Contacts of the helix formed by residues 218 - 233 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172D PRO* 5.5 1.0 - - - +
180D GLU* 2.5 31.3 + - - -
216D ALA 3.9 1.2 + - - -
217D SER* 1.3 77.9 + - - +
219D PRO* 1.3 74.5 - - - +
220D ALA* 3.5 5.8 + - - +
221D PHE* 2.9 19.0 + - - +
222D MET* 2.9 21.3 + - - +
257D MET* 4.0 1.8 - - - -
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Residues in contact with PRO 219 (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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217D SER 4.3 2.5 - - - +
218D SER* 1.3 87.2 - - - +
220D ALA* 1.3 52.1 + - - +
222D MET* 3.3 1.3 + - + -
223D GLN* 2.8 49.3 + - - +
256D GLN 3.6 19.3 - - - +
257D MET* 3.5 29.0 - - - +
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Residues in contact with ALA 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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180D GLU* 4.1 9.6 - - - +
218D SER* 3.1 7.8 - - - +
219D PRO* 1.3 81.3 - - + +
221D PHE* 1.3 61.3 + - - +
223D GLN* 3.4 13.9 + - - +
224D ARG* 3.1 30.2 + - - +
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Residues in contact with PHE 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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134D PHE* 4.1 15.7 - + - -
172D PRO* 3.6 31.4 - - + -
180D GLU* 3.8 30.7 + - + +
183D ALA* 3.6 21.8 - - + -
184D ILE* 3.3 33.2 - - + -
187D ILE* 5.0 1.6 - - + -
205D ILE* 4.0 22.0 - - + -
217D SER* 3.5 17.9 - - - +
218D SER* 2.9 21.2 + - - +
220D ALA* 1.3 73.8 - - - +
222D MET* 1.3 68.0 + - - +
224D ARG* 3.0 8.6 + - - +
225D LEU* 3.0 29.2 + - + +
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Residues in contact with MET 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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205D ILE* 4.1 18.6 - - + -
207D PRO* 4.0 15.7 - - + -
217D SER* 3.5 24.7 - - - +
218D SER 2.9 15.1 + - - +
219D PRO 3.7 4.3 - - - +
221D PHE* 1.3 78.6 - - - +
223D GLN* 1.3 57.5 + - - +
225D LEU* 3.3 23.7 + - - +
226D ARG* 2.9 29.3 + - - +
236D LEU* 4.6 4.8 - - + +
254D MET* 3.7 29.4 - - + -
257D MET* 3.6 21.8 - - + -
259D VAL* 3.6 18.8 - - + -
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Residues in contact with GLN 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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219D PRO* 2.8 32.7 + - - +
220D ALA* 3.6 11.1 - - - +
221D PHE 3.1 0.2 - - - -
222D MET* 1.3 75.8 - - - +
224D ARG* 1.3 64.2 + - + +
226D ARG* 3.4 2.6 + - - +
227D ALA* 3.1 22.2 + - - +
257D MET 3.0 21.3 + - - +
258D GLY* 4.2 7.2 - - - +
259D VAL* 3.6 28.6 - - + +
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Residues in contact with ARG 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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180D GLU* 3.9 14.1 + - - +
181D ASP* 2.7 43.4 + - - +
184D ILE* 3.7 31.7 - - + +
220D ALA* 3.1 18.4 + - - +
221D PHE* 3.0 11.2 + - - +
223D GLN* 1.3 77.2 - - + +
225D LEU* 1.3 57.7 + - - +
227D ALA* 3.4 6.8 + - - +
228D LEU* 2.9 28.9 + - - +
1005D SO4 2.7 46.0 + - - +
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Residues in contact with LEU 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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134D PHE* 4.3 8.7 - - + -
184D ILE* 4.3 5.8 - - + +
187D ILE* 3.6 31.9 - - + -
203D ILE* 3.9 23.3 - - + -
205D ILE* 3.9 28.0 - - + -
221D PHE* 3.0 19.8 + - + +
222D MET* 3.6 16.2 - - - +
223D GLN 3.2 0.2 - - - -
224D ARG* 1.3 76.1 - - - +
226D ARG* 1.3 60.3 + - - +
228D LEU* 3.6 6.2 - - + +
229D CYS* 2.9 34.9 + - - -
236D LEU* 3.8 26.5 - - + -
