Contacts of the helix formed by residues 198 - 216 (chain A) in PDB entry 3NA0
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 ILE 198 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE* 4.2 11.4 - - + -
182A LEU* 4.4 7.0 - - + -
185A ARG* 4.3 3.4 - - - +
194A TYR* 4.2 25.4 - - + +
196A GLY 3.6 4.7 + - - +
197A ASP* 1.3 75.1 + - - +
199A SER* 1.3 53.4 + - - +
200A ASP 3.4 2.7 - - - -
201A ASP* 3.2 24.7 + - + +
202A LEU* 2.8 64.9 + - + +
336A GLN* 4.9 1.1 + - - +
339A LEU* 4.1 13.7 - - + -
507A ILE 4.5 1.8 + - - -
509A PHE* 4.0 18.2 - - + -
511A PHE* 3.9 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ASP* 2.6 30.4 + - - -
198A ILE* 1.3 73.8 - - - +
200A ASP* 1.3 64.7 + - - +
202A LEU* 2.9 10.3 + - - +
203A PHE* 2.8 47.2 + - - -
333A MET* 4.6 3.9 - - - +
336A GLN* 3.8 23.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ASP 5.2 1.3 + - - +
198A ILE 3.4 0.4 - - - -
199A SER* 1.3 82.5 + - - +
201A ASP* 1.3 59.0 + - - +
203A PHE* 3.3 18.1 + - - +
204A ARG* 3.0 53.9 + - - +
231A GLN* 5.5 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE* 3.7 21.2 - - + -
181A VAL* 5.3 2.4 - - + +
185A ARG* 2.9 42.9 + - - +
197A ASP 4.1 4.2 - - - +
198A ILE* 3.2 28.3 + - + +
200A ASP* 1.3 75.1 + - - +
202A LEU* 1.3 59.1 + - - +
204A ARG* 2.8 32.0 + - - +
205A PHE* 2.8 29.5 + - - +
222A LEU* 4.5 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE* 3.8 22.0 - - + -
198A ILE* 2.8 43.8 + - + +
199A SER* 2.9 6.9 + - - +
201A ASP* 1.3 72.5 - - - +
203A PHE* 1.3 57.7 + - - +
205A PHE* 3.3 6.1 + - + +
206A ALA* 2.9 24.8 + - - +
332A SER* 3.4 26.8 - - - +
333A MET* 5.0 1.3 - - + -
335A LEU* 4.7 12.1 - - + -
336A GLN* 3.7 39.9 - - + +
339A LEU* 4.5 2.5 - - + -
475A PHE* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER* 2.8 40.0 + - - -
200A ASP* 3.6 17.0 - - - +
202A LEU* 1.3 77.2 - - - +
204A ARG* 1.3 56.5 + - - +
206A ALA* 3.4 2.6 + - - +
207A PHE* 3.0 28.6 + - - +
231A GLN* 5.8 0.4 - - - +
234A ILE* 3.7 22.8 - - + +
238A TYR* 5.0 11.7 - + + -
328A VAL* 3.8 8.9 - - + +
329A ASP* 3.3 35.0 - - + -
332A SER* 3.5 21.5 - - - -
333A MET* 3.5 26.0 - - + -
502A MET* 4.5 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ARG* 4.7 3.4 - - - +
200A ASP* 3.0 33.8 + - - +
201A ASP* 2.8 40.9 + - - +
203A PHE* 1.3 72.9 - - - +
205A PHE* 1.3 60.3 + - - +
207A PHE* 3.3 2.3 + - - +
208A GLU* 2.9 32.1 + - - +
221A MET* 3.3 34.8 + - + +
222A LEU* 4.3 6.0 - - + +
226A VAL* 4.2 14.3 - - - +
231A GLN* 3.0 37.0 + - - +
234A ILE* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU 5.2 0.9 - - - -
174A VAL* 3.6 21.1 - - + -
175A SER* 3.6 22.9 - - - -
178A PHE* 3.8 27.8 - + + -
201A ASP 2.8 18.2 + - - +
202A LEU* 3.4 10.5 - - + +
204A ARG* 1.3 76.4 - - - +
206A ALA* 1.3 65.2 + - + +
207A PHE 3.2 0.3 + - - -
208A GLU* 3.3 5.3 + - - +
209A SER* 2.8 42.4 + - - -
222A LEU* 4.0 8.4 - - + +
332A SER* 5.7 0.4 - - - -
335A LEU* 3.7 17.9 - - + -
471A GLU* 3.3 28.3 - - + -
475A PHE* 3.3 39.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU 2.9 18.2 + - - +
203A PHE 3.8 2.0 - - - +
205A PHE* 1.3 74.9 - - + +
207A PHE* 1.3 57.3 + - - +
209A SER* 3.4 1.7 + - - -
210A ILE* 3.0 31.1 + - - +
327A GLY 3.5 8.3 - - - +
328A VAL* 3.2 28.3 - - - +
331A THR* 3.4 20.6 - - - +
332A SER* 3.9 4.5 - - - -
471A GLU* 3.7 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PHE 3.0 17.9 + - - +
204A ARG 3.6 3.8 - - - +
