Contacts of the helix formed by residues 218 - 233 (chain C) in PDB entry 1SZU
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 SER 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172C PRO* 5.4 1.2 - - - +
180C GLU* 2.8 29.3 + - - -
216C ALA 3.7 2.4 + - - -
217C SER* 1.3 77.7 + - - +
219C PRO* 1.3 75.8 - - - +
220C ALA* 3.5 5.7 + - - +
221C PHE* 3.1 19.0 + - - +
222C MET* 3.0 21.1 + - - +
257C MET* 3.9 1.1 - - - -
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Residues in contact with PRO 219 (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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217C SER 4.4 1.6 - - - +
218C SER* 1.3 88.7 - - - +
220C ALA* 1.3 51.4 + - - +
222C MET* 3.2 2.6 + - - +
223C GLN* 2.8 56.3 + - - +
256C GLN 3.5 20.0 - - - +
257C MET* 3.6 20.2 - - - +
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Residues in contact with ALA 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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180C GLU* 3.9 10.8 - - - +
218C SER* 3.2 8.5 + - - +
219C PRO* 1.3 80.0 - - - +
221C PHE* 1.3 62.6 + - - +
223C GLN* 3.3 14.1 + - - +
224C ARG* 3.0 31.1 + - + +
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Residues in contact with PHE 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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134C PHE* 4.1 13.9 - + - -
172C PRO* 3.6 31.4 - - + -
180C GLU* 3.6 33.4 + - + -
183C ALA* 3.3 26.5 - - + -
184C ILE* 3.7 26.7 - - + -
187C ILE* 5.3 0.7 - - + -
205C ILE* 3.9 21.3 - - + -
217C SER* 3.5 17.0 - - - +
218C SER* 3.1 22.5 + - - +
220C ALA* 1.3 72.4 - - - +
222C MET* 1.3 67.6 + - - +
224C ARG* 3.0 9.1 + - - +
225C LEU* 2.8 33.8 + - + +
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Residues in contact with MET 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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205C ILE* 4.3 16.4 - - + -
207C PRO* 4.1 14.1 - - + -
217C SER* 3.3 30.1 - - - +
218C SER 3.0 16.7 + - - +
219C PRO 3.6 3.6 - - - +
221C PHE* 1.3 77.0 - - - +
223C GLN* 1.3 58.2 + - - +
225C LEU* 3.3 23.0 + - - +
226C ARG* 2.9 27.4 + - - +
236C LEU* 4.5 6.5 - - + -
254C MET* 3.7 30.1 - - + -
257C MET* 3.7 22.2 - - + -
259C VAL* 3.6 18.8 - - + -
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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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219C PRO* 2.8 31.5 + - - +
220C ALA* 3.5 10.4 - - - +
222C MET* 1.3 73.9 - - - +
224C ARG* 1.3 65.4 + - + +
226C ARG* 3.2 2.9 + - - +
227C ALA* 2.9 23.6 + - - +
257C MET 3.0 21.6 + - - +
258C GLY* 4.4 6.9 + - - +
259C VAL* 3.8 28.0 - - + +
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Residues in contact with ARG 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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180C GLU* 4.0 13.8 + - - +
181C ASP* 2.5 44.0 + - - +
184C ILE* 3.7 30.9 - - + +
220C ALA* 3.0 23.8 + - + +
221C PHE* 3.0 10.8 + - - +
223C GLN* 1.3 77.2 - - + +
225C LEU* 1.3 56.9 + - - +
227C ALA* 3.3 6.8 + - - +
228C LEU* 2.9 30.8 + - - +
1004C SO4 2.8 47.7 + - - +
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Residues in contact with LEU 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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134C PHE* 4.3 4.9 - - + -
184C ILE* 4.2 4.0 - - + +
187C ILE* 3.7 29.8 - - + -
203C ILE* 4.0 21.5 - - + -
205C ILE* 3.6 32.1 - - + -
221C PHE* 2.8 24.5 + - + +
