Contacts of the helix formed by residues 198 - 216 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B PHE* 4.3 11.4 - - + -
182B LEU* 4.6 6.5 - - + -
185B ARG* 4.5 1.8 - - - +
194B TYR* 4.2 17.3 - - + -
196B GLY 3.5 9.8 + - - +
197B ASP* 1.3 74.9 + - - +
199B SER* 1.3 58.6 + - - +
200B ASP 3.4 2.7 - - - -
201B ASP* 3.2 22.6 + - + +
202B LEU* 2.8 60.3 + - + +
336B GLN* 4.9 1.1 + - - +
339B LEU* 3.9 14.6 - - + -
479B MET* 5.8 0.2 - - + -
507B ILE 4.4 2.4 + - - -
509B PHE* 3.9 16.4 - - + -
511B PHE* 3.9 34.3 - - + -
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Residues in contact with SER 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ASP* 2.5 29.0 + - - -
198B ILE* 1.3 76.2 - - - +
200B ASP* 1.3 63.7 + - - +
202B LEU* 3.0 9.9 + - - +
203B PHE* 2.9 46.5 + - - -
333B MET* 4.7 3.9 - - - +
336B GLN* 3.7 23.7 + - - -
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Residues in contact with ASP 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LYS* 5.8 1.9 + - - -
197B ASP 5.1 2.3 + - - +
198B ILE 3.4 0.2 - - - -
199B SER* 1.3 82.2 + - - +
201B ASP* 1.3 59.1 + - - +
203B PHE* 3.2 20.3 + - - +
204B ARG* 3.0 53.8 + - - +
231B GLN* 5.5 5.0 + - - +
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Residues in contact with ASP 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PHE* 3.7 23.0 - - + -
181B VAL* 5.1 2.9 - - - +
185B ARG* 2.8 45.2 + - - -
197B ASP 4.5 2.3 - - - +
198B ILE* 3.2 21.4 + - + +
200B ASP* 1.3 73.9 - - - +
202B LEU* 1.3 60.5 + - - +
204B ARG* 2.6 31.1 + - - +
205B PHE* 2.9 28.2 + - - +
222B LEU* 4.3 5.1 - - + +
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PHE* 3.8 14.4 - - + -
198B ILE* 2.8 37.9 + - + +
199B SER* 3.0 8.7 + - - +
201B ASP* 1.3 74.1 - - - +
203B PHE* 1.3 59.4 + - - +
205B PHE* 3.2 9.5 + - + +
206B ALA* 2.9 25.3 + - - +
332B SER* 3.6 25.8 - - - +
333B MET* 5.3 0.7 - - + -
335B LEU* 4.9 7.4 - - + -
336B GLN* 3.6 41.7 - - + +
339B LEU* 4.7 1.6 - - + -
475B PHE* 3.8 32.8 - - + -
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Residues in contact with PHE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B SER* 2.9 39.3 + - - -
200B ASP* 3.2 19.3 + - - +
202B LEU* 1.3 75.3 - - - +
204B ARG* 1.3 62.7 + - - +
206B ALA* 3.3 3.8 + - - +
207B PHE* 3.0 23.4 + - - +
231B GLN* 5.8 0.2 - - - +
234B ILE* 3.8 24.0 - - + -
238B TYR* 5.1 10.1 - + + -
328B VAL* 3.8 7.9 - - + +
329B ASP* 3.3 35.2 - - + -
332B SER* 3.3 23.3 - - - -
333B MET* 3.6 25.6 - - + -
502B MET* 4.4 12.6 - - + -
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Residues in contact with ARG 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ARG* 4.8 1.2 - - - +
200B ASP* 3.0 39.2 + - - +
201B ASP* 2.6 45.6 + - - +
203B PHE* 1.3 74.6 - - - +
205B PHE* 1.3 62.5 + - - +
207B PHE* 3.3 2.1 + - - +
208B GLU* 2.9 27.2 + - - +
221B MET* 3.4 33.5 - - + +
222B LEU* 4.4 6.5 - - + +
226B VAL* 4.3 11.9 - - - +
231B GLN* 3.0 30.2 + - - +
234B ILE* 4.0 17.9 - - + -
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Residues in contact with PHE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 5.3 1.3 - - + -
174B VAL* 3.5 22.9 - - + -
175B SER* 3.4 28.7 - - - -
178B PHE* 3.9 28.3 - + + -
201B ASP 2.9 14.4 + - - +
202B LEU* 3.2 13.2 + - + +
204B ARG* 1.3 76.7 - - - +
206B ALA* 1.3 64.6 + - - +
207B PHE 3.2 0.2 + - - -
208B GLU* 3.3 3.7 + - - +
209B SER* 2.8 42.0 + - - -
222B LEU* 4.1 7.9 - - + +
331B THR* 4.8 1.1 - - + -
332B SER* 6.0 0.4 - - - -
335B LEU* 3.8 17.7 - - + -
471B GLU* 3.3 28.5 - - + -
475B PHE* 3.4 32.5 - + + -
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B LEU 2.9 17.7 + - - +
203B PHE 3.6 2.7 - - - +
205B PHE* 1.3 73.1 - - - +
207B PHE* 1.3 57.2 + - - +
209B SER* 3.6 1.7 - - - -
210B ILE* 3.0 31.4 + - - +
327B GLY 3.5 17.1 - - - +
328B VAL* 3.2 28.0 - - - +
331B THR* 4.1 14.1 - - + -
332B SER* 4.1 2.7 - - - -
471B GLU* 3.7 13.1 - - - +
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Residues in contact with PHE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B PHE 3.0 15.9 + - - +
