Contacts of the helix formed by residues 191 - 207 (chain D) in PDB entry 1Z6T
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 ASP 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190D GLN* 1.3 75.1 + - - +
192D LYS* 1.3 59.0 + - - +
193D SER* 3.7 5.5 + - - -
194D GLY* 2.7 35.0 + - - -
195D LEU 2.9 24.1 + - - -
249D TRP* 3.6 12.3 - - - -
524D HIS* 3.5 28.6 + - + -
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Residues in contact with LYS 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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191D ASP* 1.3 76.2 - - - +
193D SER* 1.3 58.7 + - - +
195D LEU 3.4 0.2 + - - -
196D LEU* 3.0 24.4 + - - +
220D ILE* 3.4 26.5 - - + +
249D TRP* 3.7 53.1 - - + +
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Residues in contact with SER 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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191D ASP* 3.3 6.1 + - - -
192D LYS* 1.3 76.2 - - - +
194D GLY* 1.3 60.8 + - - +
196D LEU* 3.7 9.8 - - - +
197D MET* 3.1 34.2 + - - +
520D ALA* 4.9 4.3 - - - -
521D HIS* 3.7 29.2 + - - +
524D HIS* 3.3 39.0 - - - -
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Residues in contact with GLY 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 GLN* 3.2 22.3 - - - +
191D ASP* 2.7 21.1 + - - -
193D SER* 1.3 72.8 + - - +
195D LEU* 1.3 64.6 + - - +
197D MET* 3.4 19.9 + - - +
198D LYS* 3.3 24.6 + - - +
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Residues in contact with LEU 195 (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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187D VAL* 4.3 13.7 - - + -
190D GLN* 3.7 10.3 - - + +
191D ASP 2.9 16.4 + - - +
192D LYS 3.9 3.4 - - - +
194D GLY* 1.3 75.9 - - - +
196D LEU* 1.3 57.1 + - - +
198D LYS* 3.0 11.5 + - + +
199D LEU* 2.8 41.2 + - + +
220D ILE* 4.7 4.9 - - + -
249D TRP* 3.8 25.8 - - + -
250D VAL* 3.9 27.8 - - + -
253D ALA* 3.8 27.1 - - + -
254D PHE* 4.2 14.6 - - + -
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Residues in contact with LEU 196 (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 LYS 3.0 18.2 + - - +
193D SER* 3.7 10.1 - - - +
195D LEU* 1.3 76.3 - - - +
197D MET* 1.3 57.0 + - + +
199D LEU* 3.2 3.6 + - - -
200D GLN* 2.8 58.2 + - + +
217D PRO 4.2 3.1 - - - +
218D LEU 3.6 21.1 - - - +
219D ASN* 3.6 35.4 - - - +
220D ILE* 4.0 8.7 - - + +
223D ALA* 4.5 9.6 - - + -
517D VAL 5.2 2.0 - - - +
520D ALA* 3.9 20.0 - - + -
521D HIS* 5.2 4.7 - - + +
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Residues in contact with MET 197 (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 GLN* 5.5 0.9 - - - +
193D SER 3.1 15.7 + - - +
194D GLY* 3.5 22.9 - - - +
196D LEU* 1.3 75.4 - - - +
198D LYS* 1.3 66.0 + - + +
200D GLN* 3.5 14.2 + - - +
201D ASN* 3.2 23.9 + - - +
485D ASN* 3.6 38.4 - - - +
486D PHE* 4.0 25.4 - - + -
521D HIS* 3.8 33.2 - - + +
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Residues in contact with LYS 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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185D VAL* 5.0 12.6 - - + +
186D SER* 3.0 33.9 + - - +
187D VAL* 3.8 4.6 + - + +
190D GLN* 3.6 26.0 - - + +
194D GLY 3.3 15.5 - - - +
195D LEU* 3.0 18.3 + - + +
197D MET* 1.3 78.3 - - + +
199D LEU* 1.3 66.0 + - + +
201D ASN* 3.5 8.2 + - + +
202D LEU* 3.0 23.8 + - - +
254D PHE* 6.2 0.4 - - + -
392D ASP* 2.7 29.8 + - - +
393D VAL* 5.1 1.7 - - - +
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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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195D LEU* 2.8 45.4 + - + +
196D LEU* 3.7 4.7 - - - +
198D LYS* 1.3 74.2 - - - +
200D GLN* 1.3 57.7 + - - +
202D LEU* 3.2 10.6 + - + +
203D CYS* 2.9 37.5 + - - -
220D ILE* 4.5 14.6 - - + +
223D ALA* 3.9 31.9 - - + +
224D LYS 5.1 2.0 - - - +
227D LEU* 4.8 8.5 - - + -
