Contacts of the helix formed by residues 196 - 213 (chain D) in PDB entry 1ZWS
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 LEU 196 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D HIS* 3.4 55.7 + - + +
134D LYS* 4.7 10.1 - - + -
135D ILE 3.0 44.2 - - - +
136D ALA* 3.9 11.0 - - + +
168D ILE* 4.1 16.9 - - + +
195D GLY* 1.3 70.2 - - - -
197D GLU* 1.3 68.8 + - - +
198D ALA 2.9 1.2 + - - -
199D ASP* 3.1 12.1 + - - +
200D MET* 3.7 3.1 + - - +
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Residues in contact with GLU 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D GLU* 3.9 11.1 - - - +
193D PRO 5.1 0.9 - - - +
194D LEU 4.1 0.2 - - - -
195D GLY* 2.9 35.7 + - - +
196D LEU* 1.3 79.1 + - - +
198D ALA* 1.3 64.8 + - - +
200D MET* 2.9 26.9 + - - +
260D THR* 4.0 43.3 - - + +
261D ARG* 5.1 9.5 + - - +
263D ARG* 3.0 17.1 + - + +
264D LEU 5.7 1.3 - - - +
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Residues in contact with ALA 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D PHE* 3.4 22.7 - - + -
185D ALA* 4.4 5.3 - - + +
187D GLU* 3.2 24.0 + - + +
188D ILE* 4.9 9.4 - - + -
194D LEU* 5.5 0.7 - - + -
195D GLY 3.0 15.9 + - - +
196D LEU 2.9 0.4 + - - -
197D GLU* 1.3 76.3 - - - +
199D ASP* 1.3 55.4 + - - +
200D MET 2.6 13.7 + - - -
201D TRP* 2.7 22.6 + - - +
202D SER* 3.5 5.8 + - - -
263D ARG* 3.9 3.6 - - - +
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Residues in contact with ASP 199 (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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127D VAL* 4.9 1.8 - - + -
131D HIS* 3.1 23.8 - - + -
136D ALA* 3.1 15.7 - - - +
137D HIS* 2.9 25.7 + - - +
138D PHE* 2.8 28.6 + - - -
140D LEU* 3.6 24.6 + - + +
196D LEU 3.1 9.3 + - - +
198D ALA* 1.3 76.6 - - - +
200D MET* 1.3 61.2 + - - +
202D SER* 3.3 13.4 + - - -
203D ILE* 3.2 22.8 + - - +
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Residues in contact with MET 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D LEU* 5.2 0.7 - - + -
127D VAL* 5.2 0.9 - - - -
131D HIS* 4.5 9.4 - - + +
196D LEU 4.2 7.6 - - - +
197D GLU* 2.9 20.1 + - - +
198D ALA 2.6 5.5 + - - -
199D ASP* 1.3 68.1 - - - +
201D TRP* 1.3 65.8 + - - +
202D SER 3.0 1.1 - - - -
203D ILE* 2.7 27.8 + - + +
204D GLY 3.1 9.4 + - - -
255D LEU* 3.7 21.3 - - + +
263D ARG* 4.0 12.6 - - - -
264D LEU 3.5 13.7 - - - +
265D THR* 3.4 4.5 - - - -
266D ILE* 3.3 53.8 - - + +
269D ALA* 3.3 25.1 - - + -
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Residues in contact with TRP 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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182D GLU 4.9 0.6 + - - -
183D PHE 3.6 14.3 + - - -
184D VAL 3.2 14.1 + - - -
185D ALA* 3.3 8.1 - - + -
186D PRO* 3.2 39.9 - - + -
198D ALA 2.7 12.4 + - - +
200D MET* 1.3 74.1 - - - +
202D SER* 1.3 65.0 + - - +
204D GLY* 3.1 3.5 + - - -
205D VAL* 3.0 37.4 + - + +
217D PHE* 3.2 37.3 - + - -
229D ILE* 3.9 19.3 - - + -
232D VAL* 4.3 9.9 - - + -
255D LEU 3.9 11.0 - - - -
256D LEU* 3.7 9.3 - - + +
257D VAL 3.9 29.6 - - - -
258D LYS 4.3 0.7 - - - -
263D ARG* 2.9 35.7 - - - +
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Residues in contact with SER 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D LEU* 3.8 34.7 + - - +
183D PHE* 3.2 22.2 + - - +
184D VAL* 5.2 0.5 - - - -
185D ALA 5.4 0.5 + - - -
198D ALA 3.8 6.9 + - - -
199D ASP* 3.3 16.0 + - - -
200D MET 3.0 0.6 - - - -
201D TRP* 1.3 77.6 - - - +
203D ILE* 1.3 66.7 + - - +
205D VAL* 3.0 6.8 + - - +
206D ILE* 2.8 28.7 + - - +
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Residues in contact with ILE 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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120D ILE* 4.7 10.8 - - + -
123D ILE* 4.1 15.7 - - + -
124D LEU* 4.2 22.7 - - + -
127D VAL* 4.1 21.1 - - + -
140D LEU* 3.8 18.8 - - + -
199D ASP 3.2 16.6 - - - +
200D MET* 2.7 31.8 + - + +
202D SER* 1.3 72.4 - - - +
204D GLY* 1.3 64.1 + - - +
206D ILE* 3.2 9.3 + - + +
207D THR* 2.9 32.5 + - - +
251D PHE* 4.8 1.3 - - + -
255D LEU* 4.0 14.8 - - + -
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Residues in contact with GLY 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 MET 3.1 6.9 + - - -
201D TRP 3.5 4.3 - - - -
203D ILE* 1.3 79.6 - - - +
205D VAL* 1.3 62.7 + - - +
207D THR* 2.9 7.9 + - - -
208D TYR* 2.8 24.5 + - - +
252D ILE* 3.9 6.8 - - - +
255D LEU* 3.5 25.6 - - - +
256D LEU* 4.0 10.1 - - - -