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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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222D MET 2.9 15.8 + - - +
223D GLN 3.6 6.1 - - - +
224D ARG 3.2 0.2 - - - -
225D LEU* 1.3 75.6 - - - +
227D ALA* 1.3 59.6 + - - +
229D CYS* 3.3 20.2 + - - +
230D ASP* 2.8 62.8 + - - +
234D ILE 3.8 4.0 + - - -
235D MET* 5.5 1.2 - - - +
236D LEU* 3.7 22.8 - - + +
259D VAL* 4.0 26.9 - - + -
260D ALA 3.1 29.8 + - - +
261D PRO 3.9 0.2 - - - -
262D ASP* 2.7 42.1 + - - +
282D ARG* 4.6 5.4 - - - +
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Residues in contact with ALA 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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223D GLN 3.1 16.1 + - - +
224D ARG* 3.7 7.2 - - - +
226D ARG* 1.3 76.7 - - - +
228D LEU* 1.3 64.0 + - - +
230D ASP* 3.3 9.4 + - - +
231D GLU* 3.0 26.8 + - - +
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Residues in contact with LEU 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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184D ILE* 4.1 19.1 - - + -
187D ILE* 4.0 23.3 - - + -
188D HIS* 3.9 33.0 - - + +
191D PHE* 3.7 28.9 - - + -
203D ILE* 4.2 17.9 - - + -
224D ARG 2.9 16.6 + - - +
225D LEU* 3.6 6.5 - - + +
227D ALA* 1.3 78.6 - - - +
229D CYS* 1.3 63.8 + - - +
231D GLU* 3.4 8.6 + - - +
232D HIS* 3.3 25.2 + - + +
234D ILE* 4.6 1.3 - - + -
1005D SO4 5.5 3.1 - - - +
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Residues in contact with CYS 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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203D ILE* 3.8 27.8 - - - -
225D LEU* 2.9 25.0 + - - +
226D ARG* 3.5 14.8 - - - +
228D LEU* 1.3 76.5 - - - +
230D ASP* 1.3 64.9 + - - +
232D HIS 3.1 1.7 + - - -
233D GLY* 2.9 21.5 + - - -
234D ILE* 3.0 40.8 + - - +
236D LEU* 4.0 26.2 - - - -
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Residues in contact with ASP 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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226D ARG* 2.8 57.5 + - - +
227D ALA* 3.6 8.7 - - - +
229D CYS* 1.3 77.1 - - - +
231D GLU* 1.3 63.3 + - - +
232D HIS 3.3 0.9 + - - -
233D GLY* 3.5 8.9 + - - -
282D ARG* 5.6 1.6 + - - -
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Residues in contact with GLU 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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188D HIS* 5.7 3.6 - - - -
227D ALA 3.0 17.2 + - - +
228D LEU* 3.7 9.6 - - - +
229D CYS 3.2 0.4 - - - -
230D ASP* 1.3 78.6 - - - +
232D HIS* 1.3 85.0 + - + +
233D GLY 3.6 0.2 - - - -
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Residues in contact with HIS 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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128D ARG* 2.9 27.4 + - - -
188D HIS* 5.1 5.9 - - - -
191D PHE* 3.8 26.9 - + - -
197D PRO* 3.5 30.4 - - + +
198D GLU* 5.6 0.2 - - - -
228D LEU* 3.3 25.5 + - + +
229D CYS 3.1 2.8 + - - -
231D GLU* 1.3 104.1 + - + +
233D GLY* 1.3 59.8 + - - +
234D ILE* 3.2 18.8 - - + -
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Residues in contact with GLY 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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126D THR* 3.6 17.3 - - - +
128D ARG* 3.3 14.4 + - - -
229D CYS 2.9 5.6 + - - -
230D ASP* 3.5 8.2 + - - -
231D GLU 3.6 0.6 - - - -
232D HIS* 1.3 78.9 - - - +
234D ILE* 1.3 60.9 + - - +
235D MET* 3.7 9.9 - - - +
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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