Contacts of the helix formed by residues 219 - 234 (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 ASN 219 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D LEU* 3.6 14.0 - - - +
217D PRO 3.5 0.2 - - - -
218D LEU* 1.3 82.3 + - - +
220D ILE* 1.3 66.3 + - - +
221D GLU* 3.3 11.6 + - - +
222D GLU* 2.9 52.6 + - - +
223D ALA* 3.0 24.4 + - - +
520D ALA* 5.5 3.1 - - + -
557D ARG* 4.5 3.8 - - - +
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Residues in contact with ILE 220 (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* 3.4 54.1 - - + +
195D LEU* 4.7 4.9 - - + -
196D LEU* 4.4 15.3 - - + +
199D LEU* 4.5 7.0 - - + -
219D ASN* 1.3 75.5 - - - +
221D GLU* 1.3 68.2 + - - +
223D ALA* 3.3 5.8 + - - +
224D LYS* 2.9 29.6 + - + +
249D TRP* 4.3 11.7 - - + -
253D ALA* 4.2 26.0 - - + -
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Residues in contact with GLU 221 (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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219D ASN* 3.3 8.8 + - - +
220D ILE* 1.3 88.4 - - - +
222D GLU* 1.3 57.0 + - + +
224D LYS* 3.4 19.5 + - - +
225D ASP* 3.1 28.2 + - - +
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Residues in contact with GLU 222 (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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215D ARG* 3.3 20.9 + - - -
217D PRO* 3.6 11.4 - - + +
218D LEU* 2.9 25.0 + - - +
219D ASN* 2.9 31.2 + - - +
221D GLU* 1.3 75.7 - - - +
223D ALA* 1.3 58.7 + - - +
225D ASP* 3.6 7.2 + - - +
226D ARG* 2.9 31.1 + - - +
557D ARG* 2.3 35.9 + - - -
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Residues in contact with ALA 223 (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* 4.5 3.8 - - + -
199D LEU* 3.9 32.2 - - + +
203D CYS* 4.1 4.1 - - - -
217D PRO* 3.4 26.7 - - + -
219D ASN 3.0 18.4 + - - +
220D ILE* 3.7 3.8 - - - +
222D GLU* 1.3 74.6 - - - +
224D LYS* 1.3 61.6 + - - +
226D ARG* 3.8 1.7 - - - +
227D LEU* 2.9 31.2 + - - +
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Residues in contact with LYS 224 (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* 5.1 1.5 - - - +
220D ILE* 2.9 20.0 + - + +
221D GLU* 3.7 21.7 + - - +
223D ALA* 1.3 77.2 - - - +
225D ASP* 1.3 56.9 + - - +
227D LEU* 3.3 6.0 + - - +
228D ARG* 2.9 24.8 + - + +
252D LYS* 2.6 52.2 + - - +
253D ALA* 3.4 27.6 - - + +
255D ASP 3.8 19.1 + - - -
256D SER* 3.6 12.5 + - - +
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Residues in contact with ASP 225 (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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11B GLN* 4.7 5.0 - - - +
221D GLU 3.1 17.9 + - - +
222D GLU* 3.6 7.9 - - - +
224D LYS* 1.3 75.7 - - - +
226D ARG* 1.3 64.7 + - - +
228D ARG* 3.1 35.8 + - - +
229D ILE* 3.2 30.7 + - - +
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Residues in contact with ARG 226 (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* 3.9 15.9 - - - +
207D ASP* 5.7 1.6 - - - -
212D PHE* 5.4 2.9 - - - -
213D SER* 3.6 36.1 + - - +
215D ARG* 2.6 41.2 + - - +
216D LEU* 4.0 3.6 + - - +
217D PRO* 3.6 29.1 - - + +
222D GLU* 2.9 22.6 + - - +
223D ALA* 3.4 4.7 + - - +
225D ASP* 1.3 76.1 + - - +
227D LEU* 1.3 57.9 + - - +
229D ILE* 3.2 11.0 + - + +
230D LEU* 2.9 52.3 + - + +
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Residues in contact with LEU 227 (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* 4.8 5.4 - - + -
