Contacts of the helix formed by residues 186 - 203 (chain B) in PDB entry 3E0D
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 LEU 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LEU* 4.0 21.1 - - + -
183B ASN* 4.6 1.0 - - - +
184B HIS* 2.8 19.9 + - + +
185B GLY* 1.3 74.7 - - - +
187B PRO* 1.4 73.1 - - + +
188B GLU* 3.2 12.1 - - - +
189B GLN* 3.1 49.6 + - - +
190B LYS* 3.6 4.5 + - - +
245B PRO* 3.6 43.5 - - + +
246B CYS* 4.6 7.4 - - + -
249B PHE* 5.0 2.7 - - + -
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Residues in contact with PRO 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 GLY 3.6 4.7 - - - +
186B LEU* 1.4 86.5 - - + +
188B GLU* 1.3 81.5 + - + +
189B GLN 3.2 0.2 - - - -
190B LYS* 3.5 22.4 + - + +
191B LYS* 3.7 7.1 + - - +
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 3.9 21.8 - - + -
155B LEU* 3.8 31.6 - - + +
186B LEU* 3.7 13.5 - - - +
187B PRO* 1.3 96.9 - - + +
189B GLN* 1.3 64.8 + - - +
191B LYS* 3.3 5.4 + - - +
192B VAL* 3.0 28.4 + - - +
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Residues in contact with GLN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 4.2 22.6 - - + +
182B GLN* 3.6 30.3 + - + +
183B ASN* 4.0 11.0 - - - +
184B HIS* 3.0 57.6 + - - +
186B LEU* 3.1 31.7 + - - +
188B GLU* 1.3 79.8 - - - +
190B LYS* 1.3 55.7 + - - +
192B VAL* 4.6 5.4 - - + -
193B ASN* 2.9 40.0 + - - +
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Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ASN* 5.3 1.0 + - - -
186B LEU 3.6 5.2 + - - +
187B PRO* 3.5 16.3 + - + +
188B GLU 3.2 0.2 - - - -
189B GLN* 1.3 78.5 - - - +
191B LYS* 1.3 62.5 + - + +
193B ASN* 4.3 1.6 - - - +
194B GLN* 3.2 35.9 + - - +
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Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 3.7 17.7 + - + +
155B LEU* 3.5 31.3 + - + +
157B ASP* 2.7 30.1 + - - -
159B LEU* 6.4 0.9 - - - -
187B PRO 3.7 6.2 + - - +
188B GLU* 3.3 9.0 + - - +
190B LYS* 1.3 80.1 - - + +
192B VAL* 1.3 65.8 + - + +
194B GLN* 3.7 12.2 + - - +
195B VAL* 3.4 25.7 + - + +
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 4.0 13.5 - - + -
151B PRO* 3.5 46.2 - - + +
154B ILE* 4.1 12.0 - - + +
155B LEU* 3.9 17.3 - - + -
188B GLU 3.0 20.8 + - - +
189B GLN* 4.1 6.1 - - + +
191B LYS* 1.3 77.0 - - + +
193B ASN* 1.3 56.2 + - - +
195B VAL* 3.1 4.9 + - - +
196B LEU* 2.7 52.1 + - + +
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Residues in contact with ASN 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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180B GLU 4.5 0.2 - - - +
181B ILE* 4.0 23.4 - - - +
182B GLN 3.0 29.5 + - - +
183B ASN* 4.4 7.7 + - - +
189B GLN* 2.9 27.6 + - - +
190B LYS* 4.3 2.4 - - - +
192B VAL* 1.3 78.9 - - - +
194B GLN* 1.3 55.9 + - - +
196B LEU* 3.5 21.4 - - - +
197B LYS* 2.7 37.0 + - - +
266B TRP* 3.8 23.5 - - + -
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Residues in contact with GLN 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LYS* 3.2 29.5 + - - +
191B LYS* 3.8 12.5 - - - +
193B ASN* 1.3 78.7 - - - +
195B VAL* 1.3 69.5 + - - +
197B LYS* 3.5 21.1 - - - +
198B GLU* 3.4 31.1 + - + +
266B TRP* 5.7 0.4 - - - -
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 3.8 41.3 - - + -
159B LEU* 3.8 22.0 - - + -
191B LYS* 3.4 15.2 + - + +
192B VAL 3.1 2.5 + - - +
194B GLN* 1.3 83.6 - - - +
196B LEU* 1.3 65.7 + - - +
197B LYS 3.2 0.2 - - - -
198B GLU* 3.2 21.7 + - + +
199B PHE* 3.1 35.3 + - + -
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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
