Contacts of the helix formed by residues 200 - 217 (chain D) in PDB entry 4WNP
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 GLY 200 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135D ILE* 3.6 26.2 - - - +
172D LEU* 4.5 1.4 - - - +
199D ASP* 1.3 78.7 - - - +
201D LYS* 1.3 60.4 + - - +
202D ALA 3.1 0.4 - - - -
203D ASP* 3.1 18.3 + - - +
204D LEU 3.7 0.9 + - - -
269D PHE* 3.4 33.4 - - - -
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Residues in contact with LYS 201 (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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199D ASP* 2.9 20.1 + - - +
200D GLY* 1.3 73.9 - - - +
202D ALA* 1.3 63.8 + - - +
203D ASP 3.3 0.4 - - - -
204D LEU* 3.1 23.3 + - + +
205D TRP 3.1 6.8 + - - -
263D HIS* 2.9 36.2 + - + +
264D LYS* 3.6 14.8 + - - +
266D ARG* 3.0 49.7 + - + +
267D MET 3.7 11.9 - - - +
268D ASP* 3.6 25.8 - - - +
269D PHE* 4.3 3.6 - - + -
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Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D ARG* 6.3 2.2 - - + -
189D ALA* 3.9 13.6 + - + +
191D GLU* 4.1 7.0 + - - +
192D VAL* 3.8 28.9 - - + -
198D TYR* 3.8 12.3 - - + -
199D ASP 3.1 15.6 + - - +
201D LYS* 1.3 78.2 - - - +
203D ASP* 1.3 64.0 + - - +
204D LEU 3.3 0.2 + - - -
205D TRP* 3.4 5.7 + - - +
206D SER* 3.2 21.9 + - - -
266D ARG* 3.9 2.1 - - - +
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Residues in contact with ASP 203 (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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126D MET* 3.8 20.3 - - + +
129D LEU* 4.6 0.2 - - - +
134D ILE 4.8 0.3 - - - +
135D ILE* 3.6 14.2 - - - +
136D HIS* 2.8 26.5 + - - +
137D ARG* 2.9 29.0 + - - +
139D LEU* 3.9 22.3 - - + +
199D ASP 4.5 0.2 + - - -
200D GLY 3.1 12.0 + - - +
202D ALA* 1.3 79.2 - - - +
204D LEU* 1.3 58.1 + - - +
206D SER* 3.1 8.5 + - - -
207D ILE* 2.9 32.4 + - - +
269D PHE* 5.1 0.7 - - + -
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Residues in contact with LEU 204 (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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200D GLY 4.2 1.6 - - - +
201D LYS* 3.1 14.8 + - + +
203D ASP* 1.3 75.7 - - - +
205D TRP* 1.3 65.7 + - - +
207D ILE* 3.3 16.0 + - + +
208D GLY 2.9 18.0 + - - -
258D LEU* 3.5 26.0 - - + +
266D ARG* 4.5 2.7 - - - -
267D MET 3.4 25.8 - - - +
268D ASP* 3.8 20.2 - - - +
269D PHE* 3.7 42.0 - - + +
272D PHE* 3.8 29.4 - - + -
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Residues in contact with TRP 205 (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 MET 5.1 0.8 + - - -
187D TYR* 3.7 6.9 + - - +
188D MET 3.1 13.8 + - - -
189D ALA* 3.4 27.8 - - + -
190D PRO* 3.5 32.1 - - + -
201D LYS 3.1 6.3 + - - -
202D ALA 3.5 8.7 - - - +
204D LEU* 1.3 74.9 - - - +
206D SER* 1.3 66.1 + - - +
208D GLY* 3.0 12.0 + - - -
209D THR* 3.1 24.3 + - + +
221D PHE* 3.6 29.8 - + - -
233D TYR* 3.5 21.6 + - - -
239D LEU* 4.1 8.5 - - + -
258D LEU 3.6 11.7 - - - -
259D LEU* 3.6 43.7 - - + +
260D GLN 3.6 20.4 - - - -
261D ARG 4.3 0.9 - - - -
266D ARG* 3.9 11.2 - - - +
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Residues in contact with SER 206 (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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137D ARG* 5.7 2.9 - - - -
139D LEU* 3.7 31.2 + - - +
187D TYR 2.7 28.1 + - - -
188D MET* 4.6 1.9 - - - -
189D ALA 4.8 0.2 + - - -
202D ALA 3.2 11.2 + - - -
203D ASP* 3.1 14.3 + - - -
205D TRP* 1.3 77.1 - - - +
207D ILE* 1.3 62.1 + - - +
209D THR* 2.7 21.6 + - - -
210D ILE* 3.1 14.5 + - - +
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Residues in contact with ILE 207 (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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119D LEU* 3.7 30.1 - - + -
122D ILE* 4.1 13.5 - - + -
126D MET* 3.7 33.0 - - + -
139D LEU* 3.8 18.4 - - + -
203D ASP 2.9 20.0 + - - +
204D LEU* 3.6 23.6 - - + +
205D TRP 3.2 0.2 - - - -
206D SER* 1.3 75.7 - - - +
208D GLY* 1.3 63.5 + - - +
210D ILE* 3.1 14.5 + - + +
211D VAL* 2.9 24.4 + - + +
258D LEU* 4.7 3.1 - - + -
272D PHE* 4.1 13.9 - - + -
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Residues in contact with GLY 208 (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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204D LEU 2.9 14.1 + - - -
205D TRP 3.0 5.5 + - - -
207D ILE* 1.3 76.6 - - - +
209D THR* 1.3 55.7 + - - +
211D VAL* 3.3 1.4 + - - -
212D TYR* 2.9 28.8 + - - +
255D LEU* 3.5 10.1 - - - +
258D LEU* 3.9 25.6 - - - +
259D LEU* 4.0 11.4 - - - +