202D LEU* 3.9 16.2 - - + -
203D CYS* 4.4 9.6 - - - -
206D LEU* 3.5 31.6 - - + -
223D ALA 2.9 18.6 + - - +
224D LYS 3.5 4.7 - - - +
225D ASP 3.3 0.2 - - - -
226D ARG* 1.3 78.3 - - - +
228D ARG* 1.3 63.3 + - - +
230D LEU* 3.4 3.3 + - - +
231D MET* 3.0 40.4 + - + +
240D LEU* 4.3 9.6 - - + -
253D ALA 4.3 5.6 - - - +
254D PHE* 3.6 45.5 - - + +
256D SER* 5.1 3.1 - - - +
258D CYS* 5.4 2.5 - - - -
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Residues in contact with ARG 228 (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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11B GLN* 5.8 0.2 - - - +
224D LYS 2.9 14.2 + - - +
225D ASP* 3.1 33.4 + - - +
227D LEU* 1.3 77.6 - - - +
229D ILE* 1.3 93.0 + - - +
231D MET* 4.1 2.7 - - - +
232D LEU* 3.2 38.5 + - + +
256D SER* 3.7 34.2 - - - +
257D GLN* 4.2 14.4 - - - +
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Residues in contact with ILE 229 (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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11B GLN* 3.3 43.5 - - + +
212D PHE* 3.9 32.8 - - + -
225D ASP* 3.2 15.2 + - - +
226D ARG* 3.2 12.4 + - + +
228D ARG* 1.3 111.2 - - - +
230D LEU* 1.3 62.8 + - + +
232D LEU* 4.5 5.2 - - + -
233D ARG* 2.8 37.5 + - + +
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Residues in contact with LEU 230 (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* 3.7 31.4 - - - +
206D LEU* 4.0 26.0 - - + +
207D ASP* 3.6 23.8 - - + +
212D PHE* 3.7 32.5 - - + -
226D ARG* 2.9 41.1 + - + +
227D LEU* 4.1 2.9 - - - +
229D ILE* 1.3 78.1 - - + +
231D MET* 1.3 58.8 + - - +
233D ARG* 5.1 0.2 - - - -
234D LYS* 2.8 36.4 + - + +
235D HIS* 3.0 9.9 + - - -
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Residues in contact with MET 231 (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* 5.4 1.8 - - - +
206D LEU* 3.8 26.5 - - - -
227D LEU* 3.0 28.5 + - + +
228D ARG* 4.1 3.4 - - - +
230D LEU* 1.3 77.9 - - - +
232D LEU* 1.3 58.4 + - - +
235D HIS* 3.0 38.4 - - + +
236D PRO* 3.2 5.5 - - - +
238D SER* 3.1 31.9 - - - +
239D LEU 5.2 0.7 - - - +
240D LEU* 4.3 26.2 - - + +
256D SER 5.3 1.3 - - - +
257D GLN 6.0 0.4 - - - +
258D CYS* 3.7 34.1 - - + -
259D GLN 5.9 0.7 - - - +
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Residues in contact with LEU 232 (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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228D ARG* 3.2 34.4 + - + +
229D ILE* 3.7 5.4 - - + +
231D MET* 1.3 79.7 - - - +
233D ARG* 1.3 78.1 + - + +
234D LYS 3.6 0.2 - - - -
236D PRO* 3.7 21.7 - - + +
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Residues in contact with ARG 233 (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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7B ASN* 3.4 36.6 + - - +
10B LEU* 4.2 17.8 - - - +
212D PHE* 3.5 31.1 - - + -
229D ILE* 2.8 27.5 + - + +
232D LEU* 1.3 92.8 - - + +
234D LYS* 1.3 59.7 + - - +
236D PRO* 4.4 3.8 - - - +
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Residues in contact with LYS 234 (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 LEU 3.5 13.9 + - - +
207D ASP* 3.4 24.4 + - - +
208D GLN* 3.8 4.2 - - - +
209D ASP* 2.5 39.7 + - - +
211D SER* 3.7 13.7 - - - +
212D PHE* 3.4 26.2 - - + -
230D LEU* 2.8 20.5 + - + +
233D ARG* 1.3 76.4 - - - +
235D HIS* 1.3 82.6 + - + +
236D PRO* 3.3 9.7 - - - +
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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