Contacts of the helix formed by residues 200 - 219 (chain B) in PDB entry 1EZF
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 200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B LEU* 2.8 22.8 + - + +
197B VAL* 3.8 8.1 + - - +
198B GLY 3.6 0.8 - - - -
199B GLU* 1.3 68.6 - - - +
201B THR* 1.3 62.8 + - - +
202B GLU* 3.4 11.6 + - - +
203B ARG* 3.2 43.1 + - + +
204B ALA* 3.3 18.9 + - - +
276B TYR* 5.5 0.2 - - - -
279B ARG* 2.8 37.2 + - - +
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Residues in contact with THR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ILE* 3.8 35.4 - - + +
185B ARG* 6.3 0.9 - - + -
198B GLY 4.2 10.5 - - - +
199B GLU 2.8 18.7 + - - +
200B ASP* 1.3 72.3 - - - +
202B GLU* 1.3 54.6 + - - +
204B ALA* 3.3 3.4 + - - +
205B ASN* 2.8 38.1 + - - +
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Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ASP* 3.2 9.9 + - - +
201B THR* 1.3 80.7 + - - +
203B ARG* 1.3 72.0 + - - +
205B ASN* 3.2 18.9 + - - +
206B SER* 3.0 31.9 + - - -
272B ASP* 4.4 10.9 - - - +
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Residues in contact with ARG 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ASP* 3.2 41.8 + - + +
202B GLU* 1.3 87.9 - - - +
204B ALA* 1.3 62.7 + - - +
206B SER* 3.2 5.7 + - - -
207B MET* 3.1 23.2 + - - +
272B ASP* 3.3 53.5 + - - +
275B THR* 3.5 23.3 + - + +
276B TYR* 3.9 21.3 - - + +
279B ARG* 3.8 16.6 - - - +
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B GLY 4.1 2.4 - - - +
180B GLY* 3.7 23.8 - - - -
181B ILE* 3.8 9.6 - - + +
184B SER* 3.2 28.7 - - - +
200B ASP 3.3 10.8 + - - +
201B THR* 3.8 7.2 - - - +
203B ARG* 1.3 79.9 - - - +
205B ASN* 1.3 61.8 + - - +
207B MET* 3.4 6.2 + - - +
208B GLY 3.3 15.4 + - - -
276B TYR* 3.9 12.7 - - + -
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Residues in contact with ASN 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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173B HIS* 2.7 37.9 + - + +
177B GLY* 3.2 22.7 - - - -
181B ILE* 4.2 6.2 - - + +
201B THR 2.8 18.3 + - - +
202B GLU* 3.5 20.1 + - - +
203B ARG 3.2 0.2 - - - -
204B ALA* 1.3 74.8 - - - +
206B SER* 1.3 60.9 + - - +
208B GLY* 3.1 3.5 + - - -
209B LEU* 2.8 45.9 + - - +
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Residues in contact with SER 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLU* 3.0 15.2 + - - -
203B ARG 3.2 4.0 + - - -
205B ASN* 1.3 75.0 + - - +
207B MET* 1.3 60.7 + - - +
209B LEU* 3.9 3.7 - - - +
210B PHE* 2.9 32.7 + - - +
269B HIS* 3.8 28.8 - - - +
272B ASP* 2.7 43.8 + - - -
273B VAL* 4.8 2.0 - - - -
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Residues in contact with MET 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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180B GLY* 5.4 0.2 - - - -
203B ARG 3.1 18.3 + - - +
204B ALA 3.4 9.6 - - - +
205B ASN 3.2 0.2 - - - -
206B SER* 1.3 78.2 - - - +
208B GLY* 1.3 62.3 + - - +
210B PHE* 3.9 0.7 - - - +
211B LEU* 3.5 13.7 + - - +
273B VAL* 3.9 28.5 - - - +
276B TYR* 3.6 48.9 - - + -
277B LEU* 4.2 3.1 - - + -
289B CYS* 4.0 17.5 - - + +
293B GLN* 3.1 54.9 + - + +
992B IN0 3.9 18.4 - - + -
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Residues in contact with GLY 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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176B ALA* 3.4 37.7 - - - +
204B ALA 3.3 5.2 + - - -
205B ASN 3.1 6.1 + - - -
207B MET* 1.3 78.6 - - - +
209B LEU* 1.3 63.9 + - - +
211B LEU* 3.3 3.7 + - - +
212B GLN 3.0 19.2 + - - -
992B IN0 3.6 13.6 - - - -
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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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169B ASP* 4.0 34.8 - - + +
172B CYS* 3.4 41.7 - - + +
173B HIS* 3.4 10.5 - - - +
177B GLY* 4.2 1.3 - - - -
205B ASN* 2.8 41.9 + - - +
206B SER* 3.9 2.7 - - - +
208B GLY* 1.3 70.7 - - - +
210B PHE* 1.3 57.7 + - - +
212B GLN* 3.8 0.6 - - - +
213B LYS* 2.8 39.4 + - + +
269B HIS* 3.8 30.1 - - + +
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Residues in contact with PHE 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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206B SER 2.9 19.6 + - - +
207B MET 3.9 3.8 - - - +
209B LEU* 1.3 76.5 - - - +
211B LEU* 1.3 55.2 + - - +
213B LYS* 3.6 2.2 + - - +
214B THR* 2.7 37.9 + - + +
266B ALA* 3.2 29.8 - - + -
267B LEU* 4.3 0.9 - - + -
269B HIS* 3.9 16.5 + - + -
270B ILE* 3.3 28.5 - - + -
273B VAL* 4.2 4.7 - - + -
293B GLN* 3.1 24.0 - - - +
296B ALA* 3.7 20.9 - - + -
297B ILE* 3.4 27.8 - - + -
