Contacts of the helix formed by residues 219 - 234 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196C LEU* 3.7 12.7 - - - +
217C PRO 3.6 0.6 - - - -
218C LEU* 1.3 77.8 + - - +
220C ILE* 1.3 66.0 + - - +
221C GLU* 3.2 14.8 + - - +
222C GLU* 2.8 39.8 + - - +
223C ALA* 3.0 22.5 + - - +
520C ALA* 5.6 3.1 - - + -
557C ARG* 4.0 21.6 - - - +
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Residues in contact with ILE 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C LYS* 3.6 55.2 - - + +
195C LEU* 4.6 4.0 - - + -
196C LEU* 4.1 11.8 - - + +
199C LEU* 4.5 10.7 - - + +
219C ASN* 1.3 74.8 - - - +
221C GLU* 1.3 59.2 + - - +
223C ALA* 3.2 6.9 + - - +
224C LYS* 2.8 30.3 + - + +
249C TRP* 4.4 11.4 - - + -
253C ALA* 4.1 25.4 - - + -
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Residues in contact with GLU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ASN* 3.2 12.5 + - - +
220C ILE* 1.3 81.1 - - - +
222C GLU* 1.3 62.9 + - + +
224C LYS* 3.4 7.9 + - - +
225C ASP* 3.1 23.9 + - + +
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Residues in contact with GLU 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C ARG* 3.3 22.9 + - - -
217C PRO* 3.8 9.9 - - + +
218C LEU* 3.0 22.7 + - - +
219C ASN* 2.8 26.1 + - - +
221C GLU* 1.3 80.4 - - + +
223C ALA* 1.3 56.6 + - - +
225C ASP* 3.4 6.2 + - - +
226C ARG* 2.8 34.0 + - - +
557C ARG* 2.8 31.6 + - - -
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Residues in contact with ALA 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C LEU* 4.4 4.7 - - + -
199C LEU* 3.8 34.6 - - + +
203C CYS* 4.1 4.7 - - - -
217C PRO* 3.4 26.6 - - + +
219C ASN 3.0 17.0 + - - +
220C ILE* 3.6 4.5 - - - +
222C GLU* 1.3 73.5 - - - +
224C LYS* 1.3 61.5 + - - +
226C ARG* 4.0 1.6 - - - +
227C LEU* 2.9 30.7 + - - +
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Residues in contact with LYS 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C LEU* 5.2 1.3 - - - +
220C ILE* 2.8 19.6 + - + +
221C GLU* 3.6 7.0 - - - +
223C ALA* 1.3 77.4 - - - +
225C ASP* 1.3 56.8 + - - +
227C LEU* 3.4 3.4 + - - +
228C ARG* 3.0 24.3 + - - +
252C LYS* 2.7 34.0 + - - +
253C ALA* 3.5 28.5 - - + +
255C ASP* 3.7 25.6 + - - +
256C SER* 3.5 13.0 + - - +
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Residues in contact with ASP 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C GLU* 3.1 16.1 + - + +
222C GLU* 3.7 7.0 - - - +
224C LYS* 1.3 74.9 - - - +
226C ARG* 1.3 64.7 + - - +
228C ARG* 3.3 36.5 + - - +
229C ILE* 3.1 35.6 + - - +
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Residues in contact with ARG 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C CYS* 4.2 15.0 - - - +
207C ASP* 5.8 1.1 - - - -
212C PHE* 5.4 3.1 - - - -
213C SER* 3.6 33.9 + - - +
215C ARG* 2.5 46.0 + - - +
216C LEU* 4.0 3.4 + - - +
217C PRO* 3.8 27.4 - - + +
222C GLU* 2.8 23.5 + - - +
223C ALA* 4.0 4.3 - - - +
225C ASP* 1.3 72.6 - - - +
227C LEU* 1.3 58.3 + - - +
229C ILE* 3.3 10.9 + - + +
230C LEU* 3.0 52.7 + - + +
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Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C LEU* 5.1 5.6 - - + -