----------------------------------------------------------
143B SER* 4.1 12.1 - - - +
144B GLY 5.5 1.1 - - - +
150B ILE* 4.0 17.5 - - + -
151B PRO* 4.9 5.4 - - + -
154B ILE* 3.9 16.6 - - + -
179B ILE* 3.6 27.9 - - + +
180B GLU 3.3 26.5 - - - +
181B ILE* 4.6 2.9 - - + -
192B VAL* 2.7 42.0 + - + +
193B ASN* 3.5 16.4 - - - +
195B VAL* 1.3 69.1 - - - +
197B LYS* 1.3 60.1 - - - +
199B PHE* 3.1 9.4 + - + +
200B ALA* 2.8 29.5 + - - +
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Residues in contact with LYS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ILE* 5.2 0.4 - - - +
193B ASN 2.7 18.6 + - - +
194B GLN* 3.5 21.2 - - - +
196B LEU* 1.3 74.0 - - - +
198B GLU* 1.3 60.6 + - + +
200B ALA* 3.3 2.8 + - - +
201B ARG* 3.1 66.1 + - - +
207B MET* 4.2 17.5 - - + -
265B GLU* 3.1 31.4 + - - +
266B TRP* 3.5 30.5 - - + -
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Residues in contact with GLU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLN* 3.4 25.6 - - + +
195B VAL* 3.2 27.3 + - + +
196B LEU 3.2 0.4 - - - -
197B LYS* 1.3 75.6 - - + +
199B PHE* 1.3 63.1 + - + +
201B ARG* 3.3 6.7 + - - +
202B LYS* 3.0 31.1 + - - +
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Residues in contact with PHE 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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150B ILE* 4.3 16.4 - - + -
154B ILE* 4.4 0.7 - - + -
159B LEU* 4.1 11.0 - - + -
162B ALA* 4.1 21.3 - - + -
163B GLU* 3.7 48.5 - - + -
166B LEU* 3.8 25.7 - - + +
179B ILE* 4.7 7.4 - - + -
195B VAL* 3.1 35.1 + - + -
196B LEU* 3.1 13.9 + - + +
198B GLU* 1.3 79.2 - - + +
200B ALA* 1.3 63.3 + - - +
202B LYS* 4.5 7.2 - - + -
203B TYR* 3.1 36.0 + + - +
205B LEU* 4.8 0.7 - - - +
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Residues in contact with ALA 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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179B ILE* 3.6 23.7 - - + +
196B LEU 2.8 16.4 + - - +
197B LYS 3.5 5.8 - - - +
198B GLU 3.3 0.2 - - - -
199B PHE* 1.3 77.0 - - - +
201B ARG* 1.3 58.1 + - + +
204B GLY* 3.4 4.3 + - - -
205B LEU* 2.8 32.1 + - + -
206B GLY 4.1 5.9 + - - +
207B MET* 3.7 28.0 - - + +
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Residues in contact with ARG 201 (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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197B LYS* 3.1 58.3 + - + +
198B GLU* 3.9 5.8 - - - +
199B PHE 3.1 0.4 - - - -
200B ALA* 1.3 81.4 - - + +
202B LYS* 1.3 62.0 + - - +
203B TYR 3.4 0.4 - - - -
204B GLY* 3.8 7.5 + - - +
207B MET* 5.7 3.1 - - - +
265B GLU 5.0 4.6 + - - -
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Residues in contact with LYS 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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163B GLU* 2.7 32.0 + - - +
198B GLU 3.0 17.6 + - - +
199B PHE* 3.3 7.6 + - + +
201B ARG* 1.3 78.4 - - - +
203B TYR* 1.3 80.5 + - + +
204B GLY 3.4 0.2 - - - -
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Residues in contact with TYR 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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163B GLU* 2.5 39.9 + - + +
166B LEU* 3.6 23.6 - - + -
167B ASN* 3.2 31.0 + - - -
170B LEU* 3.9 15.0 - - + -
199B PHE* 3.1 17.3 + + - +
202B LYS* 1.3 97.9 + - + +
204B GLY* 1.3 64.9 + - - +
205B LEU* 3.3 25.8 - - + +
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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