Contacts of the helix formed by residues 219 - 234 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A LEU* 3.6 14.7 - - - +
217A PRO 3.6 0.2 - - - -
218A LEU* 1.3 78.8 + - - +
220A ILE* 1.3 66.9 + - - +
221A GLU* 3.3 13.4 + - - +
222A GLU* 3.0 50.2 + - - +
223A ALA* 3.0 23.2 + - - +
520A ALA* 5.5 3.1 - - + -
557A ARG* 4.0 12.1 - - - +
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Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS* 3.5 54.5 - - + +
195A LEU* 4.7 3.8 - - + -
196A LEU* 4.4 11.4 - - + +
199A LEU* 4.5 11.2 - - + +
219A ASN* 1.3 75.0 - - - +
221A GLU* 1.3 57.9 + - - +
223A ALA* 3.2 5.9 + - - +
224A LYS* 2.8 30.3 + - + +
249A TRP* 4.3 11.4 - - + -
253A ALA* 4.2 25.8 - - + -
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Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ASN* 3.3 10.1 + - - +
220A ILE* 1.3 79.2 - - - +
222A GLU* 1.3 62.7 + - + +
224A LYS* 3.4 9.5 + - + +
225A ASP* 3.1 23.9 + - - +
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Residues in contact with GLU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ARG* 3.1 20.0 + - - -
217A PRO* 3.6 10.5 - - + +
218A LEU* 2.9 20.3 + - - +
219A ASN* 3.0 31.5 + - - +
221A GLU* 1.3 76.4 - - + +
223A ALA* 1.3 56.6 + - - +
225A ASP* 3.5 7.6 + - - +
226A ARG* 2.9 32.3 + - - +
557A ARG* 2.9 37.8 + - - -
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Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 4.5 3.1 - - + -
199A LEU* 3.8 33.5 - - + +
203A CYS* 4.1 4.4 - - - -
217A PRO* 3.4 26.0 - - + +
219A ASN 3.0 17.2 + - - +
220A ILE* 3.6 4.3 - - - +
222A GLU* 1.3 74.4 - - - +
224A LYS* 1.3 62.5 + - - +
226A ARG* 3.8 1.5 - - - +
227A LEU* 2.9 30.9 + - - +
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A LEU* 5.1 1.3 - - - +
220A ILE* 2.8 20.7 + - + +
221A GLU* 3.6 10.3 - - + +
223A ALA* 1.3 75.2 - - - +
225A ASP* 1.3 58.6 + - - +
227A LEU* 3.3 6.1 + - - +
228A ARG* 3.0 28.2 + - + +
252A LYS* 2.8 53.7 + - - +
253A ALA* 3.5 26.2 - - - +
255A ASP 3.9 18.1 + - - -
256A SER* 3.6 8.5 + - - +
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Residues in contact with ASP 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A GLU 3.1 17.1 + - - +
222A GLU* 3.6 7.5 - - - +
224A LYS* 1.3 76.3 - - - +
226A ARG* 1.3 65.2 + - - +
228A ARG* 2.7 47.6 + - - +
229A ILE* 3.2 23.2 + - - +
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Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A CYS* 4.1 14.3 - - - +
207A ASP* 5.8 1.3 - - - -
212A PHE* 5.3 3.1 - - - -
213A SER* 3.8 34.7 + - - +
215A ARG* 2.6 40.0 + - - +
216A LEU* 4.0 3.0 + - - +
217A PRO* 3.5 31.5 - - + +
222A GLU* 2.9 22.8 + - - +
223A ALA* 3.3 5.1 + - - +
225A ASP* 1.3 74.1 + - - +
227A LEU* 1.3 61.0 + - - +
229A ILE* 3.2 9.6 + - + +
230A LEU* 2.9 52.0 + - + +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A LEU* 4.7 6.1 - - + -
202A LEU* 4.4 9.2 - - + -
203A CYS* 4.4 10.3 - - - -
206A LEU* 3.7 23.3 - - + -
223A ALA 2.9 18.1 + - - +
224A LYS 3.5 4.9 - - - +
225A ASP 3.3 0.2 - - - -
226A ARG* 1.3 76.4 - - - +
228A ARG* 1.3 64.5 + - - +
230A LEU* 3.9 3.1 - - - +
231A MET* 3.0 51.6 + - + +
240A LEU* 4.3 11.0 - - + -
253A ALA 4.4 4.7 - - - +
254A PHE* 3.6 46.4 - - + +
256A SER* 5.0 2.9 - - - +
258A CYS* 5.4 2.7 - - - -
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Residues in contact with ARG 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LYS 3.0 14.1 + - - +
225A ASP* 2.7 60.2 + - - +
227A LEU* 1.3 78.1 - - - +
229A ILE* 1.3 81.4 + - - +
231A MET* 3.6 3.4 + - - +
232A LEU* 3.2 35.4 + - + +
256A SER* 3.7 31.8 - - - +
257A GLN* 3.9 18.6 - - - +
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A PHE* 3.9 31.6 - - + -
225A ASP* 3.2 31.4 + - - +
226A ARG* 3.2 11.0 + - + +
228A ARG* 1.3 99.7 - - - +
230A LEU* 1.3 61.7 + - + +
232A LEU* 3.7 6.3 - - + +
233A ARG* 2.8 37.8 + - + +
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Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A CYS* 3.6 33.4 - - + +
206A LEU* 4.0 26.5 - - + +
207A ASP* 3.6 24.2 - - + -
212A PHE* 3.7 31.6 - - + -
226A ARG* 2.9 38.2 + - + +
227A LEU* 4.0 3.4 - - - +
229A ILE* 1.3 78.3 - - + +
231A MET* 1.3 58.1 + - - +
233A ARG* 5.2 0.2 - - - -
234A LYS* 2.8 37.4 + - + +
235A HIS* 3.0 10.0 + - - -
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Residues in contact with MET 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A HIS* 5.5 2.2 - - - +
206A LEU* 4.0 16.2 - - - -
227A LEU* 3.0 43.1 + - + +
228A ARG* 4.0 3.6 - - - +
230A LEU* 1.3 73.7 - - - +
232A LEU* 1.3 61.4 + - - +
235A HIS* 3.0 38.6 - - + +
236A PRO* 3.1 6.4 - - - +
238A SER* 3.1 31.9 - - - +
239A LEU 5.3 0.4 - - - -
240A LEU* 4.4 23.8 - - + +
256A SER 5.3 1.6 - - - +
257A GLN 6.0 0.9 - - - +
258A CYS* 3.8 30.3 - - + -
259A GLN 5.9 0.4 - - - +
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ARG* 3.2 30.4 + - + +
229A ILE* 3.7 7.2 - - + +
231A MET* 1.3 82.1 - - - +
233A ARG* 1.3 73.6 + - + +
236A PRO* 3.7 19.2 - - + +
257A GLN* 6.6 0.2 - - + -
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Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A PHE* 3.5 37.8 - - + -
229A ILE* 2.8 30.2 + - + +
232A LEU* 1.3 89.5 - - + +
234A LYS* 1.3 59.5 + - - +
236A PRO* 4.4 2.9 - - - +
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Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU 3.4 22.6 + - - +
207A ASP* 3.7 13.0 - - - +
208A GLN 4.0 3.4 - - - +
209A ASP* 3.0 34.8 + - - +
211A SER* 3.6 13.0 - - - +
212A PHE* 3.4 35.0 - - + -
230A LEU* 2.8 21.2 + - + +
233A ARG* 1.3 75.8 - - - +
235A HIS* 1.3 84.1 + - + +
236A PRO* 3.3 9.2 - - - +
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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