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Residues in contact with THR 209 (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 MET 4.1 8.1 - - - +
187D TYR* 3.2 27.5 - - - -
205D TRP* 3.1 35.8 + - + +
206D SER* 2.7 20.8 + - - -
208D GLY* 1.3 76.2 - - - +
210D ILE* 1.3 57.3 + - - +
212D TYR* 3.7 7.4 - - - +
213D GLN* 2.9 29.8 + - - +
220D PRO* 3.8 26.8 - - + +
259D LEU* 3.6 11.7 - - + -
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Residues in contact with ILE 210 (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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100D LEU* 3.9 26.9 - - + -
104D LEU* 5.3 0.3 - - - +
122D ILE* 5.0 14.8 - - + -
139D LEU* 4.1 12.1 - - + -
140D LYS* 3.8 39.9 - - - +
141D PRO* 4.1 11.8 - - + +
144D ILE* 4.5 12.3 - - + -
187D TYR* 4.8 1.1 - - + -
206D SER 3.1 18.4 + - - +
207D ILE* 3.1 15.5 + - + +
209D THR* 1.3 77.8 + - - +
211D VAL* 1.3 69.4 + - + +
213D GLN* 3.2 6.3 + - - +
214D CYS* 2.9 25.6 + - - -
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Residues in contact with VAL 211 (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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115D ILE* 3.8 25.9 - - + +
119D LEU* 4.0 34.8 - - + -
122D ILE* 6.4 0.7 - - + -
207D ILE* 2.9 24.1 + - + +
208D GLY* 3.7 5.6 - - - +
210D ILE* 1.3 77.9 - - + +
212D TYR* 1.3 64.2 + - - +
214D CYS* 3.1 10.1 + - - +
215D LEU* 3.0 22.0 + - + +
251D LEU* 4.0 17.5 - - + -
254D LEU* 5.5 1.8 - - + -
255D LEU* 3.8 17.7 - - + -
258D LEU* 5.3 4.5 - - + -
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Residues in contact with TYR 212 (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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208D GLY 2.9 17.7 + - - +
209D THR* 3.7 7.0 - - - +
211D VAL* 1.3 77.4 - - - +
213D GLN* 1.3 57.0 + - - +
215D LEU* 3.1 5.5 + - + +
216D THR* 3.0 54.8 + - + +
218D LYS* 3.0 31.1 - - + +
219D ALA 3.8 2.7 - - - -
220D PRO* 3.3 32.7 + - + +
241D PRO* 3.5 28.5 - - + -
242D THR* 2.6 41.8 + - - -
243D ILE* 4.1 9.9 - - + -
255D LEU* 3.8 15.7 - - + +
259D LEU* 4.5 3.1 - - + -
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Residues in contact with GLN 213 (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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101D ALA* 5.5 4.6 - - - +
104D LEU* 3.9 21.5 - - + +
105D HIS* 5.6 6.9 + - - -
141D PRO* 3.7 16.7 - - + +
142D GLN* 5.8 1.6 - - - +
186D MET* 6.0 0.2 - - - -
187D TYR* 2.6 37.9 + - - -
209D THR 2.9 16.9 + - - +
210D ILE* 3.7 5.4 - - - +
212D TYR* 1.3 73.6 - - - +
214D CYS* 1.3 61.6 + - - +
217D GLY* 2.8 34.5 + - - -
218D LYS 3.3 25.8 - - - +
219D ALA* 4.3 11.8 + - - +
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Residues in contact with CYS 214 (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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100D LEU* 4.0 25.6 - - - -
104D LEU* 3.8 13.2 - - - -
109D THR* 3.5 5.4 - - - -
110D LEU* 2.9 54.7 + - + -
115D ILE* 4.0 15.9 - - + -
118D PHE* 5.2 4.3 - - - -
210D ILE* 2.9 20.6 + - - -
211D VAL* 3.1 12.5 + - - +
213D GLN* 1.3 77.1 - - - +
215D LEU* 1.3 59.2 + - - +
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Residues in contact with LEU 215 (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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109D THR* 3.6 15.3 - - - +
110D LEU 4.5 6.5 - - - +
112D GLU* 4.8 8.3 - - + +
115D ILE* 3.9 18.8 - - + -
211D VAL* 3.0 12.7 + - + +
212D TYR* 3.1 9.4 + - + +
214D CYS* 1.3 79.4 - - - +
216D THR* 1.3 65.7 + - + +
243D ILE* 4.3 2.2 - - + -
244D PRO* 4.2 18.9 - - + +
247D THR* 3.9 29.2 - - + +
251D LEU* 4.4 12.8 - - + -
255D LEU* 3.8 27.8 - - + -
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Residues in contact with THR 216 (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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109D THR* 3.6 11.9 - - - +
212D TYR* 3.0 47.0 + - + +
215D LEU* 1.3 91.5 - - + +
217D GLY* 1.3 59.7 + - - +
218D LYS* 3.1 30.7 + - - +
242D THR 4.4 0.9 - - - +
244D PRO* 3.9 22.9 - - + -
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Residues in contact with GLY 217 (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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104D LEU* 5.8 2.2 - - - -
108D ARG* 3.7 21.5 - - - -
109D THR* 3.7 3.9 - - - +
213D GLN* 2.8 27.3 + - - +
216D THR* 1.3 76.5 - - - +
218D LYS* 1.3 66.3 + - - +
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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