253D ALA* 4.2 14.6 - - + +
254D PHE* 3.6 36.3 - - + -
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Residues in contact with GLN 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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196D LEU* 2.8 43.4 + - + +
197D MET* 3.7 14.5 - - - +
199D LEU* 1.3 70.8 - - - +
201D ASN* 1.3 63.3 + - - +
203D CYS* 3.3 2.1 + - - +
204D THR* 3.1 26.0 + - - -
216D LEU* 3.7 28.2 - - + +
217D PRO* 2.8 38.6 + - + +
481D MET* 5.5 1.0 - - - +
485D ASN* 5.7 0.3 - - - +
517D VAL* 3.1 47.2 + - - +
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Residues in contact with ASN 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 MET 3.2 15.1 + - - +
198D LYS* 3.7 7.1 - - - +
200D GLN* 1.3 80.6 - - - +
202D LEU* 1.3 57.2 + - - +
204D THR* 3.4 9.1 + - - +
205D ARG* 3.1 50.0 + - - +
434D ARG* 5.5 5.2 + - - +
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Residues in contact with LEU 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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183D HIS* 4.9 2.2 - - + -
185D VAL* 3.7 38.6 - - + -
198D LYS 3.0 17.5 + - - +
199D LEU* 3.2 10.5 + - + +
201D ASN* 1.3 74.8 + - - +
203D CYS* 1.3 61.0 + - - +
205D ARG* 3.2 26.4 + - + +
206D LEU* 2.9 56.5 + - + +
227D LEU* 3.9 21.5 - - + -
240D LEU* 4.7 7.9 - - + -
254D PHE* 3.9 19.5 - - + -
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Residues in contact with CYS 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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199D LEU* 2.9 23.6 + - - +
200D GLN 3.9 4.0 - - - +
202D LEU* 1.3 75.7 - - - +
204D THR* 1.3 62.0 + - - +
206D LEU* 3.4 1.5 + - - -
207D ASP* 3.3 25.1 + - - +
216D LEU* 5.5 1.1 - - + -
217D PRO* 4.1 25.8 - - + -
223D ALA* 4.1 14.6 - - - -
226D ARG* 3.9 26.2 - - + +
227D LEU* 4.4 13.5 - - - -
230D LEU* 3.7 17.3 - - + +
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Residues in contact with THR 204 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200D GLN 3.1 7.7 + - - -
201D ASN* 3.7 12.9 - - - +
203D CYS* 1.3 77.1 - - - +
205D ARG* 1.3 63.6 + - + +
207D ASP 3.4 21.2 + - - +
208D GLN* 3.7 8.0 + - + +
216D LEU* 3.1 28.9 - - - +
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Residues in contact with ARG 205 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D GLU 5.8 2.7 - - - -
117D GLY 3.2 24.0 + - - -
118D GLY* 4.4 6.0 - - - -
183D HIS* 4.7 14.9 + - + +
184D TRP 2.7 33.3 + - - +
185D VAL* 4.0 8.7 - - - +
186D SER 5.2 0.8 - - - +
201D ASN* 3.1 38.6 + - - +
202D LEU* 3.2 29.9 + - + +
204D THR* 1.3 77.6 - - + +
206D LEU* 1.3 64.9 + - + +
208D GLN* 2.8 36.2 + - - +
235D HIS* 5.7 0.5 - - - -
434D ARG* 6.1 2.7 - - - +
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Residues in contact with LEU 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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183D HIS* 3.3 49.4 - - + +
202D LEU* 2.9 30.8 + - + +
203D CYS 3.4 0.2 + - - -
204D THR 3.3 0.2 - - - -
205D ARG* 1.3 76.9 - - - +
207D ASP* 1.3 58.0 + - - +
208D GLN 3.8 1.1 - - - -
227D LEU* 3.5 32.8 - - + -
230D LEU* 4.0 20.1 - - + +
231D MET* 3.8 16.4 - - - -
234D LYS* 3.5 14.4 + - - +
235D HIS* 2.8 35.8 + - + +
240D LEU* 4.9 1.1 - - + -
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Residues in contact with ASP 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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203D CYS 3.3 12.7 + - - +
204D THR* 3.5 8.6 - - - +
205D ARG 3.3 0.6 - - - -
206D LEU* 1.3 79.1 - - - +
208D GLN* 1.3 62.8 + - - +
209D ASP 3.6 0.2 - - - -
210D GLU* 3.2 11.9 + - - +
211D SER* 3.0 30.8 + - - -
212D PHE* 3.3 35.5 + - - +
213D SER 3.8 6.6 - - - +
226D ARG* 5.7 2.2 - - - -
230D LEU* 3.6 22.2 - - + +
234D LYS* 3.4 4.8 + - - +
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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