Contacts of the helix formed by residues 217 - 235 (chain D) in PDB entry 2NPP
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 GLN 217 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179D PRO* 3.6 31.1 - - + +
182D ARG* 3.8 7.4 + - - -
183D ARG* 4.2 2.5 - - - +
215D ASP* 2.5 19.2 + - - +
216D GLU* 1.3 81.9 - - - +
218D ASP* 1.3 62.5 + - - +
219D SER* 3.0 19.1 - - - +
220D VAL* 2.7 31.2 + - + +
221D ARG* 3.2 9.5 + - - +
155E LEU* 3.7 27.3 - - - +
159E GLU* 4.3 17.0 + - - +
193E GLN* 5.1 3.4 + - - +
200E ARG* 5.9 1.3 - - - +
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Residues in contact with ASP 218 (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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216D GLU 3.4 6.5 + - - -
217D GLN* 1.3 72.8 - - - +
219D SER* 1.3 80.1 + - - +
220D VAL 2.9 5.0 + - - -
221D ARG* 3.4 28.6 - - - +
222D LEU* 3.1 26.9 + - - +
256D SER* 2.8 31.8 + - - +
258D ARG* 3.4 27.4 + - - +
259D VAL* 3.9 1.8 - - + +
96E THR* 4.3 5.1 - - + +
159E GLU* 4.9 15.0 + - - +
200E ARG* 5.6 0.5 + - - -
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Residues in contact with SER 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D ARG* 2.9 42.9 + - - +
217D GLN* 3.0 9.2 + - - +
218D ASP* 1.3 87.2 + - - +
220D VAL* 1.3 56.1 + - - +
222D LEU* 2.9 23.4 - - - +
223D LEU* 3.7 5.7 - - - +
258D ARG* 6.4 1.1 - - - +
200E ARG* 3.3 33.9 + - - -
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Residues in contact with VAL 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D PRO* 4.1 5.4 - - + +
182D ARG* 4.1 7.9 - - + -
183D ARG* 3.2 37.2 - - + +
186D ALA* 4.5 5.0 - - + +
212D LEU* 3.6 40.7 - - + +
215D ASP* 3.7 20.2 - - + +
217D GLN* 2.7 17.0 + - + +
219D SER* 1.3 79.6 + - - +
221D ARG* 1.3 66.6 + - - +
222D LEU 3.2 1.8 - - - -
223D LEU* 3.0 18.8 + - - +
224D ALA* 3.3 7.8 + - - +
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Residues in contact with ARG 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D LEU 3.5 9.0 - - - -
213D ALA* 3.3 24.2 - - - +
214D SER* 3.3 10.8 - - - +
215D ASP 3.2 43.5 + - - +
216D GLU 3.5 7.5 + - - -
217D GLN 3.7 2.5 - - - +
218D ASP* 3.2 27.6 + - - +
220D VAL* 1.3 77.6 - - - +
222D LEU* 1.3 62.0 + - - +
224D ALA* 3.0 19.2 + - - +
225D VAL* 3.3 8.7 + - - +
254D ASP* 2.5 44.0 + - - +
255D LYS* 4.8 2.6 - - - +
256D SER* 3.4 19.8 - - - +
259D VAL* 4.0 7.9 - - + +
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Residues in contact with LEU 222 (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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218D ASP 3.1 6.0 + - - +
219D SER* 2.9 39.3 - - - +
221D ARG* 1.3 76.2 - - - +
223D LEU* 1.3 93.0 + - + +
225D VAL* 3.1 23.4 + - - +
226D GLU 3.6 2.6 + - - -
258D ARG* 4.4 26.9 - - + +
259D VAL* 3.6 22.8 - - + +
262D MET* 3.8 29.1 - - + +
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Residues in contact with LEU 223 (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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183D ARG* 3.3 35.9 - - + +
186D ALA* 3.9 11.7 - - + -
187D SER* 4.2 16.4 - - - +
219D SER 3.7 9.2 - - - +
220D VAL 3.0 8.5 + - - +
222D LEU* 1.3 98.9 - - + +
224D ALA* 1.3 69.0 + - - +
225D VAL 2.7 1.6 + - - -
226D GLU* 2.8 19.2 + - + +
227D ALA* 3.3 8.9 + - - +
262D MET* 5.2 4.3 - - + -
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Residues in contact with ALA 224 (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 ALA* 4.8 4.3 - - - +
189D LEU* 5.7 2.5 - - + -
209D PHE* 3.1 18.3 - - + +
212D LEU* 3.9 11.0 - - + +
213D ALA* 3.3 39.5 - - + +
220D VAL 3.3 3.2 + - - +
221D ARG 3.0 14.9 + - - +
223D LEU* 1.3 77.9 - - - +
225D VAL* 1.3 60.4 + - + +
227D ALA* 3.3 9.6 + - - +
228D CYS 2.9 17.3 + - - -
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Residues in contact with VAL 225 (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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209D PHE* 5.1 0.4 - - - -
213D ALA* 6.3 1.1 - - + -
221D ARG 3.7 9.6 - - - +
222D LEU* 3.1 14.4 - - - +
223D LEU 2.7 4.4 + - - -
224D ALA* 1.3 71.7 - - + +
226D GLU* 1.3 69.5 + - - +
228D CYS* 2.8 25.8 - - + +
229D VAL* 3.6 4.7 + - + +
248D LEU* 5.4 1.3 - - + -
251D ALA* 3.9 16.6 - - + -
259D VAL* 3.8 26.2 - - + +
262D MET* 3.9 7.6 - - + -
263D VAL* 3.8 34.8 - - + +
266D LYS* 5.6 3.8 - - + -
270D LEU* 5.0 8.3 - - + +
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Residues in contact with GLU 226 (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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222D LEU 3.6 1.8 + - - -
