.2 + - - +
189D ILE* 4.0 13.6 - - + +
191D THR* 1.3 67.9 - - - +
193D ARG* 1.3 58.6 + - - +
194D ASP 3.2 0.3 + - - -
195D ILE* 4.2 0.2 - - - +
196D HIS* 2.7 44.9 + - + +
215D PHE* 3.7 32.2 + - + +
217D LEU* 3.6 35.2 - - + +
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Residues in contact with ARG 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* 3.1 40.5 + - + +
190D GLU* 3.7 16.6 - - - +
191D THR 3.5 0.2 - - - -
192D GLN* 1.3 78.4 - - - +
194D ASP* 1.3 62.9 + - - +
196D HIS* 3.9 10.7 - - + +
197D GLN* 3.6 28.7 + - - +
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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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150D TYR* 3.7 24.5 + - - +
190D GLU* 2.9 27.1 + - + +
191D THR 3.9 0.9 - - - +
192D GLN 3.2 0.2 - - - -
193D ARG* 1.3 75.7 - - - +
195D ILE* 1.3 57.7 + - - +
197D GLN* 3.1 7.7 + - - +
198D ARG* 3.0 56.2 + - - +
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Residues in contact with ILE 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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144D ILE* 4.3 24.7 - - + -
146D ALA* 5.8 0.9 - - - -
150D TYR* 3.5 50.0 - - + -
154D LEU* 4.1 16.2 - - + -
157D LEU* 5.6 0.7 - - + -
175D VAL* 4.8 0.2 - - + -
177D ILE* 4.2 29.6 - - + -
191D THR* 3.0 28.6 + - + +
192D GLN 4.2 0.9 - - - +
194D ASP* 1.3 72.2 - - - +
196D HIS* 1.3 63.9 + - - +
197D GLN 3.4 0.7 + - - -
198D ARG* 3.5 12.9 + - - +
199D ALA* 3.6 15.6 + - + +
215D PHE* 4.3 12.9 - - + -
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Residues in contact with HIS 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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177D ILE* 5.8 0.2 - - - +
192D GLN* 2.7 34.5 + - + +
193D ARG* 3.9 7.4 - - + +
195D ILE* 1.3 71.3 - - - +
197D GLN* 1.3 70.0 + - + +
200D ASN* 2.3 39.7 + - - +
212D HIS* 6.2 2.0 - - - -
215D PHE* 3.8 34.5 - + + -
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Residues in contact with GLN 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 ARG* 3.6 20.6 + - - +
194D ASP* 3.1 4.4 + - - +
196D HIS* 1.3 91.8 - - + +
198D ARG* 1.3 56.0 + - - +
199D ALA 3.7 0.2 - - - -
200D ASN* 4.0 4.5 - - - -
201D ASP* 2.8 50.8 + - - +
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Residues in contact with ARG 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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150D TYR* 5.2 3.4 - - - -
151D MET* 3.6 32.0 - - - +
154D LEU* 3.4 35.4 - - + +
194D ASP* 3.0 38.7 + - - +
195D ILE* 3.5 2.2 + - - +
197D GLN* 1.3 76.2 - - - +
199D ALA* 1.3 57.4 + - - +
200D ASN 3.3 0.7 - - - -
201D ASP* 3.2 9.3 + - - +
202D ASP* 3.0 28.6 + - - +
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Residues in contact with ALA 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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154D LEU* 3.6 22.7 - - + +
157D LEU* 3.6 24.9 - - + -
158D HIS* 5.9 0.9 - - + +
195D ILE 3.6 8.6 + - - +
198D ARG* 1.3 74.2 - - - +
200D ASN* 1.3 58.4 + - - +
201D ASP 3.5 0.2 - - - -
202D ASP* 3.8 19.6 - - - +
203D LEU* 3.2 28.9 + - - +
213D LEU* 4.2 9.2 - - + +
215D PHE* 5.8 0.4 - - + -
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Residues in contact with ASN 200 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D HIS* 2.3 39.3 + - - +
197D GLN* 3.9 6.2 + - + +
198D ARG 3.3 0.4 - - - -
199D ALA* 1.3 76.5 - - - +
201D ASP* 1.3 62.2 + - - +
203D LEU* 3.5 18.4 - - - +
204D ALA* 3.1 26.2 + - - +
211D LEU 5.4 0.5 - - - +
212D HIS* 4.9 11.4 + - - -
213D LEU* 4.5 6.4 + - - +
215D PHE* 3.5 28.5 - - - -
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Residues in contact with ASP 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 GLN* 2.8 39.3 + - - +
198D ARG* 3.4 7.9 - - - +
200D ASN* 1.3 76.1 - - - +
202D ASP* 1.3 58.5 + - - +
203D LEU 3.3 0.2 - - - -
204D ALA* 3.5 7.5 + - - +
205D ASP* 2.7 41.4 + - - +
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Residues in contact with ASP 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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154D LEU* 2.9 29.7 - - - +
155D THR* 5.1 1.0 - - - +
158D HIS* 3.4 33.6 + - + +
198D ARG 3.0 16.5 + - - +
199D ALA* 3.8 17.7 - - - +
201D ASP* 1.3 72.6 - - - +
203D LEU* 1.3 62.5 + - - +
205D ASP* 3.1 19.4 + - - +
206D ALA* 3.2 14.6 + - - +
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Residues in contact with LEU 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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158D HIS* 4.6 9.2 - - - +
161D VAL* 4.2 10.3 - - + -
199D ALA 3.2 22.6 + - - +
200D ASN* 3.5 22.8 + - - +
201D ASP 3.3 0.8 - - - -
202D ASP* 1.3 78.4 - - + +
204D ALA* 1.3 55.2 + - - +
206D ALA 3.6 0.7 + - - -
207D GLY 3.1 8.0 + - - -
208D LEU* 2.6 69.6 + - + +
209D GLU* 4.9 2.2 - - - +
211D LEU* 3.3 38.8 - - + +
213D LEU* 4.1 20.2 - - + -
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Residues in contact with ALA 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 ASN 3.1 16.7 + - - +
201D ASP* 3.8 11.2 - - - +
202D ASP 3.3 0.2 - - - -
203D LEU* 1.3 76.0 - - - +
205D ASP* 1.3 63.0 + - - +
207D GLY* 3.8 6.4 + - - -
209D GLU* 3.8 33.6 - - + +
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Residues in contact with ASP 205 (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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201D ASP* 2.7 28.9 - - - +
202D ASP* 3.1 9.5 + - - +
204D ALA* 1.3 80.3 - - - +
206D ALA* 1.3 57.8 + - - +
207D GLY* 3.0 8.6 + - - -
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Residues in contact with ALA 206 (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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158D HIS* 3.5 36.8 - - + +
202D ASP 3.2 4.1 + - - +
203D LEU 3.6 0.6 + - - +
205D ASP* 1.3 75.2 - - - +
207D GLY* 1.3 57.6 + - - +
208D LEU* 3.4 23.3 - - + +
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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