Contacts of the helix formed by residues 185 - 202 (chain B) in PDB entry 3SDI
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 LYS 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B ALA* 3.6 3.1 - - - -
43B SER* 4.7 0.7 - - - +
44B ASP* 3.5 27.1 - - - +
183B ASP 3.8 0.6 + - - +
184B MET* 1.3 76.1 - - - +
186B VAL* 1.3 82.3 + - - +
187B ASP* 3.2 41.9 + - + +
188B ASP* 3.1 24.0 + - - +
189B ALA* 3.1 17.8 + - - +
216B ARG* 3.5 10.8 - - - +
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Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 3.5 8.5 - - + +
44B ASP* 3.3 20.0 + - - +
45B GLY* 3.3 41.3 - - - +
46B ILE 4.8 2.5 - - - +
47B VAL* 4.3 17.0 - - + -
185B LYS* 1.3 74.4 - - - +
187B ASP* 1.3 52.6 + - - +
189B ALA* 2.9 5.5 + - - +
190B ILE* 2.8 40.0 + - + +
214B THR* 4.5 7.6 - - + -
216B ARG* 3.9 32.5 - - + +
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Residues in contact with ASP 187 (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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185B LYS* 3.2 29.5 + - + +
186B VAL* 1.3 74.7 - - - +
188B ASP* 1.3 66.1 + - - +
190B ILE* 3.4 14.4 + - - +
191B GLU* 3.2 19.9 + - - +
216B ARG* 2.7 31.8 + - - -
236B THR* 5.6 1.2 - - - +
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Residues in contact with ASP 188 (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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181B LYS* 4.9 9.1 + - - +
184B MET* 3.5 19.2 - - + +
185B LYS* 3.1 32.1 + - - +
187B ASP* 1.3 80.6 - - - +
189B ALA* 1.3 58.5 + - - +
191B GLU* 3.3 13.5 + - - +
192B LEU* 2.9 26.5 + - - +
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Residues in contact with ALA 189 (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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40B ILE* 3.4 32.5 - - + +
42B ALA* 4.3 10.5 - - + -
47B VAL* 3.9 13.4 - - + +
184B MET* 3.4 13.2 - - + +
185B LYS 3.1 10.5 + - - +
186B VAL* 2.9 12.9 + - - +
188B ASP* 1.3 74.5 - - - +
190B ILE* 1.3 64.3 + - - +
192B LEU* 4.2 2.7 - - - -
193B ALA* 3.0 22.0 + - - +
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Residues in contact with ILE 190 (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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47B VAL* 3.8 18.8 - - + -
186B VAL* 2.8 25.2 + - + +
187B ASP* 3.5 17.9 - - - +
188B ASP 3.3 0.2 - - - -
189B ALA* 1.3 73.2 - - - +
191B GLU* 1.3 65.1 + - - +
193B ALA* 3.3 2.3 + - - +
194B LEU* 3.2 34.0 + - + +
212B PHE* 3.6 27.8 - - + -
214B THR* 4.1 17.3 - - + -
216B ARG* 4.8 9.9 - - - +
224B PHE* 4.7 8.7 - - + -
232B ILE* 3.9 16.6 - - + -
236B THR* 4.8 4.3 - - + -
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Residues in contact with GLU 191 (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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187B ASP 3.2 10.6 + - - +
188B ASP* 3.3 15.6 - - - +
190B ILE* 1.3 80.4 - - - +
192B LEU* 1.3 62.5 + - - +
194B LEU* 3.4 2.0 + - - +
195B LYS* 3.0 58.0 + - + +
236B THR* 3.9 31.7 - - + +
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Residues in contact with LEU 192 (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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40B ILE* 3.8 13.7 - - + -
175B LEU 4.6 2.0 - - - +
176B LEU* 4.0 18.6 - - + -
179B ASP* 4.2 24.9 - - + +
180B TYR* 4.1 24.7 - - + +
184B MET* 3.8 27.8 - - + -
188B ASP 2.9 17.3 + - - +
189B ALA* 3.7 5.8 - - - +
190B ILE 3.3 0.4 - - - -
191B GLU* 1.3 77.7 - - - +
193B ALA* 1.3 57.1 + - - +
195B LYS* 3.7 6.6 - - + +
196B THR* 2.5 46.1 + - - +
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Residues in contact with ALA 193 (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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38B ILE* 3.9 17.6 - - + +
40B ILE* 3.4 16.7 - - + +
47B VAL* 4.0 18.6 - - + -
49B ALA* 4.2 10.3 - - + -
189B ALA 3.0 17.2 + - - +
190B ILE 3.7 3.6 - - - +
192B LEU* 1.3 76.2 - - - +
194B LEU* 1.3 63.8 + - - +
196B THR* 3.3 5.5 + - - -
197B LEU* 3.1 28.8 + - - +
212B PHE* 4.8 0.7 - - + -
