Contacts of the helix formed by residues 218 - 232 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172B PRO* 5.5 0.8 - - - +
180B GLU* 2.7 29.1 + - - -
216B ALA 3.8 1.6 + - - -
217B SER* 1.3 78.3 + - - +
219B PRO* 1.3 75.2 - - - +
220B ALA* 3.4 7.0 + - - +
221B PHE* 3.0 16.4 + - - +
222B MET* 3.0 19.9 + - - +
257B MET* 4.0 1.3 - - - -
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Residues in contact with PRO 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B SER 4.3 2.5 - - - +
218B SER* 1.3 88.4 - - - +
220B ALA* 1.3 56.3 + - - +
222B MET* 3.2 1.6 + - - +
223B GLN* 2.9 50.0 + - - +
256B GLN 3.4 20.0 - - - +
257B MET* 3.5 24.2 - - + +
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B GLU* 4.0 9.6 - - - +
218B SER* 3.1 9.3 + - - +
219B PRO* 1.3 82.5 - - - +
221B PHE* 1.3 60.9 + - - +
223B GLN* 3.2 14.2 + - - +
224B ARG* 3.1 28.2 + - - +
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Residues in contact with PHE 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B PHE* 4.1 15.7 - + - -
172B PRO* 3.9 25.8 - - + -
180B GLU* 3.7 28.4 + - + -
183B ALA* 3.4 22.9 - - + -
184B ILE* 3.4 35.0 - - + -
187B ILE* 5.2 0.4 - - + -
205B ILE* 3.7 25.6 - - + -
217B SER* 3.3 18.4 - - - +
218B SER* 3.0 20.8 + - - +
220B ALA* 1.3 76.3 - - - +
222B MET* 1.3 63.8 + - - +
224B ARG* 3.0 8.9 + - - +
225B LEU* 2.9 33.9 + - + +
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Residues in contact with MET 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B ILE* 4.1 19.3 - - + -
207B PRO* 4.0 15.7 - - + -
217B SER* 3.4 30.1 - - - +
218B SER 3.0 15.5 + - - +
219B PRO 3.6 4.3 - - - +
221B PHE* 1.3 80.1 - - - +
223B GLN* 1.3 56.9 + - - +
225B LEU* 3.4 24.3 + - - +
226B ARG* 2.9 27.0 + - - +
236B LEU* 4.5 5.0 - - + +
254B MET* 3.8 28.7 - - + +
257B MET* 3.7 22.7 - - + -
259B VAL* 3.6 19.5 - - + +
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Residues in contact with GLN 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B PRO* 2.9 30.7 + - - +
220B ALA* 3.5 10.2 - - - +
222B MET* 1.3 76.7 - - - +
224B ARG* 1.3 64.6 + - + +
226B ARG* 3.6 1.7 - - - +
227B ALA* 3.0 24.3 + - - +
257B MET 2.9 23.1 + - - +
258B GLY* 4.2 6.3 - - - +
259B VAL* 3.5 28.0 - - + -
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Residues in contact with ARG 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B GLU* 4.0 14.5 + - - +
181B ASP* 2.7 42.9 + - - +
184B ILE* 3.7 33.6 - - + +
220B ALA* 3.1 18.2 + - - +
221B PHE* 3.0 11.7 + - - +
223B GLN* 1.3 75.9 - - + +
225B LEU* 1.3 58.8 + - - +
227B ALA* 3.3 7.2 + - - +
228B LEU* 2.9 29.8 + - - +
1003B SO4 3.0 44.6 + - - +
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B PHE* 4.3 4.9 - - + -
184B ILE* 4.2 5.5 - - + +
187B ILE* 3.7 29.6 - - + -
203B ILE* 4.0 22.4 - - + -
205B ILE* 3.7 31.4 - - + -
221B PHE* 2.9 25.4 + - + +
222B MET* 3.6 15.0 - - - +
224B ARG* 1.3 77.7 - - - +
226B ARG* 1.3 57.0 + - - +
228B LEU* 3.2 7.3 + - + +
229B CYS* 2.9 33.8 + - - -
236B LEU* 4.0 25.4 - - + -
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Residues in contact with ARG 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B MET 2.9 17.8 + - - +
223B GLN 3.6 4.7 - - - +
224B ARG 3.3 0.2 - - - -
225B LEU* 1.3 75.3 - - - +
227B ALA* 1.3 57.6 + - - +
229B CYS* 3.3 21.3 + - - +
230B ASP* 2.9 61.2 + - - +
234B ILE 3.8 3.2 + - - -
235B MET* 5.9 0.2 - - - +
236B LEU* 3.7 21.2 - - + +
259B VAL* 4.1 26.5 - - + -
260B ALA 3.0 30.2 + - - +
261B PRO 3.8 0.4 - - - -
262B ASP* 2.8 46.9 + - - +
282B ARG* 4.7 5.5 - - - +
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Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B GLN 3.0 17.0 + - - +
224B ARG* 3.7 6.5 - - - +
226B ARG* 1.3 77.9 - - - +
228B LEU* 1.3 62.1 + - - +
230B ASP* 3.6 10.0 - - - +
231B GLU* 3.1 25.6 + - - +
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B ILE* 4.4 12.1 - - + -
187B ILE* 4.0 26.7 - - + -
188B HIS* 3.9 32.1 - - + +
191B PHE* 3.9 23.1 - - + -
203B ILE* 3.8 27.4 - - + -
224B ARG 2.9 16.6 + - - +
225B LEU* 3.2 6.0 + - + +
227B ALA* 1.3 75.8 - - - +
229B CYS* 1.3 69.5 + - - +
231B GLU* 3.5 7.0 + - - +
232B HIS* 3.2 32.7 + - + +
234B ILE* 4.7 0.9 - - + -
1003B SO4 4.8 4.3 - - - +
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Residues in contact with CYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B ILE* 3.8 26.2 - - - -
225B LEU* 2.9 20.7 + - - +
226B ARG* 3.3 15.2 + - - +
228B LEU* 1.3 79.0 - - - +
230B ASP* 1.3 63.7 + - - +
232B HIS 3.0 1.9 + - - -
233B GLY* 3.0 4.5 + - - -
234B ILE* 3.0 57.9 + - - +
236B LEU* 3.9 27.1 - - - -
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Residues in contact with ASP 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ARG* 2.9 57.0 + - - +
227B ALA* 3.6 9.4 - - - +
229B CYS* 1.3 77.0 - - - +
231B GLU* 1.3 63.6 - - - +
232B HIS 3.2 0.5 + - - -
233B GLY* 3.4 9.0 + - - +
282B ARG* 5.4 3.8 + - - -
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ALA 3.1 16.7 + - - +
228B LEU* 3.7 9.2 - - - +
229B CYS 3.2 0.2 - - - -
230B ASP* 1.3 77.2 - - - +
232B HIS* 1.3 85.0 + - + +
233B GLY 3.6 0.2 - - - -
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Residues in contact with HIS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ARG* 2.9 29.8 + - - -
188B HIS* 5.4 5.3 + - - -
191B PHE* 4.0 24.5 - + - -
197B PRO* 3.5 31.8 - - + +
228B LEU* 3.2 26.7 + - + +
229B CYS 3.0 3.4 + - - -
231B GLU* 1.3 107.9 + - + +
233B GLY* 1.3 60.4 + - - +
234B ILE* 3.0 19.1 - - + -
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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