Contacts of the helix formed by residues 200 - 219 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 3.0 16.2 + - + +
197A VAL* 3.9 7.8 + - - +
198A GLY 3.5 1.2 - - - -
199A GLU* 1.3 72.8 - - - +
201A THR* 1.3 60.0 + - - +
202A GLU* 3.4 6.4 + - - +
203A ARG* 3.1 45.2 + - + +
204A ALA* 3.1 21.0 + - - +
276A TYR* 5.3 0.6 - - + -
279A ARG* 2.7 42.3 + - - +
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Residues in contact with THR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ILE* 3.0 43.2 - - + +
185A ARG* 3.8 14.4 - - - +
198A GLY 4.2 9.6 - - - +
199A GLU 2.9 16.0 + - - +
200A ASP* 1.3 68.2 - - - +
202A GLU* 1.3 57.9 + - - +
204A ALA* 4.4 1.1 - - - -
205A ASN* 2.7 33.9 + - - +
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Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ASP* 3.2 9.8 - - - +
201A THR* 1.3 81.9 + - - +
203A ARG* 1.3 71.7 + - - +
205A ASN* 3.6 12.3 + - - +
206A SER* 3.0 37.5 + - - -
272A ASP* 4.1 8.7 - - - +
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Residues in contact with ARG 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ASP* 3.1 44.5 + - + +
202A GLU* 1.3 92.5 - - - +
204A ALA* 1.3 64.6 + - - +
206A SER* 3.3 4.7 + - - -
207A MET* 3.2 24.9 + - - +
272A ASP* 3.4 54.6 + - - +
275A THR* 3.9 11.7 + - + +
276A TYR* 3.9 25.1 - - + +
279A ARG* 3.7 22.4 - - - +
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Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLY 4.0 0.2 - - - +
180A GLY* 3.5 26.5 - - - +
181A ILE* 3.6 15.5 - - + +
184A SER* 3.2 27.8 - - - +
200A ASP 3.1 11.5 + - - +
201A THR* 4.4 0.9 - - - -
203A ARG* 1.3 78.1 - - - +
205A ASN* 1.3 63.4 + - - +
207A MET* 3.3 17.6 - - - +
208A GLY 3.4 4.5 + - - -
276A TYR* 3.8 12.0 - - + -
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Residues in contact with ASN 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A HIS* 2.8 36.3 + - + +
177A GLY* 3.3 18.9 - - - -
181A ILE* 3.6 9.8 - - + +
201A THR 2.7 22.3 + - - +
202A GLU* 3.6 14.3 + - - +
204A ALA* 1.3 74.8 - - - +
206A SER* 1.3 60.0 + - - +
208A GLY* 3.0 4.7 + - - -
209A LEU* 2.9 51.8 + - - +
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Residues in contact with SER 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A GLU* 3.0 14.8 + - - -
203A ARG 3.3 5.8 + - - -
205A ASN* 1.3 74.4 + - - +
207A MET* 1.3 67.9 + - - +
209A LEU* 3.3 10.0 + - - +
210A PHE* 2.9 25.5 + - - +
269A HIS* 3.9 22.5 - - - +
272A ASP* 2.8 45.1 + - - +
273A VAL* 4.5 1.8 - - - -
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Residues in contact with MET 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ARG 3.2 16.6 + - - +
204A ALA* 3.3 9.9 - - - +
205A ASN 3.2 0.4 - - - -
206A SER* 1.3 79.9 - - - +
208A GLY* 1.3 62.8 + - - +
210A PHE* 3.3 1.4 + - - +
211A LEU* 3.3 13.3 + - - +
273A VAL* 3.8 25.5 - - + +
276A TYR* 3.5 48.9 - - + -
277A LEU* 4.1 3.4 - - + -
289A CYS* 4.0 19.1 - - + +
293A GLN* 3.1 56.0 + - + +
991A IN0 3.9 17.9 - - + -
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Residues in contact with GLY 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ALA* 3.2 39.0 - - - +
