Contacts of the helix formed by residues 197 - 210 (chain D) in PDB entry 1Z1G
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 CYS 197 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195D SER 3.5 2.4 + - - -
196D PRO* 1.3 72.3 - - - +
198D TRP* 1.3 66.5 + - - +
199D LEU 3.2 0.9 + - - -
200D ARG* 3.3 28.3 + - - +
201D LEU* 3.6 9.0 + - + +
265D ILE* 3.7 33.9 - - + -
266D LEU* 4.0 11.0 - - + -
275D THR* 6.0 6.3 - - - -
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Residues in contact with TRP 198 (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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196D PRO* 4.0 22.3 - - + +
197D CYS* 1.3 77.2 - - - +
199D LEU* 1.3 104.2 + - + +
201D LEU* 3.1 4.3 + - - +
202D ALA* 2.6 36.7 + - + +
266D LEU* 3.7 26.9 - - + -
272D ILE* 4.2 6.7 - - + +
273D ALA 2.8 30.3 - - - +
274D SER* 3.8 14.5 + - - +
275D THR* 4.0 13.6 + - - +
280D LEU* 3.6 33.7 - - + +
284D THR* 5.3 5.8 - - + -
285D VAL* 5.0 16.2 - - + -
288D TYR* 4.1 34.1 - + + -
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Residues in contact with LEU 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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192D ALA* 3.7 15.5 - - + -
195D SER* 3.2 31.2 - - - +
196D PRO 3.4 13.0 - - - +
197D CYS 3.1 0.2 - - - -
198D TRP* 1.3 103.0 - - + +
200D ARG* 1.3 65.9 + - + +
202D ALA* 3.1 6.1 + - + +
203D MSE 2.8 43.3 + - + +
285D VAL* 4.4 6.5 - - + +
288D TYR* 4.3 15.9 - - + +
289D PHE* 3.9 27.4 - - + +
292D ALA* 4.5 5.6 - - + -
307D PHE* 6.0 1.6 - - + -
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Residues in contact with ARG 200 (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 TYR* 3.7 53.8 + - + -
190D GLN* 4.2 4.6 + - - +
192D ALA* 3.7 26.1 + - + +
193D GLU* 3.4 32.2 + - - +
195D SER 5.4 0.9 - - - -
196D PRO 4.7 0.7 - - - +
197D CYS* 3.6 19.3 - - - +
199D LEU* 1.3 74.6 - - + +
201D LEU* 1.3 65.0 + - + +
203D MSE 2.9 23.5 + - - +
204D GLU* 2.9 21.3 + - - +
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Residues in contact with LEU 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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197D CYS* 3.6 8.2 + - + +
198D TRP* 3.1 7.9 + - - +
200D ARG* 1.3 80.9 - - + +
202D ALA* 1.3 53.3 + - - +
204D GLU* 3.3 7.2 + - - +
205D LEU* 2.7 36.8 + - - +
258D THR* 3.7 32.9 - - + +
261D LYS* 3.8 29.4 - - + +
262D CYS* 3.8 22.0 - - - +
265D ILE* 4.8 9.4 - - + -
266D LEU* 3.8 33.0 - - + -
272D ILE* 4.0 11.4 - - + -
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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
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198D TRP* 2.6 22.3 + - + +
199D LEU* 3.4 7.6 - - + +
201D LEU* 1.3 71.5 - - - +
203D MSE 1.3 53.3 + - + +
205D LEU* 3.2 3.2 + - - +
206D ALA* 2.6 39.1 + - - +
216D LEU* 4.2 5.0 - - + +
272D ILE* 3.5 24.8 - - + +
285D VAL* 4.6 20.4 - - + -
307D PHE* 4.7 12.1 - - + -
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Residues in contact with MSE 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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185D TYR* 3.8 26.0 - - + +
188D ILE* 3.7 5.4 - - + -
189D TYR* 3.7 33.4 - - + +
192D ALA* 4.1 13.9 - - - -
199D LEU* 2.8 37.9 + - + +
200D ARG* 2.9 10.4 + - - +
202D ALA* 1.3 74.2 - - - +
204D GLU* 1.3 66.1 + - - +
206D ALA* 3.1 8.8 + - - +
207D VAL* 3.1 26.4 + - - +
289D PHE* 3.5 42.2 - - + -
292D ALA* 5.8 0.2 - - - -
307D PHE* 4.9 2.2 - - + -
310D LEU* 4.6 8.0 - - + +
