Contacts of the helix formed by residues 192 - 215 (chain A) in PDB entry 3NJ8
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 192 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.0 13.6 - - - +
146A TYR* 3.7 26.0 - - - +
149A ALA* 4.4 5.3 - - - +
190A GLY 3.1 2.2 - - - -
191A GLY* 1.3 77.4 - - - +
193A MET* 1.3 53.0 + - - +
194A SER* 3.2 4.0 + - - +
195A SER* 3.1 13.3 + - - -
196A ALA* 2.7 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA* 3.8 11.2 - - + -
131A GLY* 3.8 26.0 - - - -
134A VAL* 3.7 19.7 - - + -
149A ALA* 4.0 8.1 - - + -
153A SER* 3.5 27.4 - - - +
189A TYR* 3.4 33.2 - - + +
190A GLY 3.3 16.9 + - - +
191A GLY 3.3 1.6 + - - +
192A GLY* 1.3 76.5 - - - +
194A SER* 1.3 57.2 + - - +
196A ALA* 3.0 4.2 + - - +
197A LYS* 2.8 50.8 + - - +
501A NJ8 4.2 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 5.2 7.6 - - - +
181A ALA* 3.5 31.2 - - - -
182A ALA* 3.6 13.5 - - - +
185A VAL* 6.5 0.2 - - - -
186A VAL 6.2 0.7 - - - -
189A TYR* 3.5 24.2 + - - -
190A GLY* 5.7 0.5 - - - -
192A GLY* 4.7 2.8 + - - -
193A MET* 1.3 78.6 - - - +
195A SER* 1.3 73.3 + - - +
197A LYS* 3.5 1.2 + - - +
198A ALA* 3.2 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.2 10.4 - - - +
146A TYR* 3.3 38.6 + - - -
192A GLY* 3.1 12.4 + - - -
194A SER* 1.3 82.3 + - - +
196A ALA* 1.3 56.1 + - - +
198A ALA* 2.8 28.0 + - - +
199A ALA* 3.0 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ALA* 4.2 7.0 - - + +
150A SER* 4.0 32.8 - - - +
153A SER* 4.4 12.1 - - - -
154A ALA* 3.5 12.3 + - + +
192A GLY 2.7 16.3 + - - +
193A MET* 3.0 13.7 + - - +
195A SER* 1.3 73.6 - - - +
197A LYS* 1.3 58.4 + - - +
199A ALA* 3.5 6.0 + - - -
200A LEU* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A HIS* 5.6 0.2 - - - -
128A LEU 4.2 1.6 + - - -
129A ALA* 3.6 8.5 - - - +
153A SER* 4.2 8.9 - - - -
177A LEU 3.4 23.2 + - - +
178A SER* 3.8 20.5 + - - +
179A TYR 4.2 7.4 - - - +
182A ALA* 3.9 9.4 - - + +
189A TYR* 3.4 25.4 - - + +
193A MET* 2.8 36.2 + - - +
194A SER* 4.0 5.2 - - - +
196A ALA* 1.3 69.9 - - - +
198A ALA* 1.3 60.0 + - - +
200A LEU* 3.2 15.9 - - + +
201A GLU* 2.9 32.4 + - - +
316A NAD 2.6 38.1 + - - -
501A NJ8 4.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA* 3.7 24.2 - - + +
194A SER 3.2 12.7 + - - +
195A SER* 2.8 12.6 + - - +
197A LYS* 1.3 74.7 - - - +
199A ALA* 1.3 66.8 + - - +
201A GLU* 3.2 7.1 + - - +
202A SER* 3.1 23.8 + - - -
205A ARG* 4.7 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A SER* 5.2 4.7 - - - +
154A ALA* 4.2 10.8 - - + -
195A SER 3.0 10.5 + - - +
196A ALA* 3.5 11.9 - - - +
198A ALA* 1.3 73.9 - - - +
200A LEU* 1.3 52.6 + - - +
202A SER* 3.2 5.6 + - - -
203A ASP* 2.8 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A HIS* 4.9 0.4 - - + -
153A SER 3.9 17.5 - - - +
154A ALA* 4.3 9.8 - - + +
157A PHE* 3.5 37.2 - - + -
176A THR* 3.2 28.7 - - + +
177A LEU 3.2 28.7 - - - +
178A SER* 4.8 2.7 - - - -
196A ALA 3.0 13.9 + - - +
197A LYS* 3.2 23.8 - - + +
198A ALA 3.1 0.2 - - - -
199A ALA* 1.3 76.7 - - - +
201A GLU* 1.3 56.7 + - - +
203A ASP* 3.3 6.1 + - + +
204A THR* 2.6 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A SER* 2.7 33.9 + - - +
179A TYR 4.1 2.6 - - - +
180A LEU* 5.6 0.5 - - - -
182A ALA* 3.5 18.1 - - - +
183A GLU* 3.5 30.1 - - - +
197A LYS 2.9 15.9 + - - +
198A ALA* 3.2 5.7 + - - +
200A LEU* 1.3 77.0 - - - +
202A SER* 1.3 60.4 + - - +
204A THR* 3.3 10.7 - - - -
205A ARG* 3.3 36.4 + - - +
221A ALA* 4.8 4.9 - - + -
223A SER* 4.2 3.5 + - - -
285A THR* 4.1 34.0 + - + +
287A TYR* 5.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ALA 3.1 15.4 + - - -
199A ALA* 3.6 6.5 - - - -
201A GLU* 1.3 75.5 - - - +
203A ASP* 1.3 57.5 + - - +
204A THR 2.9 4.3 - - - -
205A ARG* 3.0 26.0 + - - +
206A THR* 2.7 40.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ALA* 4.8 8.1 - - - +
155A TYR* 5.6 0.3 - - - -
157A PHE* 5.4 4.5 - - + -