204B ARG 3.6 3.6 - - - +
206B ALA* 1.3 73.9 - - - +
208B GLU* 1.3 56.0 + - - +
210B ILE* 3.5 6.2 - - + +
211B THR* 2.5 55.4 + - + +
219B GLN* 4.0 16.6 - - + -
221B MET* 3.6 31.2 - - + -
230B ALA* 4.0 14.6 - - + -
233B PHE* 3.4 36.3 - + - -
234B ILE* 3.8 20.2 - - + -
280B TYR* 3.9 25.4 - + - -
324B LEU* 5.3 1.1 - - + -
328B VAL* 4.0 17.0 - - + +
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Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL* 3.5 20.6 - - + -
204B ARG 2.9 18.3 + - - +
205B PHE 3.6 4.3 - - - +
207B PHE* 1.3 72.5 - - - +
209B SER* 1.3 54.4 + - - +
211B THR* 2.9 4.7 + - - -
212B ASN* 2.8 38.1 + - - +
217B GLU 5.3 0.2 - - - +
218B ARG* 2.7 34.1 + - - +
219B GLN* 3.1 28.9 + - - +
220B GLY* 3.4 10.5 + - - -
221B MET* 2.9 35.6 + - + +
222B LEU* 4.1 17.0 - - + -
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Residues in contact with SER 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 4.0 13.8 + - - +
174B VAL* 3.6 13.4 - - - +
205B PHE* 2.8 40.2 + - - -
206B ALA 3.6 1.8 - - - -
208B GLU* 1.3 75.7 - - - +
210B ILE* 1.3 62.7 + - - +
212B ASN* 3.1 11.8 + - - +
213B VAL* 3.1 18.2 + - - +
467B ILE* 6.0 0.2 - - - -
471B GLU* 3.5 29.1 + - - -
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Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ALA 3.0 18.1 + - - +
207B PHE* 3.5 16.2 - - + +
209B SER* 1.3 75.0 - - - +
211B THR* 1.3 65.4 + - + +
213B VAL* 3.2 11.3 - - + +
214B ILE* 3.1 39.6 + - + +
323B MET* 3.6 24.9 - - + +
324B LEU* 4.2 24.0 - - + +
327B GLY* 4.3 13.2 - - - +
328B VAL* 4.7 1.6 - - + -
467B ILE* 4.1 27.6 - - + -
471B GLU* 4.6 3.7 + - - +
601B HEM 4.1 16.6 - - + -
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Residues in contact with THR 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B PHE* 2.5 54.0 + - + +
208B GLU* 2.9 12.6 + - - -
210B ILE* 1.3 74.7 - - + +
212B ASN* 1.3 60.4 + - - +
215B PHE* 2.8 49.4 + - + +
216B GLY 3.8 0.2 + - - -
217B GLU 4.0 2.8 + - - +
219B GLN* 3.3 27.0 - - + +
280B TYR* 5.3 2.0 - - + -
324B LEU* 3.7 22.0 - - + -
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Residues in contact with ASN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU* 2.7 53.3 + - + +
173B ALA* 4.9 3.6 - - - +
174B VAL* 3.8 5.6 - - + +
208B GLU 2.8 21.4 + - - +
209B SER* 3.1 4.7 + - - +
211B THR* 1.3 78.5 + - - +
213B VAL* 1.3 58.3 + - - +
216B GLY* 2.8 30.8 + - - -
217B GLU* 3.3 26.1 + - - +
218B ARG* 3.4 26.8 + - - +
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B PHE* 3.7 34.5 - - + -
170B LEU* 4.2 15.3 - - + -
171B LEU* 3.8 27.1 - - + -
209B SER 3.1 9.4 + - - +
210B ILE* 3.2 29.8 - - + +
212B ASN* 1.3 76.4 - - - +
214B ILE* 1.3 58.4 + - - +
216B GLY 4.4 0.2 - - - -
298B TYR* 4.1 1.9 + - - -
300B GLY* 3.4 6.6 - - - -
301B ILE* 2.9 38.0 + - + +
467B ILE* 4.2 13.2 - - + -
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ILE* 3.1 33.6 + - + +
213B VAL* 1.3 78.1 - - - +
215B PHE* 1.3 89.9 + - + +
216B GLY 3.6 0.2 - - - -
284B PHE* 5.0 0.3 - - - -
300B GLY* 3.9 1.0 - - - -
301B ILE* 3.4 16.0 + - + +
302B LEU* 3.0 37.8 + - + +
303B TYR 4.5 0.9 + - - -
320B VAL* 4.2 14.8 - - + +
323B MET* 3.7 38.8 - - + -
324B LEU* 3.8 22.9 - - + -
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Residues in contact with PHE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B THR* 2.8 37.8 + - + +
214B ILE* 1.3 86.4 - - + +
216B GLY* 1.3 62.6 + - - +
217B GLU* 3.2 22.0 + - + +
219B GLN* 4.6 9.9 - - - +
280B TYR* 3.6 40.6 - + + -
281B THR 4.3 1.1 - - - -
284B PHE* 3.5 30.4 - + + -
299B ARG 3.7 6.5 - - - +
302B LEU* 3.5 31.9 - - + -
320B VAL* 3.9 16.4 - - + -
324B LEU* 3.8 26.9 - - + -
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Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU* 4.9 11.5 - - - +
212B ASN* 2.8 26.7 + - - -
213B VAL 4.4 0.8 - - - -
214B ILE 3.6 1.4 - - - -
215B PHE* 1.3 76.4 - - - +
217B GLU* 1.3 61.2 + - - +
299B ARG* 3.4 20.0 + - - +
300B GLY* 4.8 0.7 - - - -
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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