Contacts of the helix formed by residues 181 - 203 (chain D) in PDB entry 2NS8
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 GLY 181 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D PHE* 2.8 30.2 + - - -
178D ASP 4.8 0.6 + - - -
179D HIS 3.9 0.2 - - - -
180D GLN* 1.3 87.6 + - - +
182D ALA* 1.3 63.9 + - - -
183D GLU 3.7 0.2 + - - -
184D PRO* 4.0 1.0 - - - +
185D ALA* 4.8 1.4 + - - +
5F ALA* 3.3 16.6 - - - +
6F TYR* 4.3 13.2 - - - -
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Residues in contact with ALA 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ARG* 4.7 4.7 - - - +
148D ASP* 3.2 32.3 - - - +
181D GLY* 1.3 74.3 - - - -
183D GLU* 1.3 60.0 + - - +
184D PRO 3.5 0.4 - - - -
185D ALA* 3.4 7.5 + - - +
186D PHE* 2.9 30.0 + - + +
4F ASN* 5.5 0.2 - - - +
5F ALA* 3.4 11.5 - - + +
6F TYR* 3.4 27.9 + - + +
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Residues in contact with GLU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ARG* 3.8 33.3 + - - +
180D GLN 4.5 1.5 + - - +
182D ALA* 1.3 77.4 - - - +
184D PRO* 1.3 67.4 - - + +
186D PHE* 3.2 4.5 + - + +
187D LEU* 2.8 55.5 + - + +
6F TYR* 5.1 0.2 + - - -
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Residues in contact with PRO 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C TYR* 3.4 8.5 - - + +
180D GLN* 3.4 50.9 - - + +
181D GLY 4.0 2.2 - - - +
182D ALA 3.7 1.3 - - - -
183D GLU* 1.3 95.5 - - + +
185D ALA* 1.3 51.4 + - - +
187D LEU* 3.1 11.4 + - + +
188D HIS* 2.7 37.9 + - - +
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Residues in contact with ALA 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C TYR* 3.6 33.6 - - + +
135C SER* 4.3 18.6 + - - +
136C ALA* 5.8 0.2 - - - +
140D PHE* 4.3 2.0 - - - -
177D PHE* 4.5 17.0 - - + -
180D GLN* 4.5 1.0 - - - +
181D GLY 4.8 1.1 + - - +
182D ALA* 3.4 10.6 + - - +
183D GLU 3.3 0.6 - - - -
184D PRO* 1.3 76.0 - - - +
186D PHE* 1.3 61.7 + - - +
188D HIS* 4.0 0.2 - - - +
189D GLY* 2.8 29.3 + - - -
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Residues in contact with PHE 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ALA* 4.1 17.3 - - + -
84D LYS* 4.4 9.6 - - + -
87D ARG* 3.4 48.9 - - - +
140D PHE* 3.4 33.2 - + - -
141D THR* 3.9 20.4 - - + -
144D SER* 3.9 17.3 - - - +
148D ASP* 6.1 0.7 - - - +
182D ALA* 2.9 15.5 + - + +
183D GLU* 3.4 8.3 - - - +
185D ALA* 1.3 76.7 - - - +
187D LEU* 1.3 72.7 + - + +
190D LEU* 2.7 52.1 + - + +
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Residues in contact with LEU 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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80D ARG* 6.1 0.9 - - + -
84D LYS* 4.2 23.3 - - + -
183D GLU* 2.8 49.7 + - + +
184D PRO* 3.6 8.1 - - + +
186D PHE* 1.3 89.2 - - + +
188D HIS* 1.3 61.1 + - - +
190D LEU* 3.3 9.1 + - + +
191D GLU* 2.9 28.8 + - - +
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Residues in contact with HIS 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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129C ASN* 3.1 28.5 + - - +
132C TYR* 3.2 44.4 - + + +
133C ALA 5.3 0.2 - - - -
197C PHE* 5.7 3.1 - + - -
200C GLN* 3.1 31.7 - - + +
206C GLN* 3.5 8.9 + - - -
207C ILE* 3.9 18.0 + - + +
184D PRO 2.7 19.7 + - - +
185D ALA 4.0 0.2 - - - +
187D LEU* 1.3 74.0 - - - +
189D GLY* 1.3 58.2 + - - +