205A PHE 3.1 0.2 - - - -
206A ALA* 1.3 74.5 - - - +
208A GLU* 1.3 56.7 + - - +
210A ILE* 3.4 6.8 - - + +
211A THR* 2.6 64.0 + - + +
219A GLN* 4.0 10.5 - - + -
221A MET* 3.7 22.4 - - + -
230A ALA* 4.0 21.8 - - + -
233A PHE* 3.3 30.7 - + - -
234A ILE* 3.8 23.6 - - + -
280A TYR* 3.8 24.2 - + - -
324A LEU* 5.2 2.0 - - + -
328A VAL* 3.9 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A VAL* 3.5 22.0 - - + -
204A ARG 2.9 19.1 + - - +
205A PHE 3.6 3.1 - - - +
207A PHE* 1.3 72.4 - - - +
209A SER* 1.3 58.1 + - - +
211A THR* 3.0 4.4 + - - -
212A ASN* 2.9 32.2 + - - +
217A GLU 5.3 0.2 - - - +
218A ARG* 2.7 34.2 + - - +
219A GLN* 3.0 34.4 + - - +
220A GLY 3.5 2.7 + - - -
221A MET* 2.9 37.0 + - + +
222A LEU* 4.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 3.8 15.7 + - - +
174A VAL* 3.5 16.5 - - - +
205A PHE* 2.8 42.2 + - - -
206A ALA 3.6 1.8 - - - -
208A GLU* 1.3 76.3 - - - +
210A ILE* 1.3 62.4 + - - +
212A ASN* 3.3 2.9 + - - +
213A VAL* 3.2 27.8 + - - +
467A ILE* 5.9 0.2 - - - -
471A GLU* 3.6 26.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ALA 3.0 17.8 + - - +
207A PHE* 3.4 16.4 - - + +
209A SER* 1.3 76.0 - - - +
211A THR* 1.3 65.5 + - + +
213A VAL* 3.6 4.5 - - + +
214A ILE* 3.2 41.3 + - + +
323A MET* 3.5 24.2 - - + +
324A LEU* 4.1 22.0 - - + +
327A GLY* 4.5 9.4 - - - +
328A VAL* 4.7 5.2 - - + -
467A ILE* 4.1 37.2 - - + -
471A GLU* 4.8 2.5 + - - +
601A HEM 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A PHE* 2.6 58.3 + - + +
208A GLU* 3.0 12.6 + - - -
210A ILE* 1.3 76.1 - - + +
212A ASN* 1.3 54.0 + - - +
215A PHE* 2.7 51.1 + - + +
217A GLU 4.2 2.3 + - - +
219A GLN* 3.2 32.3 - - + +
280A TYR* 5.4 2.0 - - + -
324A LEU* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 2.8 50.8 + - + +
173A ALA* 4.7 3.4 - - - +
174A VAL* 3.9 6.5 - - + +
208A GLU 2.9 19.5 + - - +
209A SER 3.3 4.7 + - - +
211A THR* 1.3 78.3 + - - +
213A VAL* 1.3 58.0 + - - +
216A GLY* 2.8 32.6 + - - +
217A GLU 3.4 30.5 + - - +
218A ARG* 3.6 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PHE* 4.0 25.8 - - + -
170A LEU* 3.9 21.0 - - + +
171A LEU* 3.9 29.8 - - + -
209A SER 3.2 11.4 + - - +
210A ILE* 3.6 15.5 - - + +
212A ASN* 1.3 75.7 - - - +
214A ILE* 1.3 61.3 + - - +
298A TYR* 4.1 2.3 + - - -
300A GLY* 3.3 5.5 - - - -
301A ILE* 2.8 39.8 + - + +
467A ILE* 4.0 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ILE* 3.2 40.0 + - + +
211A THR 4.0 1.8 - - - +
213A VAL* 1.3 77.1 - - - +
215A PHE* 1.3 88.9 + - + +
284A PHE* 5.1 0.2 - - - -
299A ARG 4.8 0.2 - - - +
300A GLY 3.9 1.2 - - - -
301A ILE* 3.5 25.8 + - + -
302A LEU* 3.0 36.9 + - + +
303A TYR 4.6 0.5 + - - -
320A VAL* 4.3 15.5 - - + +
323A MET* 4.0 22.9 - - + -
324A LEU* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A THR* 2.7 39.3 + - + +
214A ILE* 1.3 86.9 - - + +
216A GLY* 1.3 60.8 + - - +
217A GLU* 3.2 25.7 + - + +
219A GLN* 4.7 7.4 - - - +
280A TYR* 3.5 45.8 - + + -
281A THR* 4.3 0.9 - - - -
284A PHE* 3.4 30.9 - + + -
299A ARG 3.6 7.4 - - - +
302A LEU* 3.5 33.4 - - + -
320A VAL* 4.1 14.4 - - + -
324A LEU* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 4.7 11.4 - - - +
212A ASN* 2.8 31.2 + - - +
214A ILE 3.6 1.4 - - - -
215A PHE* 1.3 72.8 - - - +
217A GLU* 1.3 60.3 + - - +
299A ARG 3.4 19.5 + - - -
300A GLY* 4.4 1.0 - - - -
----------------------------------------------------------
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