Contacts of the helix formed by residues 189 - 207 (chain B) in PDB entry 3IEU
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 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B LYS* 5.3 7.9 + - - -
187B ASP* 2.7 23.6 + - - -
188B ARG* 1.3 81.6 - - - +
190B GLN* 1.3 60.6 + - - +
191B ARG* 4.0 4.2 + - - +
192B PHE* 3.1 18.9 + - - +
193B MET* 3.0 24.4 + - - +
305B SO4 3.4 24.5 - - - -
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Residues in contact with GLN 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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188B ARG 3.5 3.0 + - - +
189B SER* 1.3 68.9 - - - +
191B ARG* 1.3 66.2 + - - +
193B MET* 3.0 11.3 + - - +
194B ALA* 2.9 22.0 + - - +
221B PHE* 3.8 23.8 - - + -
229B TYR* 3.6 25.9 + - - -
269B PHE* 3.5 37.4 - - + +
305B SO4 3.0 24.0 + - - +
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Residues in contact with ARG 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 4.8 6.0 + - - -
39B LYS* 4.4 40.0 - - - +
189B SER* 4.2 5.6 - - - +
190B GLN* 1.3 81.2 - - - +
192B PHE* 1.3 61.5 + - - +
194B ALA* 3.3 10.4 + - - +
195B SER* 3.4 13.6 + - - +
218B ILE* 3.1 43.5 + - + +
219B GLU 4.5 3.2 + - - -
220B ARG* 4.5 3.0 - - - +
221B PHE* 3.6 49.6 + - + +
305B SO4 3.3 20.3 + - - +
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Residues in contact with PHE 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 30.5 - - + -
185B ILE* 4.2 15.7 - - + -
187B ASP* 3.4 57.7 - - + +
189B SER* 3.1 10.0 + - - +
191B ARG* 1.3 79.7 - - - +
193B MET* 1.3 72.7 + - - +
195B SER* 3.0 11.1 + - - -
196B GLU* 3.0 47.4 + - + -
199B ARG* 4.6 3.4 - - - -
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Residues in contact with MET 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ILE* 4.9 18.4 - - - -
188B ARG* 4.6 10.1 - - - +
189B SER 3.0 14.4 + - - +
190B GLN* 3.0 14.6 + - - +
192B PHE* 1.3 88.4 - - + +
194B ALA* 1.3 61.6 + - - +
196B GLU* 3.4 19.0 + - + -
197B ILE* 3.2 35.8 + - + +
268B MET* 3.6 39.7 - - + +
269B PHE* 4.2 5.4 - - + -
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Residues in contact with ALA 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 GLN 2.9 11.0 + - - +
191B ARG 3.5 10.8 - - - +
192B PHE 3.1 0.2 - - - -
193B MET* 1.3 74.9 - - - +
195B SER* 1.3 66.7 + - - +
197B ILE* 3.0 13.0 + - - +
198B ILE* 3.0 16.3 + - - +
218B ILE* 3.5 20.6 - - + -
221B PHE* 4.4 13.2 - - + -
231B ILE* 4.8 1.1 - - + -
265B MET* 4.2 27.7 - - - +
269B PHE* 4.3 3.3 - - + -
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Residues in contact with SER 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* 3.2 38.4 - - - +
36B THR 5.2 0.3 + - - -
191B ARG* 3.4 6.9 + - - +
192B PHE* 3.0 9.3 + - - -
194B ALA* 1.3 78.6 - - - +
196B GLU* 1.3 63.5 + - - +
198B ILE* 3.0 4.1 + - - +
199B ARG* 2.9 23.7 + - - +
216B VAL* 4.0 17.6 - - - +
218B ILE* 3.3 23.8 + - - +
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Residues in contact with GLU 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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35B ILE* 3.9 3.8 - - - +
185B ILE* 6.1 3.8 - - + +
192B PHE* 3.0 31.7 + - + +
193B MET* 3.7 26.9 - - + +
194B ALA 3.2 0.4 - - - -
195B SER* 1.3 77.5 - - - +
197B ILE* 1.3 57.9 + - + +
199B ARG* 3.0 42.7 + - - +
200B GLU* 3.0 32.4 + - + +
203B MET* 5.1 3.3 - - - +
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Residues in contact with ILE 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 MET* 3.2 23.5 + - + +
194B ALA 3.0 7.0 + - - +
196B GLU* 1.3 76.1 - - + +
198B ILE* 1.3 59.8 + - - +
200B GLU* 3.1 10.1 + - - +
201B LYS* 2.9 32.0 + - + +
261B ALA* 3.8 33.0 - - + +
264B ASP* 3.8 37.7 - - + +
265B MET* 3.8 21.1 - - + -
268B MET* 4.6 17.5 - - + -
269B PHE* 5.5 1.3 - - + -
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Residues in contact with ILE 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 ALA 3.0 8.4 + - - +
195B SER 3.0 6.1 + - - +
197B ILE* 1.3 73.9 - - - +
199B ARG* 1.3 55.6 + - - +
201B LYS* 3.0 7.4 + - - +
202B LEU* 2.7 38.3 + - + +
216B VAL* 3.9 29.4 - - + -
218B ILE* 4.0 26.7 - - + -
233B GLY* 4.4 8.3 - - - -
235B ILE* 4.2 20.9 - - + -
257B ILE* 5.0 2.6 - - + +
261B ALA* 4.5 7.4 - - + -
265B MET* 4.3 16.8 - - + -
275B LEU* 5.0 1.3 - - + -
