Contacts of the helix formed by residues 184 - 200 (chain B) in PDB entry 5L5E
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 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ALA* 3.7 4.9 - - - -
40B SER* 3.3 23.1 - - - +
41B ASP* 3.4 18.6 - - + +
182B ASP* 3.7 13.9 - - - +
183B MET* 1.3 76.9 - - - +
185B VAL* 1.3 61.6 + - - +
186B ASP* 3.4 5.4 - - + +
187B ASP* 3.2 19.5 + - - +
188B ALA* 2.9 27.2 + - - +
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 4.2 3.8 - - + -
41B ASP* 3.1 21.0 + - - +
42B GLY* 3.4 45.5 - - - +
43B ILE 4.4 0.9 - - - +
44B VAL* 4.4 7.9 - - + -
184B LYS* 1.3 74.3 - - - +
186B ASP* 1.3 55.0 + - - +
188B ALA* 3.0 6.0 + - - +
189B ILE* 2.8 43.8 + - + +
214B THR* 4.7 5.2 - - + -
216B ARG* 3.4 46.2 - - + +
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Residues in contact with ASP 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASP* 5.4 0.3 - - - +
184B LYS* 3.4 3.6 - - + +
185B VAL* 1.3 75.0 + - - +
187B ASP* 1.3 65.2 - - - +
189B ILE* 3.6 12.2 - - - +
190B GLU* 3.4 19.9 + - - +
216B ARG* 2.8 34.7 + - - -
240B LYS* 4.9 19.3 + - - +
241B THR* 5.7 0.9 - - - +
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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
----------------------------------------------------------
180B LYS* 4.4 13.8 + - - +
183B MET* 3.6 25.4 - - + +
184B LYS* 3.2 30.3 + - - +
185B VAL 3.2 0.4 - - - -
186B ASP* 1.3 79.4 - - - +
188B ALA* 1.3 58.6 + - - +
190B GLU* 3.2 11.6 + - - +
191B LEU* 3.0 22.9 + - - +
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Residues in contact with ALA 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.6 29.4 - - + +
39B ALA* 4.5 8.1 - - + -
44B VAL* 3.7 14.1 - - + +
183B MET* 4.0 13.4 - - - +
184B LYS 2.9 13.5 + - - +
185B VAL* 3.0 10.3 + - - +
187B ASP* 1.3 74.7 - - - +
189B ILE* 1.3 65.4 + - - +
191B LEU* 3.2 2.6 + - - -
192B ALA* 2.9 26.5 + - - +
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Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.7 17.7 - - + +
185B VAL* 2.8 37.8 + - + +
186B ASP* 3.6 11.4 - - - +
188B ALA* 1.3 73.8 - - - +
190B GLU* 1.3 63.5 + - - +
192B ALA* 3.5 2.4 + - - +
193B LEU* 3.2 29.1 + - + +
212B PHE* 3.8 24.9 - - + -
214B THR* 4.1 11.0 - - + -
216B ARG* 3.9 13.7 - - - +
229B PHE* 5.0 4.7 - - + -
237B ILE* 3.7 38.1 - - + -
240B LYS* 5.9 0.7 - - - -
241B THR* 4.7 3.1 - - + -
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ASP 3.4 10.4 + - - +
187B ASP* 3.2 14.9 + - - +
189B ILE* 1.3 77.9 - - - +
191B LEU* 1.3 59.6 + - - +
193B LEU* 3.5 2.3 + - - +
194B LYS* 3.0 68.1 + - + +
240B LYS* 5.6 2.9 + - - -
241B THR* 4.0 30.9 - - + +
243B ILE* 5.4 0.2 - - - +
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Residues in contact with LEU 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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37B ILE* 3.9 15.9 - - + -
174B LEU* 4.5 6.1 - - + +
175B LEU* 4.1 13.5 - - + +
178B ASP* 4.1 25.1 - - + +
179B TYR* 4.2 28.3 - - + +
183B MET* 3.8 25.8 - - + -
187B ASP 3.0 13.2 + - - +
188B ALA 3.2 7.6 + - - +
190B GLU* 1.3 76.0 - - - +
192B ALA* 1.3 54.6 + - - +
194B LYS* 3.4 8.1 + - + +
195B THR* 2.6 51.7 + - - +
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 4.0 11.4 - - + +
37B ILE* 3.5 16.7 - - + +
44B VAL* 4.1 12.8 - - + -
46B ALA* 4.0 21.1 - - + -
188B ALA 2.9 17.2 + - - +
189B ILE 3.7 4.3 - - - +
191B LEU* 1.3 77.4 - - - +
193B LEU* 1.3 61.9 + - - +
195B THR* 3.5 4.2 + - - -
196B LEU* 3.2 29.9 + - - +
212B PHE* 4.6 1.1 - - + -