222C MET* 3.5 18.2 - - - +
223C GLN 3.2 0.2 - - - -
224C ARG* 1.3 78.9 - - - +
226C ARG* 1.3 54.7 + - - +
228C LEU* 3.5 6.0 + - + +
229C CYS* 3.0 34.7 + - - -
236C LEU* 3.8 26.7 - - + -
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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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222C MET 2.9 15.9 + - - +
223C GLN 3.2 5.4 + - - +
225C LEU* 1.3 75.7 - - - +
227C ALA* 1.3 60.0 + - - +
229C CYS* 3.3 21.6 + - - +
230C ASP* 2.8 64.7 + - - +
234C ILE 3.7 4.9 + - - -
235C MET* 6.0 0.2 - - - +
236C LEU* 3.9 20.0 - - + +
259C VAL* 4.1 26.2 - - + -
260C ALA 3.1 29.1 + - - +
261C PRO 3.9 0.6 - - - -
262C ASP* 2.6 42.8 + - - +
282C ARG* 4.4 6.8 - - - +
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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 2.9 15.8 + - - +
224C ARG* 3.3 7.4 + - - +
226C ARG* 1.3 75.8 - - - +
228C LEU* 1.3 64.6 + - - +
230C ASP* 3.2 10.2 + - - +
231C GLU* 2.9 26.2 + - - +
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Residues in contact with LEU 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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184C ILE* 4.5 13.5 - - + -
187C ILE* 3.9 28.9 - - + -
188C HIS* 4.0 28.3 - - + +
191C PHE* 4.1 21.8 - - + -
203C ILE* 3.9 26.9 - - + -
224C ARG 2.9 17.1 + - - +
225C LEU* 3.6 6.7 - - + +
227C ALA* 1.3 78.5 - - - +
229C CYS* 1.3 65.1 + - - +
231C GLU* 3.6 6.4 + - - +
232C HIS* 3.2 33.5 + - + -
234C ILE* 4.7 1.1 - - + -
1004C SO4 5.3 3.8 - - - +
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Residues in contact with CYS 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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203C ILE* 4.1 24.7 - - - -
225C LEU* 3.0 27.0 + - - +
226C ARG* 3.5 13.9 - - - +
228C LEU* 1.3 76.2 - - - +
230C ASP* 1.3 66.4 + - - +
232C HIS 2.9 3.5 + - - -
233C GLY 2.9 21.1 + - - -
234C ILE* 3.2 36.3 + - - +
236C LEU* 4.0 27.6 - - - -
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Residues in contact with ASP 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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226C ARG* 2.8 62.0 + - - +
227C ALA* 3.5 8.4 - - - +
229C CYS* 1.3 74.6 - - - +
231C GLU* 1.3 61.6 + - - +
232C HIS 3.2 0.2 + - - -
233C GLY* 3.5 9.2 + - - +
282C ARG* 5.8 0.9 + - - -
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Residues in contact with GLU 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 2.9 16.8 + - - +
228C LEU* 3.8 8.5 - - - +
230C ASP* 1.3 76.4 - - - +
232C HIS* 1.3 84.5 + - + +
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Residues in contact with HIS 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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128C ARG* 3.0 27.4 + - - -
188C HIS* 5.2 6.9 - - - -
191C PHE* 4.0 24.7 - + - -
197C PRO* 3.4 37.0 - - + +
228C LEU* 3.2 27.4 + - + +
229C CYS 2.9 3.4 + - - -
231C GLU* 1.3 104.3 + - + +
233C GLY* 1.3 59.3 + - - +
234C ILE* 3.8 14.4 - - + -
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Residues in contact with GLY 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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126C THR* 3.5 18.4 - - - +
128C ARG* 3.5 14.5 + - - -
229C CYS 2.9 5.5 + - - -
230C ASP* 3.5 9.0 + - - -
231C GLU 3.6 0.4 - - - -
232C HIS* 1.3 79.8 - - - +
234C ILE* 1.3 62.0 + - - +
235C MET* 3.5 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