223D LEU* 2.8 16.3 + - - +
225D VAL* 1.3 74.3 - - - +
227D ALA* 1.3 65.9 + - - +
229D VAL* 2.8 34.5 + - - +
230D ASN* 3.3 20.0 + - - +
262D MET* 3.9 19.2 - - + +
266D LYS* 3.5 34.7 - - - +
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Residues in contact with ALA 227 (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 ALA 4.6 5.6 - - - +
187D SER 5.7 0.7 - - - +
189D LEU* 4.2 22.0 - - + -
190D GLY* 4.2 24.4 - - - +
223D LEU 3.3 5.8 + - - +
224D ALA* 3.4 13.2 - - - +
226D GLU* 1.3 81.8 - - - +
228D CYS* 1.3 62.6 + - - +
230D ASN* 3.4 8.9 + - - +
231D ILE* 3.0 28.8 + - + +
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Residues in contact with CYS 228 (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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209D PHE* 3.3 34.3 - - + -
224D ALA 2.9 5.2 + - - +
225D VAL* 2.8 23.6 + - + +
226D GLU 2.8 0.2 + - - -
227D ALA* 1.3 76.7 - - - +
229D VAL* 1.3 62.7 + - - +
231D ILE* 3.1 3.4 + - - +
232D ALA* 2.8 22.6 + - - +
244D VAL* 3.8 22.6 - - - +
248D LEU* 4.2 17.9 - - + -
270D LEU* 4.2 15.9 - - + -
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Residues in contact with VAL 229 (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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225D VAL 4.6 2.5 - - - +
226D GLU* 2.8 21.6 + - - +
228D CYS* 1.3 75.2 - - - +
230D ASN* 1.3 70.9 + - - +
232D ALA* 2.8 17.9 + - - +
233D GLN* 3.0 35.0 + - - +
266D LYS* 4.6 9.9 - - + -
269D GLU* 4.1 31.0 - - + +
270D LEU* 3.3 33.0 - - + -
273D ALA* 4.2 1.8 - - + -
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Residues in contact with ASN 230 (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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190D GLY* 4.3 25.6 + - - +
193D ALA* 6.0 0.2 - - + -
194D LYS* 3.5 34.4 - - + +
226D GLU* 3.3 26.3 - - - +
227D ALA* 3.4 9.5 + - - +
229D VAL* 1.3 81.4 - - - +
231D ILE* 1.3 62.2 + - + +
233D GLN* 3.3 24.5 + - - +
234D LEU* 3.1 22.0 + - + +
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Residues in contact with ILE 231 (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 LEU* 4.4 9.2 - - + +
190D GLY* 5.6 0.7 - - - -
193D ALA* 4.5 9.0 - - + -
201D VAL* 4.6 8.1 - - + -
205D ILE* 3.4 29.6 - - + -
206D ILE* 3.9 25.6 - - + -
209D PHE* 3.6 35.7 - - + -
227D ALA* 3.0 17.4 + - + +
228D CYS* 3.5 6.7 - - - +
230D ASN* 1.3 72.9 - - + +
232D ALA* 1.3 60.6 + - - +
234D LEU* 2.7 30.5 + - - +
235D LEU* 3.3 18.0 + - + +
244D VAL* 4.3 5.8 - - + -
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Residues in contact with ALA 232 (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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228D CYS* 2.8 17.6 + - - +
229D VAL* 2.8 10.2 + - - +
231D ILE* 1.3 72.5 - - - +
233D GLN* 1.3 61.7 + - - +
234D LEU 3.1 1.2 + - - -
235D LEU 3.3 18.2 + - - +
240D LEU* 3.8 26.6 - - + +
244D VAL* 4.5 13.4 - - + +
270D LEU* 5.7 1.1 - - + -
273D ALA* 3.8 27.5 - - + +
274D VAL* 4.7 7.2 - - + +
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Residues in contact with GLN 233 (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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194D LYS* 5.7 2.8 + - - -
229D VAL* 3.0 28.5 + - - +
230D ASN* 3.6 24.6 + - - +
231D ILE 3.1 0.4 - - - -
232D ALA* 1.3 75.0 - - - +
234D LEU* 1.3 68.0 + - + +
235D LEU 4.5 2.3 - - - +
269D GLU 5.1 1.6 + - - -
272D LYS* 6.0 1.6 - - - +
273D ALA* 3.4 26.3 - - + +
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Residues in contact with LEU 234 (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 ALA* 3.1 47.8 - - + +
194D LYS* 3.8 19.3 - - + +
196D LEU 5.5 0.2 - - - +
198D LEU* 3.1 24.3 - - + +
201D VAL* 4.3 17.0 - - + -
230D ASN 3.1 16.6 - - - +
231D ILE* 2.7 18.0 + - - +
233D GLN* 1.3 83.1 - - + +
235D LEU* 1.3 58.4 + - - +
236D PRO* 4.1 1.2 - - - +
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Residues in contact with LEU 235 (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 LEU* 4.4 5.4 - - + -
201D VAL* 3.8 24.2 - - + -
202D LYS* 3.8 29.4 - - + -
206D ILE* 3.9 17.9 - - + -
231D ILE* 3.3 14.2 + - + +
232D ALA 3.3 11.3 + - - +
233D GLN 4.5 2.4 - - - +
234D LEU* 1.3 81.6 - - - +
236D PRO* 1.3 73.6 - - + +
237D GLN 3.8 0.3 + - - -
239D ASP* 4.5 4.9 - - + +
240D LEU* 3.9 16.0 - - + +
243D LEU* 4.2 10.1 - - + -
244D VAL* 3.6 31.2 - - + -
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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