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Residues in contact with GLU 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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185D TYR* 3.4 19.7 + - - +
189D TYR* 3.6 28.5 + - + -
200D ARG* 2.9 19.3 + - - +
201D LEU* 3.7 8.4 - - - +
203D MSE 1.3 69.9 - - - +
205D LEU* 1.3 64.5 - - - +
207D VAL* 2.9 7.4 + - - +
208D VAL* 2.9 26.1 + - - +
253D ILE* 3.3 41.3 - - + +
258D THR* 3.3 23.1 + - + +
261D LYS* 3.7 23.5 + - - -
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Residues in contact with LEU 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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201D LEU 2.7 20.3 + - - +
202D ALA 3.3 4.0 - - - +
204D GLU* 1.3 71.5 - - - +
206D ALA* 1.3 52.4 + - - +
208D VAL* 3.0 12.1 - - + +
209D THR* 2.5 59.2 + - + +
216D LEU* 3.7 13.9 - - + -
219D MSE 4.6 8.7 - - - -
255D MSE 5.1 1.3 - - + -
258D THR* 3.9 13.3 - - + +
259D LEU* 3.9 26.2 - - + -
262D CYS* 4.9 5.6 - - - -
271D ILE* 3.6 20.6 - - + -
272D ILE* 3.6 32.1 - - + -
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Residues in contact with ALA 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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202D ALA 2.6 20.6 + - - +
203D MSE 3.1 6.3 + - - +
205D LEU* 1.3 73.2 - - - +
207D VAL* 1.3 54.1 + - - +
209D THR* 3.8 1.3 - - - -
210D GLY* 2.7 34.3 + - - -
211D GLN 3.6 2.7 + - - +
216D LEU* 3.7 15.7 - - + +
307D PHE* 3.5 30.1 - - + -
310D LEU* 4.1 14.4 - - + -
311D ARG* 4.4 3.8 - - + +
314D SER* 4.2 1.0 - - - -
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Residues in contact with VAL 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D TYR* 3.8 27.4 - - + -
203D MSE 3.2 14.6 - - - +
204D GLU* 2.9 7.6 + - - +
206D ALA* 1.3 75.3 - - - +
208D VAL* 1.3 60.9 + - - +
248D ILE* 4.4 18.7 - - + +
251D LEU* 4.6 11.7 - - + -
253D ILE* 5.8 4.9 - - + -
310D LEU* 3.9 19.7 - - + +
313D LEU* 4.5 12.8 - - + -
314D SER* 2.6 50.1 + - - +
317D LEU* 5.4 0.4 - - + -
318D TYR* 4.2 4.3 - - - -
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Residues in contact with VAL 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 GLU 2.9 10.9 + - - +
205D LEU* 3.0 26.5 - - + +
207D VAL* 1.3 80.2 - - - +
209D THR* 1.3 73.9 + - + +
242D ILE* 5.2 0.5 - - - +
246D LEU* 4.4 10.4 - - + +
247D HIS* 4.9 1.1 - - - -
248D ILE* 4.7 8.3 - - + -
253D ILE* 4.5 17.3 - - + +
254D SER 4.7 0.9 - - - -
255D MSE 3.6 47.0 - - + +
258D THR* 5.3 2.2 - - - -
318D TYR* 3.4 33.0 + - - +
330D LEU* 4.3 3.3 - - - +
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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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205D LEU* 2.5 40.7 + - + +
206D ALA* 3.7 2.3 + - - -
208D VAL* 1.3 86.4 - - + +
210D GLY* 1.3 67.1 + - - +
211D GLN* 3.0 36.9 + - - +
216D LEU* 4.7 2.3 - - - +
219D MSE 4.2 13.6 - - + +
229D LEU* 4.6 0.9 - - + -
242D ILE* 4.2 11.2 - - + +
255D MSE 3.6 26.2 - - + -
314D SER* 4.4 0.4 - - - -
330D LEU* 3.9 16.8 - - - +
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Residues in contact with GLY 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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206D ALA 2.7 18.4 + - - -
207D VAL 3.5 1.4 + - - -
208D VAL 3.4 2.2 - - - -
209D THR* 1.3 77.0 - - - +
211D GLN* 1.3 51.7 + - - -
311D ARG* 2.8 41.8 + - - +
314D SER* 3.1 24.9 - - - -
330D LEU* 5.5 0.4 - - - -
331D LEU* 4.0 13.5 - - - +
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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