202C LEU* 4.2 15.9 - - + -
203C CYS* 4.4 9.8 - - - -
206C LEU* 3.4 30.7 - - + -
223C ALA 2.9 19.3 + - - +
224C LYS* 3.5 6.3 - - - +
226C ARG* 1.3 76.7 - - - +
228C ARG* 1.3 63.3 + - - +
230C LEU* 4.6 1.6 - - - +
231C MET* 3.0 42.8 + - + +
240C LEU* 4.1 12.1 - - + -
253C ALA 4.6 3.4 - - - +
254C PHE* 3.8 42.2 - - + +
256C SER* 4.9 4.0 - - - +
258C CYS* 5.0 3.1 - - - -
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Residues in contact with ARG 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B VAL* 6.2 4.0 - - - -
224C LYS 3.0 13.6 + - - +
225C ASP* 3.3 33.6 + - - +
227C LEU* 1.3 77.3 - - - +
229C ILE* 1.3 94.7 + - - +
231C MET* 4.1 2.5 - - - +
232C LEU* 3.1 44.8 + - + +
256C SER* 3.7 33.6 - - - +
257C GLN* 4.1 15.5 - - + +
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Residues in contact with ILE 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C PHE* 4.0 29.2 - - + -
225C ASP* 3.1 23.1 + - - +
226C ARG* 3.3 10.7 + - + +
228C ARG* 1.3 106.7 - - - +
230C LEU* 1.3 54.8 + - + +
232C LEU* 3.3 5.6 + - + +
233C ARG* 2.8 47.9 + - + +
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Residues in contact with LEU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C CYS* 3.7 34.1 - - + +
206C LEU* 4.0 24.5 - - + +
207C ASP* 3.8 21.5 - - + -
212C PHE* 3.9 31.9 - - + -
226C ARG* 3.0 40.3 + - + +
227C LEU* 4.1 3.1 - - - +
229C ILE* 1.3 77.1 - - + +
231C MET* 1.3 58.4 + - - +
233C ARG* 5.0 0.7 - - - -
234C LYS* 2.8 36.6 + - + +
235C HIS* 3.1 10.6 + - + -
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Residues in contact with MET 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C HIS* 5.5 1.8 - - - +
206C LEU* 3.7 27.4 - - - -
227C LEU* 3.0 30.2 + - + +
228C ARG 4.2 2.5 - - - +
230C LEU* 1.3 76.2 - - - +
232C LEU* 1.3 57.8 + - - +
235C HIS* 3.0 39.2 - - + +
236C PRO* 3.2 6.1 - - - +
238C SER* 3.3 33.0 - - - +
239C LEU 5.1 0.4 - - - -
240C LEU* 4.0 28.7 - - + +
256C SER 5.5 1.1 - - - +
258C CYS* 3.7 32.8 - - + -
259C GLN 5.8 0.2 - - - +
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Residues in contact with LEU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C ARG* 3.1 36.3 + - + +
229C ILE* 3.6 4.7 - - + +
231C MET* 1.3 80.4 - - - +
233C ARG* 1.3 71.4 + - + +
236C PRO* 3.8 19.2 - - + +
257C GLN* 6.5 1.6 - - + -
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Residues in contact with ARG 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C PHE* 3.6 40.3 - - + -
229C ILE* 2.8 33.2 + - + +
232C LEU* 1.3 87.2 - - + +
234C LYS* 1.3 60.8 + - - +
236C PRO* 4.3 3.9 - - - +
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Residues in contact with LYS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C LEU 3.5 13.9 - - - +
207C ASP* 2.7 42.4 + - - +
208C GLN 3.6 2.6 - - - +
209C ASP* 3.0 27.4 + - - +
211C SER* 3.6 14.8 - - - +
212C PHE* 3.6 24.2 - - + -
230C LEU* 2.8 22.3 + - + +
233C ARG* 1.3 74.1 - - + +
235C HIS* 1.3 81.9 + - + +
236C PRO* 3.3 8.7 - - - +
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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