191D GLU* 3.1 6.0 + - - +
192D SER* 2.8 46.5 + - - -
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Residues in contact with GLY 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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132C TYR 5.1 1.2 + - - -
136C ALA* 4.2 19.3 - - - -
193C LEU* 4.4 2.3 - - - +
140D PHE* 3.6 16.6 - - - -
185D ALA 2.8 17.1 + - - -
186D PHE 3.6 1.1 - - - -
188D HIS* 1.3 79.4 - - - +
190D LEU* 1.3 62.8 + - - +
192D SER* 3.3 12.9 + - - -
193D LEU* 3.3 17.3 + - - +
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Residues in contact with LEU 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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79D LEU 4.5 3.6 - - - +
80D ARG* 3.6 43.1 - - + +
83D ALA* 3.6 26.5 - - + -
84D LYS* 4.1 8.1 - - + -
137D VAL* 4.2 15.0 - - + -
140D PHE* 3.3 15.3 - - + -
186D PHE* 2.7 34.8 + - + +
187D LEU* 3.5 11.9 - - + +
189D GLY* 1.3 73.8 - - - +
191D GLU* 1.3 64.7 + - - +
193D LEU* 3.2 6.2 + - + +
194D ILE* 3.1 31.8 + - + +
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Residues in contact with GLU 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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207C ILE* 3.6 45.1 - - + +
80D ARG* 3.0 45.9 + - - +
187D LEU 2.9 17.1 + - - +
188D HIS* 3.7 4.9 - - - +
190D LEU* 1.3 76.8 - - - +
192D SER* 1.3 57.5 + - - +
194D ILE* 3.1 5.1 + - - +
195D ARG* 2.9 52.9 + - + +
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Residues in contact with SER 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C SER 3.8 2.7 - - - +
193C LEU* 4.5 4.9 - - - -
196C GLY* 3.2 20.2 + - - -
197C PHE* 4.0 30.7 - - - -
207C ILE* 4.3 7.7 - - - +
188D HIS* 2.8 39.0 + - - -
189D GLY* 3.6 8.3 - - - -
190D LEU 3.2 0.4 - - - -
191D GLU* 1.3 75.7 - - - +
193D LEU* 1.3 51.8 + - - +
196D GLY* 2.7 30.8 + - - -
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Residues in contact with LEU 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C PHE* 5.5 2.0 - - + -
189C GLY 4.1 4.0 - - - +
192C SER* 4.1 17.7 - - - -
193C LEU* 3.3 33.0 - - + -
136D ALA* 3.8 40.4 - - + +
137D VAL* 4.1 11.0 - - + +
140D PHE* 3.9 28.7 - - + -
189D GLY 3.3 4.7 + - - +
190D LEU* 3.2 9.9 + - + +
192D SER* 1.3 77.0 - - - +
194D ILE* 1.3 51.4 + - - +
196D GLY* 2.9 3.5 + - - -
197D PHE* 2.7 51.4 + - + -
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Residues in contact with ILE 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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75D TRP* 3.8 2.0 - - + -
76D GLN* 3.7 38.8 - - + +
79D LEU* 3.4 40.4 - - + -
80D ARG* 3.9 22.0 - - - +
137D VAL* 5.2 0.4 - - + -
190D LEU* 3.1 28.4 + - + +
191D GLU* 3.5 14.4 - - - +
193D LEU* 1.3 76.0 - - - +
195D ARG* 1.3 65.4 + - - +
197D PHE* 3.2 19.8 + - + +
198D GLU* 3.3 18.3 + - - +
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Residues in contact with ARG 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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196C GLY* 4.3 3.6 - - - -
199C VAL* 3.7 39.3 - - + +
207C ILE* 4.0 23.9 - - + +
80D ARG* 5.7 0.2 - - - +
191D GLU* 2.9 48.1 + - + +
192D SER 3.9 2.5 - - - +
194D ILE* 1.3 71.8 - - - +
196D GLY* 1.3 66.5 + - - +
198D GLU* 3.1 45.5 + - - +
199D VAL* 3.2 18.2 + - - +
