Contacts of the helix formed by residues 193 - 210 (chain B) in PDB entry 3E4E
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 ASP 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B PHE* 3.1 30.2 - - + -
190B ASP* 2.8 31.1 + - + +
192B ASN* 1.3 77.2 - - - +
194B GLU* 1.3 69.6 + - - +
195B LYS* 3.5 13.4 + - - +
196B PHE* 3.1 17.3 + - + +
197B LEU* 3.0 21.5 + - - +
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Residues in contact with GLU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ASN 3.3 9.7 + - - +
193B ASP* 1.3 73.3 + - - +
195B LYS* 1.3 61.9 + - - +
197B LEU* 3.4 15.5 + - + +
198B ARG* 2.9 28.2 + - - +
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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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189B PHE* 5.1 2.7 - - + -
193B ASP* 3.3 14.1 + - - +
194B GLU* 1.3 76.0 - - - +
196B PHE* 1.3 65.4 + - - +
198B ARG* 3.0 17.0 + - + +
199B LEU* 2.9 35.6 + - + +
241B GLU* 4.5 19.2 + - - +
245B TYR* 4.0 42.6 - - + +
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Residues in contact with PHE 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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174B CYS* 3.6 37.0 - - + -
177B CYS* 3.5 30.7 - - + -
178B ASN* 3.5 26.9 - - - -
189B PHE* 3.2 50.4 - + + -
190B ASP 3.5 13.2 - - - -
191B TYR* 4.2 6.5 - - - -
193B ASP* 3.1 25.9 + - + +
195B LYS* 1.3 80.0 - - - +
197B LEU* 1.3 63.0 + - - +
198B ARG 3.0 0.9 + - - -
199B LEU* 3.1 8.7 + - + +
200B MET* 3.0 36.0 + - + +
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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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170B PHE* 4.0 26.3 - - + +
191B TYR 3.8 19.1 - - - +
192B ASN* 4.1 16.4 - - - +
193B ASP 3.0 13.8 + - - +
194B GLU* 3.5 17.3 - - + +
196B PHE* 1.3 76.9 - - - +
198B ARG* 1.3 56.4 + - - +
200B MET* 3.4 20.1 + - + +
201B TYR* 2.9 29.9 + - - +
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Residues in contact with ARG 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 GLU 2.9 15.4 + - - +
195B LYS* 3.0 28.4 + - + +
197B LEU* 1.3 74.5 - - - +
199B LEU* 1.3 66.3 + - + +
201B TYR* 3.0 34.6 + - - +
202B LEU* 2.9 46.2 + - + +
234B LYS* 5.6 5.5 - - - +
238B ASN* 4.9 2.2 + - - -
241B GLU* 2.8 43.1 + - - +
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Residues in contact with LEU 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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177B CYS* 5.4 2.2 - - - -
189B PHE* 4.8 6.7 - - + -
195B LYS* 2.9 30.3 + - + +
196B PHE* 3.5 9.2 - - + +
198B ARG* 1.3 73.0 - - + +
200B MET* 1.3 65.3 + - + +
202B LEU* 3.2 18.4 + - + +
203B PHE* 2.9 41.0 + - + -
241B GLU* 5.4 0.9 - - + +
242B VAL* 5.0 11.7 - - + -
245B TYR* 3.7 56.8 - - + +
297B PHE* 3.9 24.5 - - + -
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Residues in contact with MET 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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170B PHE* 3.7 21.8 - - + +
173B GLY* 3.7 11.4 - - - +
174B CYS* 3.6 49.1 - - - -
177B CYS* 4.0 22.9 - - + -
196B PHE* 3.0 35.8 + - + +
197B LEU* 3.7 25.1 - - + +
199B LEU* 1.3 75.8 - - - +
201B TYR* 1.3 59.2 + - - +
203B PHE* 3.2 9.5 + - - +
204B ASN* 2.8 32.4 + - - +
301B THR* 4.6 6.1 - - + -
302B GLU* 4.2 1.7 - - - +
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Residues in contact with TYR 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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170B PHE* 3.7 26.2 - + + -
197B LEU 2.9 15.3 + - - +
198B ARG* 3.2 39.7 - - - +
200B MET* 1.3 77.1 - - - +
202B LEU* 1.3 62.5 + - + +
204B ASN* 3.3 4.0 + - - +
205B GLU* 2.8 57.2 + - + +
234B LYS* 6.2 1.3 - - - -
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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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198B ARG* 2.9 45.7 + - + +
199B LEU* 3.7 16.4 - - + +
201B TYR* 1.3 79.1 - - + +
203B PHE* 1.3 67.6 + - - +
205B GLU* 4.1 3.1 - - - +
206B ASN* 2.9 30.2 + - - +
