Contacts of the helix formed by residues 221 - 232 (chain C) in PDB entry 1ZWS
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 THR 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219C GLY 4.4 0.7 - - - -
220C ASP* 1.3 90.4 - - + +
222C LYS* 1.3 58.5 + - - +
223C GLN* 3.5 22.9 + - - +
224C GLU* 2.5 43.0 + - - +
225C THR* 2.7 15.3 + - - -
57D SER* 4.8 5.2 - - - +
59D GLU* 5.4 10.1 - - + +
60D GLU* 3.3 28.0 - - + +
63D ARG* 5.0 3.8 - - - +
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Residues in contact with LYS 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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181C PRO* 4.0 26.7 - - + -
221C THR* 1.3 69.2 - - - +
223C GLN* 1.3 67.5 + - - +
225C THR* 2.8 21.7 + - - -
226C LEU* 2.9 32.1 + - + +
164D LEU* 6.4 0.2 - - - -
176D ASN* 3.6 21.5 - - - +
177D ILE* 2.6 31.8 + - + +
178D PHE* 3.8 12.3 - - - +
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Residues in contact with GLN 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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221C THR* 3.5 16.4 + - - +
222C LYS* 1.3 81.0 - - - +
224C GLU* 1.3 62.4 + - - +
226C LEU* 3.9 3.8 + - - +
227C ALA* 3.7 14.9 + - - +
59D GLU* 5.1 1.6 + - - -
63D ARG* 3.6 26.9 - - - +
166D HIS* 4.3 3.5 + - - -
174D PHE* 3.3 37.3 - - + -
175D LYS 4.3 7.6 - - - +
176D ASN* 3.3 27.1 + - - +
191D TYR* 4.3 2.6 + - - -
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Residues in contact with GLU 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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219C GLY* 3.8 9.3 - - - -
220C ASP* 3.0 46.7 + - - +
221C THR* 2.5 27.8 + - - +
223C GLN* 1.3 76.1 - - + +
225C THR* 1.3 65.4 + - - +
227C ALA* 3.1 19.9 + - - +
228C ASN* 2.9 17.2 + - - +
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Residues in contact with THR 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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181C PRO* 4.3 24.2 - - + +
182C GLU* 4.4 10.8 - - + +
217C PHE* 3.4 21.1 - - + +
218C LEU* 4.3 5.7 - - + +
219C GLY* 2.9 21.8 + - - +
221C THR 2.7 17.3 + - - -
222C LYS* 2.8 11.8 + - - -
224C GLU* 1.3 71.8 - - - +
226C LEU* 1.3 54.4 + - - +
228C ASN* 2.5 37.9 + - - +
229C ILE* 3.0 17.1 + - + -
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Residues in contact with LEU 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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181C PRO* 4.4 22.2 - - + +
184C VAL* 5.5 0.7 - - + -
189C VAL* 4.1 21.3 - - + -
222C LYS* 2.9 34.3 + - + +
223C GLN 4.0 2.2 - - - +
225C THR* 1.3 71.0 - - - +
227C ALA* 1.3 50.9 + - - +
229C ILE* 3.4 6.4 + - + +
230C THR* 2.7 41.8 + - - +
176D ASN* 3.0 26.9 - - - +
177D ILE* 3.6 32.8 - - + +
191D TYR* 3.2 22.0 - - + +
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Residues in contact with ALA 227 (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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223C GLN 3.7 7.0 + - - +
224C GLU* 3.1 12.9 + - - +
225C THR 3.0 0.4 - - - -
226C LEU* 1.3 75.0 - - - +
228C ASN* 1.3 54.6 + - - +
230C THR* 2.8 6.9 + - - -
231C SER* 2.6 44.8 + - - +
191D TYR* 3.1 11.5 + - - +
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Residues in contact with ASN 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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216C PRO 5.6 0.2 - - - -
217C PHE* 3.2 40.4 + - + +
219C GLY* 4.2 3.6 - - - -
224C GLU* 2.9 34.1 + - - +
225C THR* 2.5 15.5 + - - +
227C ALA* 1.3 71.6 - - - +
229C ILE* 1.3 51.7 + - - +
231C SER* 2.9 6.4 + - - -
232C VAL* 2.4 33.1 + - - -
233C SER* 2.8 28.1 + - - +
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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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181C PRO 3.1 28.9 - - - +
182C GLU 4.0 8.5 - - - +
184C VAL* 3.3 27.1 - - + +
186C PRO* 3.7 29.4 - - + +
189C VAL* 4.0 15.7 - - + -
201C TRP* 3.9 6.6 - - + -
217C PHE* 3.8 29.4 - - + -
225C THR* 3.0 13.7 + - + +
226C LEU* 3.8 8.7 - - + +
228C ASN* 1.3 76.9 - - - +
230C THR* 1.3 59.9 + - - +
232C VAL* 2.8 25.8 + - - +
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Residues in contact with THR 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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186C PRO* 4.9 3.8 - - + -
189C VAL* 3.3 18.2 - - + -
190C ASN* 3.2 35.9 - - - +
226C LEU 2.7 27.4 + - - +
227C ALA* 2.8 17.5 + - - -
229C ILE* 1.3 73.8 - - - +
231C SER* 1.3 58.7 + - - +
232C VAL* 3.4 7.6 + - - +
258C LYS* 4.2 17.7 + - - +
191D TYR* 3.3 21.5 - - + -
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Residues in contact with SER 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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227C ALA* 2.6 27.6 + - - -
228C ASN* 2.9 8.3 + - - -
230C THR* 1.3 72.3 + - - +
232C VAL* 1.3 73.2 + - - +
233C SER* 2.6 25.5 + - - -
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Residues in contact with VAL 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C PRO* 4.8 0.7 - - + -
201C TRP* 4.3 18.6 - - + -
217C PHE* 4.2 5.2 - - - -
228C ASN 2.4 13.9 + - - -
229C ILE 2.8 14.7 + - - +
230C THR 3.6 7.4 - - - +
231C SER* 1.3 83.3 - - - +
233C SER* 1.3 57.4 + - - +
234C TYR* 4.0 17.7 + - + -
256C LEU 4.4 14.6 - - - +
258C LYS* 4.1 28.9 - - + +
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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