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Residues in contact with GLY 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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192C SER* 3.1 29.2 - - - -
195C ARG* 3.9 3.9 - - - +
196C GLY* 3.6 9.1 - - - -
192D SER 2.7 15.3 + - - -
193D LEU 3.2 3.8 - - - -
195D ARG* 1.3 75.5 - - - +
197D PHE* 1.3 58.1 + - - +
199D VAL* 3.3 3.6 + - - +
200D GLN* 2.9 31.9 + - - +
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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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188C HIS* 6.0 1.8 - + - -
192C SER* 3.2 31.6 - - - -
75D TRP* 3.7 13.0 - + + -
79D LEU* 3.7 31.9 - - + -
125D PHE* 4.4 10.4 - + + -
132D TYR 4.7 1.1 - - - -
133D ALA* 3.6 38.4 - - + -
136D ALA* 4.1 10.1 - - + -
137D VAL* 3.8 13.5 - - + -
193D LEU* 2.7 39.9 + - + -
194D ILE* 3.6 12.3 - - + +
195D ARG 3.1 0.4 - - - -
196D GLY* 1.3 73.5 - - - +
198D GLU* 1.3 52.6 + - - +
200D GLN* 3.3 7.0 + - + +
201D LEU* 2.7 38.0 + - - +
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Residues in contact with GLU 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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75D TRP* 3.6 22.4 - - + -
76D GLN* 3.2 29.1 + - - +
80D ARG* 5.8 0.2 + - - -
194D ILE* 3.6 14.8 - - - +
195D ARG* 3.1 38.3 + - - +
197D PHE* 1.3 78.8 - - - +
199D VAL* 1.3 57.8 + - + +
201D LEU* 3.4 5.6 + - - +
202D THR* 3.0 36.5 + - + +
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Residues in contact with VAL 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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195C ARG* 3.7 31.6 - - + +
198C GLU* 5.8 0.4 - - - +
199C VAL* 3.7 25.1 - - + -
195D ARG* 3.2 14.0 + - - +
196D GLY 3.6 6.5 - - - +
198D GLU* 1.3 74.4 - - + +
200D GLN* 1.3 65.9 + - - +
202D THR* 3.0 19.2 + - - +
203D ALA* 3.1 15.8 + - + +
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Residues in contact with GLN 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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188C HIS* 3.0 50.5 + - + +
191C GLU* 3.5 8.5 - - - +
192C SER* 2.8 35.3 + - - +
195C ARG* 3.2 30.1 - - - +
129D ASN* 5.7 4.6 + - - +
196D GLY 2.9 11.7 + - - +
197D PHE* 3.4 9.3 - - + +
199D VAL* 1.3 80.4 - - - +
201D LEU* 1.3 61.4 + - - +
203D ALA* 3.6 15.6 + - - +
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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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75D TRP* 4.1 29.4 - - + +
123D GLN 4.8 9.6 - - - +
124D GLY 3.5 23.6 - - - +
125D PHE* 3.7 39.3 - - + -
126D SER 5.3 0.4 - - - +
129D ASN* 5.6 7.6 - - + +
197D PHE 2.7 19.2 + - - +
198D GLU* 3.7 4.9 - - - +
199D VAL 3.2 0.2 - - - -
200D GLN* 1.3 76.2 - - - +
202D THR* 1.3 62.4 + - + +
203D ALA 4.3 3.1 - - - +
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Residues in contact with THR 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 GLU* 3.0 22.0 + - + +
199D VAL* 3.0 14.9 + - - +
201D LEU* 1.3 77.0 - - + +
203D ALA* 1.3 68.4 + - - +
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Residues in contact with ALA 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D VAL* 3.1 19.8 + - + +
200D GLN* 3.7 12.8 - - - +
201D LEU 3.4 5.0 - - - +
202D THR* 1.3 85.6 + - - +
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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