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ILE* 3.2 28.3 + - + +
190B GLU 4.1 2.5 - - - +
192B ALA* 1.3 77.5 - - - +
194B LYS* 1.3 60.5 + - - +
196B LEU* 3.4 10.1 + - + +
197B SER* 2.9 30.0 + - - -
205B LEU* 3.8 6.3 - - + +
210B LEU* 4.0 15.3 - - + -
212B PHE* 3.6 26.5 - - + -
234B ILE* 5.8 0.2 - - + -
237B ILE* 4.0 19.1 - - + +
238B LEU* 3.8 29.6 - - + -
241B THR* 4.0 16.8 - - + +
243B ILE* 3.6 15.0 - - + +
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Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ASP* 6.1 0.9 - - - +
190B GLU* 3.0 52.7 + - + +
191B LEU* 3.8 9.6 - - + +
193B LEU* 1.3 75.6 - - - +
195B THR* 1.3 62.9 + - - +
197B SER* 3.4 7.5 + - - -
198B LYS* 3.2 32.8 + - + +
241B THR* 3.6 21.8 + - - -
242B GLY 5.6 0.6 + - - -
243B ILE* 4.6 12.9 - - + +
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Residues in contact with THR 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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35B ILE* 3.7 20.0 - - + -
171B ALA* 3.8 34.3 - - + +
174B LEU* 4.1 19.4 - - + +
175B LEU* 3.7 8.8 - - + +
191B LEU* 2.6 37.9 + - - +
192B ALA 3.7 5.2 - - - -
194B LYS* 1.3 74.3 - - - +
196B LEU* 1.3 57.8 + - - +
198B LYS* 3.4 2.5 + - - +
199B THR* 2.7 33.4 + - - +
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR* 4.0 35.2 - - + +
35B ILE* 3.7 21.1 - - + -
46B ALA* 3.7 29.8 - - + -
47B ALA* 4.1 6.7 - - - +
48B GLU* 4.7 9.9 - - + +
192B ALA 3.2 15.7 + - - +
193B LEU* 3.8 8.1 - - + +
195B THR* 1.3 78.9 - - - +
197B SER* 1.3 58.5 + - - +
199B THR* 3.5 3.6 - - - +
200B THR* 2.9 36.3 + - - -
205B LEU* 4.1 13.0 - - + -
210B LEU* 3.8 24.5 - - + -
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Residues in contact with SER 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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193B LEU 2.9 18.7 + - - -
194B LYS* 3.5 9.4 - - - -
195B THR 3.3 0.2 - - - -
196B LEU* 1.3 76.5 - - - +
198B LYS* 1.3 61.0 + - - +
200B THR* 3.4 17.8 - - - +
205B LEU* 3.8 19.2 + - - +
243B ILE* 4.0 22.4 - - - +
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Residues in contact with LYS 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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174B LEU* 3.7 37.5 - - + +
194B LYS* 3.2 20.4 + - + +
195B THR* 3.9 3.8 - - - +
196B LEU 3.2 0.6 - - - -
197B SER* 1.3 80.9 - - - +
199B THR* 1.3 61.2 + - - +
200B THR 3.5 3.8 + - - +
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Residues in contact with THR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR* 4.9 7.4 + - - +
35B ILE* 5.3 0.2 - - - +
48B GLU* 5.7 0.3 + - - -
167B ASN* 2.9 39.6 + - - +
170B ALA* 4.2 11.2 - - + -
171B ALA* 3.8 37.9 - - + +
174B LEU* 3.9 12.8 - - + -
195B THR* 2.7 23.0 + - - +
196B LEU* 3.4 13.9 + - - +
198B LYS* 1.3 75.1 - - - +
200B THR* 1.3 66.8 + - - +
201B ASP* 4.1 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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33B THR* 6.0 0.4 - - - -
48B GLU* 2.6 37.7 + - - -
167B ASN* 5.0 0.7 - - - +
196B LEU 2.9 15.7 + - - +
197B SER* 3.4 24.7 - - - +
198B LYS 4.4 3.1 - - - +
199B THR* 1.3 80.8 + - - +
201B ASP* 1.3 61.4 + - - +
202B SER* 3.1 29.0 + - - +
203B SER 5.6 0.4 - - - +
204B ALA* 5.1 1.3 - - - -
205B LEU* 4.3 17.1 - - + +
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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
------------------------------------------------------------
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