Contacts of the helix formed by residues 178 - 194 (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 THR 178 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D PHE* 4.4 6.6 - - + +
144D ARG* 2.9 16.6 + - - -
176D ASP* 2.4 24.0 + - - -
177D ASP* 1.3 81.0 - - - +
179D PRO* 1.3 67.2 - - + +
180D MET* 3.1 44.6 - - + -
181D VAL* 2.9 17.0 + - - +
182D ARG* 2.9 18.2 + - - +
196E ASN* 4.0 11.2 - - - +
199E TYR* 5.5 1.1 - - + -
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Residues in contact with PRO 179 (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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177D ASP 4.2 1.1 - - - +
178D THR* 1.3 83.5 - - - +
180D MET* 1.3 65.4 + - + +
182D ARG* 3.4 19.5 - - + +
183D ARG* 2.7 65.2 + - - +
217D GLN* 3.6 31.4 - - + +
220D VAL* 4.7 2.0 - - + -
193E GLN* 5.0 4.5 - - - +
196E ASN* 3.3 29.8 - - + +
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Residues in contact with MET 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D PHE* 4.0 27.4 - - + -
145D THR* 3.9 6.9 + - - +
178D THR* 3.1 26.7 - - + -
179D PRO* 1.3 92.2 - - + +
181D VAL* 1.3 61.9 + - - +
183D ARG* 3.2 28.9 - - - +
184D ALA* 3.5 14.7 + - - +
196E ASN* 3.5 38.6 - - + +
199E TYR* 3.8 33.2 - - + -
200E ARG 4.8 0.7 - - - +
204E GLU* 3.9 16.3 - - - +
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Residues in contact with VAL 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D PHE* 3.9 28.7 - - + +
144D ARG* 3.8 17.0 - - + +
145D THR* 4.2 5.4 - - - +
148D CYS* 4.7 5.8 - - - -
173D LEU* 3.7 28.3 - - + +
176D ASP* 3.3 44.0 - - + +
178D THR* 2.9 6.4 + - - +
180D MET* 1.3 75.7 - - - +
182D ARG* 1.3 57.7 + - - +
184D ALA* 2.6 25.6 + - - +
185D ALA 2.8 12.2 + - - +
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Residues in contact with ARG 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D LEU 4.4 1.1 - - - -
174D CYS 3.3 23.3 - - - +
175D SER* 4.5 2.0 - - - +
176D ASP 2.8 41.9 + - - +
177D ASP* 3.4 6.1 + - - +
178D THR 2.9 26.6 + - - +
179D PRO* 3.4 15.4 - - - +
181D VAL* 1.3 75.6 - - - +
183D ARG* 1.3 65.7 + - - +
185D ALA* 3.6 8.7 - - - +
186D ALA* 2.8 26.2 + - - +
212D LEU* 4.1 8.6 - - + +
215D ASP* 2.4 38.6 + - - -
216D GLU* 4.6 10.1 + - - +
217D GLN* 3.8 15.8 + - - -
220D VAL* 4.1 11.0 - - + -
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Residues in contact with ARG 183 (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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179D PRO* 2.7 40.2 + - - +
180D MET* 3.2 27.0 - - - +
182D ARG* 1.3 73.0 - - - +
184D ALA* 1.3 62.3 + - - +
186D ALA* 3.2 4.0 - - - +
187D SER* 3.0 19.4 + - - -
217D GLN* 4.2 5.1 - - - +
219D SER* 2.9 39.4 + - - +
220D VAL* 3.2 24.9 - - + +
223D LEU* 3.3 18.3 - - + +
200E ARG* 3.5 32.5 - - - +
204E GLU* 2.9 39.8 + - - +
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Residues in contact with ALA 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D THR* 4.1 20.4 - - + +
148D CYS* 3.9 18.2 - - + -
180D MET 3.5 9.6 + - - +
181D VAL* 2.6 17.3 + - - +
183D ARG* 1.3 69.7 - - - +
185D ALA* 1.3 69.9 + - - +
186D ALA 2.9 1.1 - - - -
187D SER* 2.8 28.9 + - - -
188D LYS* 3.0 5.0 + - + +
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Residues in contact with ALA 185 (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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148D CYS* 3.6 18.6 - - - -
170D PHE* 3.6 11.5 - - + -
173D LEU* 3.9 10.1 - - + +
174D CYS* 3.7 42.4 - - - +
181D VAL 2.8 12.2 + - - +
182D ARG* 3.6 6.5 - - - +
184D ALA* 1.3 72.3 - - - +
186D ALA* 1.3 57.8 + - - +
188D LYS 3.2 2.6 + - - -
189D LEU* 2.8 26.1 + - - +
212D LEU* 5.1 0.4 - - + -
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Residues in contact with ALA 186 (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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182D ARG 2.8 18.2 + - - +
183D ARG* 3.2 7.9 - - - +
184D ALA 2.8 0.4 + - - -
185D ALA* 1.3 74.1 - - - +
187D SER* 1.3 69.3 + - - +