277B LEU* 4.2 26.7 - - + -
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Residues in contact with ARG 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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31B GLN* 3.9 26.8 - - - +
33B ILE* 2.6 62.9 + - + -
34B SER* 4.3 4.2 - - - +
35B ILE* 3.5 24.7 - - + +
192B PHE* 4.6 5.5 - - - -
195B SER 2.9 15.1 + - - +
196B GLU* 3.0 35.6 + - - +
198B ILE* 1.3 77.5 - - - +
200B GLU* 1.3 61.5 + - - +
202B LEU* 3.5 5.0 + - - +
203B MET* 3.0 56.5 + - - +
216B VAL* 4.1 11.8 - - + +
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Residues in contact with GLU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLU* 3.0 22.8 + - + +
197B ILE* 3.5 8.6 - - - +
198B ILE 3.1 0.2 - - - -
199B ARG* 1.3 77.8 - - - +
201B LYS* 1.3 82.1 + - - +
203B MET* 3.2 18.1 + - + +
204B ARG* 2.7 66.2 + - - +
264B ASP* 3.9 4.9 - - - +
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Residues in contact with LYS 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 ILE* 2.9 22.1 + - + +
198B ILE* 3.7 5.2 - - - +
200B GLU* 1.3 101.8 + - - +
202B LEU* 1.3 64.3 + - - +
204B ARG* 3.5 20.1 - - + +
205B PHE* 3.0 40.1 + - + +
257B ILE* 4.1 19.8 - - + +
260B GLU* 3.7 37.9 - - + -
261B ALA* 4.0 9.2 - - + +
264B ASP* 2.7 38.2 + - - -
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Residues in contact with LEU 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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33B ILE* 3.7 13.5 - - + -
198B ILE* 2.7 22.8 + - + +
199B ARG 3.6 5.6 - - - +
201B LYS* 1.3 72.7 - - - +
203B MET* 1.3 57.3 + - - +
206B LEU* 2.9 53.9 + - + +
210B LEU* 4.6 0.4 - - - -
214B VAL* 4.2 13.5 - - + -
216B VAL* 3.9 28.3 - - + -
235B ILE* 4.0 36.1 - - + -
246B VAL* 4.6 6.5 - - + -
257B ILE* 3.5 28.7 - - + +
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Residues in contact with MET 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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31B GLN* 5.5 8.1 - - - +
32B LYS* 6.1 3.1 - - - -
33B ILE* 3.3 23.3 - - + -
196B GLU* 5.1 3.6 - - - +
199B ARG* 3.0 45.2 + - - +
200B GLU* 3.6 17.0 - - + +
202B LEU* 1.3 76.7 - - - +
204B ARG* 1.3 63.8 + - - +
207B GLY* 3.8 13.2 + - - +
210B LEU* 4.6 7.9 - - + -
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Residues in contact with ARG 204 (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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200B GLU* 2.7 42.2 + - - +
201B LYS* 3.5 24.3 - - - +
202B LEU 3.1 0.2 - - - -
203B MET* 1.3 81.2 - - - +
205B PHE* 1.3 85.2 + - + +
207B GLY* 4.1 2.3 + - - -
306B SO4 3.9 16.5 + - - -
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Residues in contact with PHE 205 (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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201B LYS* 3.0 39.1 + - + +
204B ARG* 1.3 98.8 - - + +
206B LEU* 1.3 65.2 + - - +
209B GLU* 4.2 4.5 - - - +
253B LYS* 3.8 29.6 + - + +
256B THR* 3.5 22.4 - - + -
257B ILE* 4.1 22.9 - - + -
260B GLU* 3.7 33.0 - - + -
306B SO4 4.2 14.0 + - - -
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Residues in contact with LEU 206 (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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202B LEU* 2.9 34.5 + - + +
205B PHE* 1.3 83.3 - - - +
207B GLY* 1.3 62.1 + - - +
208B ALA 3.1 0.3 + - - -
209B GLU* 2.8 41.8 + - + +
210B LEU* 3.4 40.8 - - + -
211B PRO* 4.8 4.5 - - + -
214B VAL* 5.7 3.6 - - + -
245B MET* 4.1 21.1 - - + +
246B VAL* 4.2 26.0 - - + -
253B LYS* 4.2 14.4 - - + -
257B ILE* 4.7 4.9 - - + -
306B SO4 4.6 0.8 + - - -
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Residues in contact with GLY 207 (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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32B LYS* 5.6 1.2 + - - -
203B MET 3.8 14.7 + - - -
204B ARG 4.1 1.5 + - - -
205B PHE 3.5 1.4 - - - -
206B LEU* 1.3 78.2 - - - +
208B ALA* 1.3 61.3 + - - -
209B GLU 3.6 0.2 + - - -
210B LEU* 3.7 14.9 + - - +
306B SO4 3.7 17.5 - - - -
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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
------------------------------------------------------------
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