238B ASN* 3.4 34.8 - - + +
241B GLU* 3.7 37.2 - - + +
242B VAL* 3.9 24.2 - - + +
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Residues in contact with PHE 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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177B CYS* 4.2 10.5 - - - -
199B LEU* 2.9 26.3 + - + -
200B MET* 3.4 6.3 - - - +
202B LEU* 1.3 76.9 - - - +
204B ASN* 1.3 57.1 - - - +
206B ASN* 3.3 3.8 + - - +
207B PHE* 3.0 26.5 + - - +
242B VAL* 4.0 32.3 - - + -
297B PHE* 3.6 35.2 - + - -
298B PHE* 3.6 42.8 - + + -
301B THR* 3.2 43.1 - - + -
302B GLU* 3.2 16.4 - - + +
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Residues in contact with ASN 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B THR* 3.9 21.2 - - + +
170B PHE* 4.0 19.9 - - + -
200B MET 2.8 17.4 + - - +
201B TYR* 3.7 5.8 - - - +
203B PHE* 1.3 73.4 - - - +
205B GLU* 1.3 70.5 + - - +
207B PHE* 3.3 2.1 + - - +
208B HIS* 3.0 28.5 + - - +
302B GLU* 3.5 24.2 + - - +
309B ARG* 4.0 11.9 - - - +
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Residues in contact with GLU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B TYR* 2.8 48.9 + - + +
202B LEU* 4.1 1.1 - - - +
204B ASN* 1.3 77.2 + - - +
206B ASN* 1.3 57.3 + - - +
208B HIS* 3.3 6.4 + - + +
209B LEU* 2.8 45.1 + - + +
234B LYS* 3.1 29.1 - - - +
238B ASN* 2.8 31.3 + - - +
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Residues in contact with ASN 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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106B PHE* 4.9 4.3 - - + -
202B LEU* 2.9 22.2 + - - +
203B PHE* 3.6 5.2 - - - +
205B GLU* 1.3 78.1 - - - +
207B PHE* 1.3 57.6 + - - +
209B LEU* 4.4 2.6 - - - +
210B LEU* 2.9 46.7 + - + +
235B VAL* 3.4 21.7 - - - +
238B ASN* 3.0 42.2 + - - +
239B VAL* 3.8 21.0 - - - +
242B VAL* 5.1 4.0 - - - +
298B PHE* 4.6 10.8 - - + -
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Residues in contact with PHE 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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203B PHE 3.0 16.9 + - - +
204B ASN 3.8 3.4 - - - +
206B ASN* 1.3 77.9 - - - +
208B HIS* 1.3 56.2 + - - +
210B LEU* 3.8 4.8 + - - +
211B SER* 2.7 30.1 + - - -
298B PHE* 4.5 11.4 - + + -
302B GLU* 3.7 19.1 - - + +
303B THR* 4.3 17.7 - - + -
306B THR* 3.9 22.9 - - + -
363B LEU* 4.2 28.0 - - + -
364B VAL* 5.4 3.6 - - + -
478B PHE* 3.6 36.6 - + - -
479B GLY* 3.8 17.5 - - - -
481B ILE* 3.3 30.2 - - + +
501B 4PZ 5.7 1.3 - - + -
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Residues in contact with HIS 208 (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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204B ASN* 3.0 25.1 + - - +
205B GLU* 3.4 8.4 - - - +
207B PHE* 1.3 76.6 - - - +
209B LEU* 1.3 73.4 + - + +
211B SER* 3.0 24.6 + - - -
212B THR* 3.4 15.5 - - + +
474B ILE* 4.7 0.9 - - + +
475B HIS* 3.4 38.2 + + - +
481B ILE* 4.0 25.3 - - + +
484B ARG* 3.1 30.2 + - - -
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Residues in contact with LEU 209 (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 GLU* 2.8 44.5 + - + +
208B HIS* 1.3 84.0 - - + +
210B LEU* 1.3 58.1 + - - +
211B SER 3.0 7.6 + - - -
212B THR* 2.8 29.4 + - + +
215B LEU* 2.9 23.8 - - + +
231B SER* 3.8 36.6 - - - +
234B LYS* 3.9 18.2 - - + -
235B VAL* 3.8 11.0 - - + +
238B ASN* 5.0 0.4 - - - +
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Residues in contact with LEU 210 (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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103B LEU* 4.3 15.9 - - + -
105B ALA* 4.0 24.9 - - + -
106B PHE* 3.7 26.9 - - + -
206B ASN* 2.9 34.2 + - + +
207B PHE* 4.1 4.9 - - - +
208B HIS 3.2 0.4 - - - -
209B LEU* 1.3 76.8 - - - +
211B SER* 1.3 57.2 + - - +
212B THR 3.4 0.9 - - - -
215B LEU* 4.2 15.0 - - + +
216B GLN* 3.6 17.4 + - - +
219B ASN* 6.2 1.6 - - + -
235B VAL* 4.4 10.3 - - + -
298B PHE* 5.0 2.0 - - + -
478B PHE* 3.2 47.6 + - + +
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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