189D LEU* 2.8 24.8 + - - +
190D GLY 4.1 1.6 + - - -
212D LEU* 4.2 22.0 - - + +
220D VAL* 4.5 6.7 - - + +
223D LEU* 3.9 21.9 - - + +
224D ALA* 4.8 5.2 - - - +
227D ALA* 4.6 6.9 - - - +
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Residues in contact with SER 187 (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 3.0 12.2 + - - -
184D ALA* 2.8 20.9 + - - -
186D ALA* 1.3 74.3 - - - +
188D LYS* 1.3 84.7 + - - +
189D LEU 3.4 0.2 + - - -
190D GLY* 3.8 7.3 + - - -
191D GLU* 4.8 1.7 + - - +
223D LEU* 4.2 14.9 - - - +
227D ALA* 5.7 0.9 - - - +
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Residues in contact with LYS 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D ARG* 3.7 23.6 - - - +
148D CYS* 3.9 33.0 - - + +
149D GLY* 3.8 11.9 - - - +
170D PHE* 4.1 6.3 - - + -
184D ALA* 3.0 7.1 + - + +
185D ALA 3.5 6.1 - - - +
187D SER* 1.3 94.5 + - - +
189D LEU* 1.3 64.5 + - - +
190D GLY 3.0 4.6 + - - -
191D GLU* 3.2 29.5 + - + +
192D PHE* 3.1 21.8 + - - +
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Residues in contact with LEU 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D PHE* 3.7 25.1 - - + -
174D CYS* 4.7 2.5 - - - -
185D ALA 2.8 11.4 + - - +
186D ALA* 2.8 18.4 + - - +
188D LYS* 1.3 78.0 - - - +
190D GLY* 1.3 62.0 + - - +
192D PHE* 3.6 0.5 + - - +
193D ALA* 3.3 19.1 + - - +
205D ILE* 4.2 20.4 - - + +
208D MET* 4.1 21.1 - - + -
209D PHE* 3.8 35.0 - - + +
212D LEU* 4.5 9.6 - - + -
224D ALA* 5.7 2.7 - - - -
227D ALA* 4.2 17.0 - - + -
231D ILE* 4.4 4.1 - - + +
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Residues in contact with GLY 190 (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 4.1 1.0 + - - -
187D SER 3.8 6.3 + - - -
188D LYS 3.1 1.4 - - - -
189D LEU* 1.3 80.5 - - - +
191D GLU* 1.3 62.9 + - - +
192D PHE 3.1 0.9 + - - -
193D ALA* 3.2 15.6 + - - +
194D LYS* 3.4 17.0 + - - +
227D ALA* 4.2 15.1 - - - +
230D ASN* 4.3 24.0 - - - +
231D ILE* 5.6 0.9 - - - -
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Residues in contact with GLU 191 (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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113D ARG* 3.1 36.0 + - - -
148D CYS 4.8 0.7 - - - +
149D GLY 3.7 7.3 - - - +
152D SER* 3.1 33.6 + - - +
187D SER 4.8 1.6 + - - +
188D LYS* 3.2 36.5 + - + +
190D GLY* 1.3 75.5 - - - +
192D PHE* 1.3 65.9 + - + +
194D LYS* 3.5 25.0 + - + +
195D VAL* 4.0 5.9 + - - +
230D ASN* 5.2 0.4 - - - +
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Residues in contact with PHE 192 (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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151D PHE* 4.5 20.0 - + + -
152D SER* 4.6 4.3 - - - -
155D TYR* 4.0 27.1 - + + -
167D ARG* 4.4 14.8 - - - -
170D PHE* 3.1 57.0 - + + -
188D LYS* 3.1 16.1 + - + +
189D LEU 4.0 4.0 - - - +
190D GLY 3.1 0.8 - - - -
191D GLU* 1.3 79.6 - - + +
193D ALA* 1.3 62.3 + - - +
195D VAL* 2.9 33.3 + - + +
196D LEU* 3.3 39.9 + - + +
205D ILE* 4.5 9.0 - - + -
208D MET* 5.0 2.9 - - + -
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Residues in contact with ALA 193 (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 3.3 10.4 + - - +
190D GLY 3.2 9.7 + - - +
192D PHE* 1.3 78.9 - - - +
194D LYS* 1.3 58.9 + - - +
195D VAL 3.0 5.4 + - - -
196D LEU* 3.2 17.8 + - - +
201D VAL* 3.8 5.1 - - + +
205D ILE* 3.9 36.7 - - + +
230D ASN 5.9 0.2 - - - -
231D ILE* 4.5 9.6 - - + +
234D LEU* 3.1 26.2 - - + +
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Residues in contact with LYS 194 (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 3.4 11.8 + - - +
191D GLU* 3.7 16.4 - - + +
192D PHE 3.1 1.4 - - - -
193D ALA* 1.3 75.9 - - - +
195D VAL* 1.3 62.6 + - + +
196D LEU 4.8 0.8 - - - +
230D ASN* 3.5 29.4 - - + +
233D GLN* 5.7 3.7 + - - +
234D LEU* 3.9 23.6 - - + -
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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
------------------------------------------------------------
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