158A VAL* 4.1 26.2 - - + +
199A ALA* 2.8 35.0 + - - +
200A LEU* 3.3 7.7 + - + +
202A SER* 1.3 80.6 + - - +
204A THR* 1.3 57.1 + - - +
205A ARG 3.3 0.2 - - - -
206A THR* 3.9 10.5 + - - -
207A LEU* 3.0 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 3.7 6.3 - - - -
176A THR* 3.5 18.4 - - + +
200A LEU 2.6 17.9 + - - -
201A GLU* 3.3 15.0 - - - +
202A SER 2.9 0.6 - - - -
203A ASP* 1.3 79.8 - - - +
205A ARG* 1.3 58.5 + - - +
208A ALA* 3.0 26.3 + - - +
219A VAL* 4.0 11.0 - - + +
220A ASN* 3.6 41.1 - - - +
221A ALA* 3.7 8.1 - - + +
283A GLY* 3.8 5.4 - - - +
284A VAL 4.6 3.8 - - - +
285A THR* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLU* 4.7 9.7 + - - -
198A ALA 4.7 2.0 + - - -
201A GLU* 3.3 28.8 + - - +
202A SER* 3.0 34.9 + - - +
204A THR* 1.3 77.1 - - - +
206A THR* 1.3 64.7 + - - +
208A ALA* 3.6 5.7 - - - +
209A TRP* 3.4 17.0 + - - +
283A GLY 3.7 20.8 + - - +
285A THR* 4.5 9.3 + - - -
293B HIS* 5.9 1.1 - - - -
294B ALA* 4.3 34.7 - - + +
295B MET* 5.6 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A SER* 2.7 21.8 + - - -
203A ASP* 3.9 9.6 + - - -
205A ARG* 1.3 75.2 - - - +
207A LEU* 1.3 63.0 + - + +
209A TRP* 2.9 28.1 + - + +
210A GLU* 3.0 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 4.4 15.5 - - + -
158A VAL* 4.1 41.3 - - + -
161A LEU* 4.3 22.9 - - + -
162A GLN* 6.3 1.6 - - + -
203A ASP* 3.0 28.5 + - + +
206A THR* 1.3 74.8 - - + +
208A ALA* 1.3 63.2 + - - +
210A GLU* 4.2 19.3 - - + +
211A ALA* 2.6 40.2 + - + +
219A VAL* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A THR 3.0 22.2 + - - +
205A ARG 3.6 6.7 - - - +
206A THR 3.2 0.4 - - - -
207A LEU* 1.3 77.3 - - - +
209A TRP* 1.3 56.9 + - - +
212A GLY* 3.0 25.6 + - - -
217A VAL 4.3 0.5 - - - +
219A VAL* 3.8 16.9 - - - +
282A SER* 3.3 23.8 + - - +
283A GLY* 3.7 13.9 - - - +
256B PRO* 3.5 14.6 - - + +
294B ALA* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ARG 3.4 8.3 + - - +
206A THR* 2.9 14.8 + - + +
208A ALA* 1.3 77.9 - - - +
210A GLU* 1.3 90.9 + - + +
212A GLY* 3.4 0.5 + - - -
213A GLN* 3.1 57.2 + - + +
253B ASN 5.5 0.2 - - - -
254B ASN 3.7 11.9 - - - -
255B ALA 3.5 20.2 - - - -
256B PRO* 3.6 21.4 - - + +
295B MET* 3.3 38.1 - - + +
299B VAL* 3.5 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A THR* 3.0 34.6 + - - +
207A LEU* 4.0 15.9 - - + +
209A TRP* 1.3 91.0 - - + +
211A ALA* 1.3 65.6 + - - +
213A GLN* 3.0 5.4 + - - +
214A LYS* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 4.5 16.4 - - + -
207A LEU* 2.6 25.9 + - + +
210A GLU* 1.3 74.2 - - - +
212A GLY* 1.3 55.9 + - - +
214A LYS* 5.0 0.2 - - - -
215A TYR* 3.0 39.9 + - + +
216A GLY 3.1 6.1 + - - -
217A VAL* 3.3 13.5 + - + +
219A VAL* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA 3.0 25.0 + - - -
209A TRP 3.7 0.7 - - - -
210A GLU 3.1 0.2 - - - -
211A ALA* 1.3 78.5 - - - +
213A GLN* 1.3 56.9 + - - +
216A GLY* 3.4 15.8 - - - -
217A VAL 3.2 16.3 + - - -
256B PRO 2.9 19.5 - - - +
257B LEU* 4.1 12.0 - - - +
258B ARG 4.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A TRP* 3.1 58.1 + - + +
210A GLU* 3.0 4.9 + - - +
212A GLY* 1.3 79.8 + - - +
214A LYS* 1.3 68.6 + - - +
215A TYR 3.4 0.2 + - - -
216A GLY* 4.0 2.9 + - - -
253B ASN 5.5 2.3 - - - +
255B ALA 3.9 5.9 + - - +
256B PRO 3.1 21.3 + - - +
258B ARG* 4.3 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLU 2.9 15.9 + - - +
213A GLN* 1.3 78.0 - - - +
215A TYR* 1.3 98.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 5.6 1.3 - - + -
162A GLN 4.8 0.8 + - - -
165A GLY* 3.5 20.2 - - - -
166A PRO* 3.2 51.6 - - + +
168A MET 4.8 7.7 - - - +
169A ASN 4.9 0.3 - - - -
170A GLU* 3.6 25.6 - - - +
211A ALA* 3.0 23.1 + - + +
213A GLN 4.6 0.2 - - - -
214A LYS* 1.3 109.6 - - + +
216A GLY* 1.3 63.5 + - - +
217A VAL* 3.5 18.9 - - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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