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Residues in contact with LEU 194 (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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190B ILE* 3.2 24.4 + - + +
191B GLU 4.0 2.5 - - - +
193B ALA* 1.3 77.3 - - - +
195B LYS* 1.3 64.5 + - - +
197B LEU* 3.4 5.1 + - + -
198B SER* 2.9 26.4 + - - -
205B LEU* 3.8 5.9 - - + +
210B LEU* 3.8 22.4 - - + -
212B PHE* 3.6 23.6 - - + -
229B ILE* 5.6 2.2 - - + -
232B ILE* 3.6 31.6 - - + +
233B LEU* 3.8 21.8 - - + -
236B THR* 4.0 17.0 - - + +
238B ILE* 4.3 14.3 - - + +
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Residues in contact with LYS 195 (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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191B GLU* 3.0 59.6 + - + +
192B LEU* 3.7 8.5 - - + +
194B LEU* 1.3 75.2 - - - +
196B THR* 1.3 57.6 + - - +
198B SER* 3.3 7.4 + - - -
199B LYS* 3.0 37.8 + - + +
236B THR* 4.5 15.1 + - - +
237B GLY 5.8 1.2 + - - -
238B ILE* 4.7 11.6 - - + +
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Residues in contact with THR 196 (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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38B ILE* 3.9 10.5 - - + -
172B ALA* 3.8 37.2 - - + +
175B LEU* 3.8 20.3 - - + +
176B LEU* 3.8 9.3 - - + +
192B LEU* 2.5 39.9 + - - +
193B ALA 3.7 4.7 - - - -
194B LEU 3.2 0.2 - - - -
195B LYS* 1.3 75.3 - - - +
197B LEU* 1.3 62.1 + - - +
199B LYS* 3.5 5.5 + - - +
200B THR* 3.0 26.7 + - - +
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Residues in contact with LEU 197 (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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36B THR* 3.7 45.3 - - + +
38B ILE* 3.6 12.1 - - + -
49B ALA* 3.7 34.3 - - + +
50B ALA* 4.3 0.4 - - - +
51B GLU* 4.2 16.9 - - + +
193B ALA 3.1 15.6 + - - +
194B LEU* 3.9 3.8 - - + +
196B THR* 1.3 73.4 - - - +
198B SER* 1.3 59.1 + - - +
200B THR* 3.0 6.1 + - - +
202B THR* 2.7 35.9 + - - -
205B LEU* 3.8 15.3 - - + -
210B LEU* 3.8 22.4 - - + -
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Residues in contact with SER 198 (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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194B LEU 2.9 18.9 + - - -
195B LYS* 3.4 9.6 - - - -
197B LEU* 1.3 77.9 - - - +
199B LYS* 1.3 61.0 + - - +
202B THR* 3.1 17.7 + - - +
205B LEU* 3.6 18.8 + - - +
238B ILE* 4.0 26.3 - - - +
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Residues in contact with LYS 199 (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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175B LEU* 4.0 36.4 - - + +
195B LYS* 3.0 23.2 + - + +
196B THR* 3.9 5.6 - - - +
197B LEU 3.2 0.4 - - - -
198B SER* 1.3 77.2 - - - +
200B THR* 1.3 59.9 + - - +
202B THR 5.1 1.0 - - - +
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Residues in contact with THR 200 (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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36B THR* 4.9 10.4 + - - +
51B GLU* 5.2 1.2 + - - -
168B ASN* 3.0 39.3 + - - +
171B ALA* 3.8 21.8 - - + -
172B ALA* 3.9 15.0 - - - +
175B LEU* 3.7 20.6 - - + -
196B THR 3.0 19.3 + - - +
197B LEU* 3.0 10.6 + - - +
199B LYS* 1.3 80.5 - - - +
202B THR* 1.3 68.9 + - - +
203B ASP* 4.4 1.2 - - - +
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Residues in contact with THR 202 (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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51B GLU* 3.1 36.3 - - - +
168B ASN* 5.1 0.4 - - - +
197B LEU 2.7 19.6 + - - -
198B SER* 3.1 17.0 + - - +
199B LYS 3.7 1.8 - - - +
200B THR* 1.3 76.9 - - - +
203B ASP* 1.3 57.7 + - - +
204B SER* 3.1 41.1 + - - +
205B LEU* 4.0 14.9 + - + +
209B ARG* 3.7 2.9 - - - +
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Residues in contact with ASP 203 (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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51B GLU* 4.4 4.2 + - - +
167B ALA* 4.8 6.9 - - - +
168B ASN* 3.3 27.9 + - - +
200B THR 4.7 0.7 - - - +
202B THR* 1.3 75.0 - - - +
204B SER* 1.3 61.1 + - - +
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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