Contacts of the helix formed by residues 217 - 233 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A PRO* 3.6 29.9 - - + +
182A ARG* 3.8 9.0 + - - -
183A ARG* 4.4 2.2 - - - +
215A ASP* 2.8 23.3 + - - +
216A GLU* 1.3 79.7 - - - +
218A ASP* 1.3 62.4 + - - +
219A SER* 3.6 20.4 - - - +
220A VAL* 2.8 28.2 + - + +
221A ARG 3.3 7.8 + - - -
155B LEU* 3.6 29.2 - - - +
159B GLU* 4.1 17.3 + - - +
193B GLN* 4.8 4.5 + - - +
200B ARG* 6.2 0.9 - - - +
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Residues in contact with ASP 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLU 3.6 5.5 + - - -
217A GLN* 1.3 69.6 - - - +
219A SER* 1.3 72.8 + - - -
220A VAL 2.8 15.9 + - - -
221A ARG* 3.0 28.6 + - - +
222A LEU* 3.0 18.9 + - - +
256A SER* 2.7 39.7 + - - +
258A ARG* 3.5 26.5 + - + +
259A VAL* 4.3 2.3 - - + +
96B THR* 4.2 6.1 - - - +
159B GLU* 4.8 12.4 + - - +
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Residues in contact with SER 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ARG* 3.2 33.4 + - - +
217A GLN* 3.6 12.4 - - - +
218A ASP* 1.3 86.8 + - - +
220A VAL* 1.3 57.3 + - - +
222A LEU* 2.9 26.4 - - - +
223A LEU* 3.5 9.4 - - - +
258A ARG* 6.6 0.2 - - - +
200B ARG* 3.4 33.4 - - - -
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Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A PRO* 4.2 5.8 - - + +
182A ARG* 4.2 10.1 - - + -
183A ARG* 3.4 32.5 - - + +
186A ALA* 4.3 6.1 - - + +
212A LEU* 3.8 30.0 - - + +
215A ASP* 3.8 31.9 - - + +
217A GLN* 2.8 17.7 + - + +
218A ASP 2.8 0.6 + - - -
219A SER* 1.3 81.3 - - - +
221A ARG* 1.3 66.1 + - - +
222A LEU 3.3 0.4 - - - -
223A LEU* 3.2 16.3 + - - +
224A ALA* 3.3 8.0 + - - +
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Residues in contact with ARG 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LEU 3.5 8.5 - - - +
213A ALA* 3.2 24.9 - - - +
214A SER* 3.3 5.6 - - - +
215A ASP 3.0 48.4 + - - +
216A GLU* 3.5 14.6 + - - +
217A GLN 3.6 3.1 - - - +
218A ASP* 3.0 16.8 + - - +
220A VAL* 1.3 77.2 - - - +
222A LEU* 1.3 58.1 + - - +
224A ALA* 2.8 25.6 + - - +
225A VAL* 3.2 10.1 + - - +
254A ASP* 2.6 40.2 + - - +
255A LYS* 5.4 2.0 - - - +
256A SER* 3.4 21.0 - - - +
259A VAL* 4.1 6.4 - - + +
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ASP 3.0 10.7 + - - +
219A SER* 2.9 39.7 - - - +
221A ARG* 1.3 77.4 - - - +
223A LEU* 1.3 93.2 + - + +
225A VAL* 3.4 23.0 + - - +
258A ARG* 4.1 31.0 - - + +
259A VAL* 3.9 23.6 - - + +
262A MET* 3.6 27.4 - - + +
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ARG* 3.2 47.8 - - + +
186A ALA* 3.8 12.3 - - + -
187A SER* 4.2 14.6 - - - +
219A SER 3.5 7.2 - - - +
220A VAL 3.4 5.8 - - - +
221A ARG 3.0 0.4 - - - -
222A LEU* 1.3 104.7 - - + +
224A ALA* 1.3 56.3 + - - +
226A GLU* 2.7 36.2 + - - +
227A ALA* 3.4 5.4 + - - +
262A MET* 5.3 2.9 - - + -
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ALA* 4.8 4.3 - - - +
189A LEU* 5.5 3.1 - - + -
209A PHE* 2.9 31.5 - - + +
212A LEU* 3.9 9.4 - - + -
213A ALA* 3.3 38.8 - - + +
220A VAL 3.3 3.5 + - - +
221A ARG* 2.8 14.9 + - - +
223A LEU* 1.3 78.8 - - - +
225A VAL* 1.3 59.6 + - - +
227A ALA* 3.4 7.8 + - - +
228A CYS 3.0 7.4 + - - -
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Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A PHE* 4.9 0.9 - - - -
213A ALA* 6.2 2.0 - - + -
221A ARG 3.7 11.4 - - - +
222A LEU* 3.5 10.3 - - - +
223A LEU 2.9 0.8 + - - -
224A ALA* 1.3 78.0 - - + +
226A GLU* 1.3 60.3 + - - +