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Residues in contact with VAL 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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182D GLU 4.1 13.2 - - - +
183D PHE* 3.7 29.4 - - + +
201D TRP* 3.0 41.4 + - + +
202D SER* 3.5 8.7 - - - +
204D GLY* 1.3 72.9 - - - +
206D ILE* 1.3 62.7 + - - +
208D TYR* 3.3 2.6 + - - +
209D ILE* 3.0 34.2 + - + +
215D SER* 4.6 3.8 - - - +
216D PRO* 4.1 18.8 - - + -
217D PHE* 4.2 10.3 - - + -
256D LEU* 3.7 9.0 - - + +
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Residues in contact with ILE 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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101D LEU* 6.2 0.4 - - + -
102D PHE* 4.3 19.9 - - + -
120D ILE* 4.8 6.7 - - + -
123D ILE* 4.8 20.0 - - + -
140D LEU* 4.1 6.3 - - + +
141D LYS* 3.9 11.2 - - - +
142D PRO* 3.4 37.9 - - + -
145D ILE* 5.3 9.2 - - + -
183D PHE* 3.9 10.5 - - + -
202D SER* 2.8 27.5 + - - +
203D ILE* 3.3 10.8 - - + +
205D VAL* 1.3 71.4 - - - +
207D THR* 1.3 55.6 + - - +
209D ILE* 3.2 7.1 + - - +
210D LEU* 2.6 36.1 + - + +
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Residues in contact with THR 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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120D ILE* 3.4 31.6 - - + +
203D ILE* 2.9 16.9 + - - +
204D GLY* 3.4 7.6 - - - -
206D ILE* 1.3 76.2 - - - +
208D TYR* 1.3 54.3 + - - +
210D LEU* 3.1 0.8 + - - -
211D LEU* 2.7 47.0 + - + +
248D ALA 6.4 0.2 - - - -
251D PHE* 4.1 10.7 - - + -
252D ILE* 3.5 21.1 - - + -
274D TRP* 4.0 32.3 - - + -
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Residues in contact with TYR 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 GLY 2.8 16.5 + - - +
205D VAL 3.4 8.5 - - - +
207D THR* 1.3 73.1 - - - +
209D ILE* 1.3 63.0 + - - +
211D LEU* 3.8 2.3 - - - +
212D SER* 2.9 40.0 + - - -
214D ALA* 2.8 36.7 - - + +
215D SER 4.1 0.8 + - - -
216D PRO* 3.4 44.2 - - + +
234D TYR* 3.8 9.0 - + - -
235D ASP* 2.7 35.4 + - - -
236D PHE* 4.2 4.0 - + - -
237D ASP* 4.6 0.7 + - - +
240D PHE* 5.8 0.5 - - - -
241D PHE* 3.2 26.8 - + - -
252D ILE* 3.6 29.0 - - + +
256D LEU* 4.5 0.7 - - + -
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Residues in contact with ILE 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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102D PHE* 3.5 24.7 - - + -
142D PRO* 4.8 3.8 - - + -
182D GLU* 4.1 11.7 - - - +
183D PHE* 3.6 35.0 - - + -
205D VAL* 3.0 20.0 + - + +
206D ILE* 3.5 6.3 - - - +
208D TYR* 1.3 75.1 - - - +
210D LEU* 1.3 61.6 + - - +
213D GLY* 2.6 43.7 + - - +
214D ALA 3.4 17.9 - - - +
215D SER* 3.9 10.5 - - - +
216D PRO* 4.3 1.6 - - + -
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Residues in contact with LEU 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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101D LEU* 5.4 3.4 - - + -
102D PHE* 4.4 13.4 - - + -
105D LEU* 4.4 18.8 - - + +
111D LEU* 3.2 34.2 - - + +
116D ALA* 3.7 10.1 - - + +
119D PHE* 5.0 8.1 - - + -
120D ILE* 3.3 34.1 - - + -
123D ILE* 6.0 1.1 - - + -
206D ILE* 2.6 25.8 + - + +
207D THR* 3.3 6.3 - - - +
209D ILE* 1.3 75.6 - - - +
211D LEU* 1.3 83.4 + - + +
213D GLY* 4.3 1.6 + - - -
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Residues in contact with LEU 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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111D LEU* 5.3 1.6 - - + -
113D GLU* 5.0 9.4 - - + -
116D ALA* 4.1 15.3 - - + -
207D THR* 2.7 33.1 + - + +
208D TYR* 3.9 2.2 - - - +
210D LEU* 1.3 94.4 - - + +
212D SER* 1.3 62.9 + - - +
240D PHE 5.3 0.7 - - - +
241D PHE* 5.0 7.2 - - + -
244D THR* 4.3 20.0 - - + +
248D ALA* 3.6 31.4 - - + -
252D ILE* 4.9 7.6 - - + -
274D TRP* 4.0 16.6 - - + -
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Residues in contact with SER 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D TYR* 2.9 24.1 + - - -
211D LEU* 1.3 79.1 - - - +
213D GLY* 1.3 61.6 + - - +
214D ALA* 3.0 18.5 + - - +
240D PHE* 3.4 42.8 - - - +
241D PHE* 3.4 26.6 - - - -
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Residues in contact with GLY 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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209D ILE* 2.6 34.9 + - - +
210D LEU 4.9 1.1 - - - -
211D LEU 3.6 0.2 - - - -
212D SER* 1.3 72.5 + - - +
214D ALA* 1.3 59.0 - - - +
240D PHE* 5.5 1.3 - - - -
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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