300B LEU* 3.7 30.7 - - + -
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Residues in contact with LEU 211 (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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207B MET 3.5 2.6 + - - +
208B GLY 3.3 6.5 + - - +
210B PHE* 1.3 79.1 - - - +
212B GLN* 1.3 59.1 + - - +
214B THR* 3.6 4.1 + - - -
215B ASN* 2.7 37.6 + - - +
292B PRO* 3.5 35.4 - - + +
293B GLN* 3.5 26.9 - - - +
296B ALA* 3.6 14.1 - - + -
992B IN0 3.5 65.3 - - + +
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Residues in contact with GLN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B TYR* 4.5 14.1 - - + -
172B CYS* 3.5 33.2 - - + -
175B VAL* 4.4 10.8 - - + +
176B ALA* 3.7 12.1 - - + +
208B GLY 3.0 16.0 + - - +
209B LEU 3.8 2.7 - - - +
211B LEU* 1.3 78.6 - - - +
213B LYS* 1.3 57.0 + - - +
215B ASN* 3.2 10.3 + - - +
216B ILE* 2.9 58.6 + - + +
230B PHE* 5.4 2.4 - - - -
992B IN0 3.3 27.9 - - - +
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Residues in contact with LYS 213 (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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168B TRP* 3.5 38.1 - - + -
169B ASP* 3.0 29.5 + - - -
172B CYS* 4.1 11.0 - - - -
209B LEU* 2.8 24.6 + - - +
210B PHE 4.0 2.9 - - - +
212B GLN* 1.3 73.0 - - - +
214B THR* 1.3 64.0 + - - +
216B ILE* 3.2 3.9 + - - +
217B ILE* 2.9 28.6 + - - +
265B ASN* 2.8 33.3 + - - +
266B ALA* 4.2 14.6 - - + -
269B HIS* 2.8 39.2 + - + +
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Residues in contact with THR 214 (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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210B PHE* 2.7 34.0 + - + +
211B LEU 4.1 2.8 + - - +
213B LYS* 1.3 75.7 - - - +
215B ASN* 1.3 60.5 + - - +
217B ILE* 3.6 2.3 - - - +
218B ARG* 2.8 35.2 + - - +
266B ALA* 5.0 1.1 - - + -
296B ALA* 3.9 21.0 - - + +
299B THR* 3.4 18.6 + - - -
300B LEU* 3.5 46.2 - - + +
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Residues in contact with ASN 215 (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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211B LEU* 2.7 36.3 + - - +
212B GLN* 3.5 12.3 + - - +
213B LYS 3.2 0.2 - - - -
214B THR* 1.3 80.6 + - - +
216B ILE* 1.3 52.3 + - + +
218B ARG* 2.7 41.7 + - - +
219B ASP* 2.8 46.8 + - - +
992B IN0 4.5 19.8 + - - +
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Residues in contact with ILE 216 (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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168B TRP* 3.5 36.8 - - + +
171B TYR* 5.1 3.6 - - + -
172B CYS* 4.0 7.4 - - - -
212B GLN* 2.9 51.6 + - + +
213B LYS 3.5 4.0 - - - +
215B ASN* 1.3 78.6 - - + +
217B ILE* 1.3 61.4 + - - +
219B ASP* 3.5 4.5 + - - +
220B TYR* 3.5 10.4 + - - -
223B ASP* 5.1 3.8 - - - +
230B PHE* 3.5 34.8 - - + -
231B TRP* 2.9 36.7 + - + -
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Residues in contact with ILE 217 (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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168B TRP* 4.5 8.7 - - + -
213B LYS 2.9 23.2 + - - +
214B THR* 3.6 4.5 - - - +
216B ILE* 1.3 76.7 - - - +
218B ARG* 1.3 66.4 - - - +
219B ASP 3.4 0.3 + - - -
220B TYR* 3.5 5.7 + - - +
231B TRP* 3.4 24.2 - - + +
259B LEU* 3.5 29.4 - - + -
262B LEU* 3.7 46.2 - - + +
263B ILE* 3.8 17.3 - - + +
266B ALA* 4.3 4.5 - - + -
300B LEU* 4.0 15.9 - - + -
303B CYS* 4.7 6.5 - - + -
309B VAL* 4.0 5.8 - - + +
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Residues in contact with ARG 218 (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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214B THR* 2.8 20.3 + - - +
215B ASN* 2.7 30.9 + - - +
217B ILE* 1.3 80.9 - - - +
219B ASP* 1.3 95.7 + - - +
220B TYR 3.4 4.2 + - - -
221B LEU* 4.7 2.6 + - - +
299B THR* 5.1 21.1 - - + +
303B CYS* 4.3 23.1 - - - -
309B VAL* 4.9 10.6 - - - +
314B VAL* 6.5 0.7 - - + -
992B IN0 3.7 20.8 + - - +
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Residues in contact with ASP 219 (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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215B ASN* 2.8 28.6 + - - +
216B ILE* 4.0 3.6 - - - +
217B ILE 3.3 0.4 - - - -
218B ARG* 1.3 109.2 + - - +
220B TYR* 1.3 65.1 + - - +
221B LEU 3.3 2.7 - - - -
222B GLU* 3.1 24.6 + - + +
223B ASP* 2.8 41.4 + - - +
228B ARG* 5.3 2.8 + - - -
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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
------------------------------------------------------------
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