228A CYS* 2.9 26.6 - - + +
229A VAL* 3.8 6.2 + - - +
248A LEU* 5.4 1.8 - - + -
251A ALA* 3.7 17.9 - - + -
259A VAL* 3.7 27.4 - - + +
262A MET* 3.8 16.4 - - + +
263A VAL* 3.7 28.3 - - + +
266A LYS* 5.5 3.5 - - + +
270A LEU* 5.0 7.3 - - + +
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Residues in contact with GLU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A SER 6.1 0.7 - - - +
222A LEU 3.8 1.2 + - - -
223A LEU* 2.7 18.2 + - - +
225A VAL* 1.3 70.0 - - - +
227A ALA* 1.3 67.0 + - - +
228A CYS 2.8 5.8 + - - -
229A VAL* 2.9 23.1 + - - +
230A ASN* 3.0 21.3 + - - +
262A MET* 3.7 19.9 - - + +
266A LYS* 3.7 33.6 - - - +
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Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ALA 4.7 3.8 - - - +
187A SER 5.7 0.7 - - - +
189A LEU* 4.0 24.2 - - + -
190A GLY* 3.8 30.7 - - - +
223A LEU 3.4 6.1 + - - +
224A ALA* 3.7 9.2 - - - +
226A GLU* 1.3 82.5 - - - +
228A CYS* 1.3 62.1 + - - +
230A ASN* 3.1 7.4 + - - +
231A ILE* 2.9 30.0 + - + +
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Residues in contact with CYS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A PHE* 3.3 29.8 - - + -
224A ALA 3.0 5.8 + - - +
225A VAL* 2.9 20.6 - - + +
226A GLU 2.8 2.0 + - - -
227A ALA* 1.3 77.4 - - - +
229A VAL* 1.3 55.0 + - - +
231A ILE* 3.2 5.1 + - - +
232A ALA* 2.8 29.2 + - - +
244A VAL* 3.7 27.1 - - - +
248A LEU* 4.3 16.4 - - - -
270A LEU* 3.9 18.6 - - + -
274A VAL* 6.5 0.2 - - - -
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A VAL 4.5 3.8 - - - +
226A GLU* 2.9 18.2 + - - +
228A CYS* 1.3 75.3 - - - +
230A ASN* 1.3 69.4 + - - +
232A ALA* 3.2 5.8 + - - +
233A GLN* 2.9 49.5 + - - +
266A LYS* 4.3 11.9 - - + +
269A GLU* 4.1 15.7 - - + +
270A LEU* 3.3 41.7 - - + +
273A ALA* 4.0 9.0 - - + -
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Residues in contact with ASN 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A GLY* 4.2 25.2 - - - +
191A GLU 5.3 0.2 - - - +
194A LYS* 3.4 34.0 - - + +
226A GLU* 3.0 27.0 - - - +
227A ALA* 3.1 9.9 + - - +
229A VAL* 1.3 83.8 - - - +
231A ILE* 1.3 63.2 + - - +
233A GLN* 3.2 19.9 + - - +
234A LEU* 3.2 25.6 + - - +
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Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 4.5 8.5 - - + +
190A GLY* 5.5 0.4 - - - -
193A ALA* 4.6 7.4 - - + -
201A VAL* 4.4 10.8 - - + -
205A ILE* 3.5 26.7 - - + -
206A ILE* 3.7 27.8 - - + -
209A PHE* 3.7 37.5 - - + -
227A ALA* 2.9 24.1 + - + +
228A CYS* 3.7 4.0 - - - +
230A ASN* 1.3 73.8 - - + +
232A ALA* 1.3 68.9 + - - +
234A LEU* 2.8 21.9 + - - +
235A LEU* 3.2 16.8 + - + +
244A VAL* 4.6 5.4 - - + -
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A CYS* 2.8 20.5 + - - +
229A VAL* 3.4 6.7 - - - +
231A ILE* 1.3 77.2 - - - +
233A GLN* 1.3 63.0 + - - +
234A LEU 3.0 1.6 + - - -
235A LEU* 3.1 21.0 + - - +
240A LEU* 3.8 23.5 - - + +
244A VAL* 4.5 11.8 - - + +
270A LEU* 5.5 0.9 - - + -
273A ALA* 4.0 25.4 - - + +
274A VAL* 4.7 9.0 - - + +
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Residues in contact with GLN 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LYS* 5.8 1.6 - - - -
229A VAL* 2.9 31.3 + - - +
230A ASN* 3.2 30.5 + - - +
231A ILE 3.2 0.2 - - - -
232A ALA* 1.3 74.1 - - - +
234A LEU* 1.3 64.4 + - + +
235A LEU 3.5 3.6 - - - +
269A GLU 5.0 1.6 + - - -
273A ALA* 3.3 26.2 - - + +
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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