204A ALA 3.4 3.6 + - - -
205A ASN 3.0 7.9 + - - -
207A MET* 1.3 77.6 - - - +
209A LEU* 1.3 58.8 + - - +
210A PHE 3.4 0.2 + - - -
211A LEU* 3.4 2.4 + - - +
212A GLN 2.9 25.3 + - - -
991A IN0 3.5 14.1 - - - -
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASP* 3.8 24.5 - - + +
172A CYS* 3.5 16.6 - - + +
173A HIS* 3.4 36.1 - - - +
177A GLY* 4.5 0.4 - - - -
205A ASN* 2.9 38.3 + - - +
206A SER* 3.3 5.1 + - - +
208A GLY* 1.3 75.4 - - - +
210A PHE* 1.3 63.6 + - - +
213A LYS* 3.0 34.6 + - - +
269A HIS* 3.3 35.2 - - + +
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Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A SER 2.9 17.4 + - - +
207A MET 3.6 5.2 - - - +
208A GLY 3.2 0.2 - - - -
209A LEU* 1.3 80.2 - - - +
211A LEU* 1.3 60.0 + - - +
213A LYS* 4.2 2.2 - - - +
214A THR* 2.8 30.3 + - + +
266A ALA* 3.4 27.8 - - + -
267A LEU* 4.5 1.3 - - + -
269A HIS* 4.0 14.3 + - + -
270A ILE* 3.5 26.0 - - + -
273A VAL* 4.1 8.1 - - + -
293A GLN* 3.1 22.7 - - + +
296A ALA* 3.5 20.6 - - + -
297A ILE* 3.4 30.5 - - + -
300A LEU* 3.5 33.4 - - + -
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A MET 3.3 3.4 + - - +
208A GLY 3.9 3.4 - - - +
210A PHE* 1.3 78.4 - - - +
212A GLN* 1.3 61.8 + - - +
214A THR* 3.1 18.4 + - - -
215A ASN* 3.0 20.7 + - - +
292A PRO* 3.4 41.1 - - + +
293A GLN* 3.4 25.1 - - - +
296A ALA* 3.7 12.8 - - + -
991A IN0 3.5 65.5 - - + +
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Residues in contact with GLN 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A TYR* 5.2 1.4 - - - -
172A CYS* 3.8 24.7 - - + -
175A VAL* 3.6 27.1 - - + +
176A ALA* 3.4 12.9 - - + +
208A GLY 2.9 17.9 + - - +
209A LEU 4.0 0.9 - - - +
211A LEU* 1.3 77.4 - - - +
213A LYS* 1.3 63.0 + - - +
215A ASN* 3.3 12.7 + - - +
216A ILE* 2.9 39.8 + - + +
991A IN0 3.0 32.9 - - - +
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Residues in contact with LYS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A TRP* 3.6 30.7 - - + -
169A ASP* 2.7 30.8 + - - +
172A CYS* 3.7 20.2 - - - -
209A LEU* 3.0 24.6 + - - +
210A PHE 4.2 1.6 - - - +
212A GLN* 1.3 74.8 - - - +
214A THR* 1.3 65.2 + - - +
216A ILE* 3.1 3.3 + - - +
217A ILE* 2.9 29.3 + - - +
265A ASN* 2.8 34.9 + - - +
266A ALA* 4.4 12.3 - - + -
269A HIS* 2.9 33.8 + - + +
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Residues in contact with THR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PHE* 2.8 29.3 + - + +
211A LEU* 3.1 9.4 + - - -
213A LYS* 1.3 75.7 - - - +
215A ASN* 1.3 65.0 + - - +
217A ILE* 3.4 2.5 + - - +
218A ARG* 2.9 32.0 + - - +
266A ALA* 4.9 2.0 - - + -
296A ALA* 3.9 28.8 - - + +
299A THR* 4.8 9.0 - - - +
300A LEU* 3.6 46.9 - - + +
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Residues in contact with ASN 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LEU* 3.0 23.0 + - - +
212A GLN* 3.6 15.9 - - - +
214A THR* 1.3 83.9 + - - +
216A ILE* 1.3 56.3 + - - +
218A ARG* 2.9 31.2 + - - +
219A ASP* 2.7 50.0 + - - +
991A IN0 4.0 25.9 + - - +
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Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A TRP* 3.8 28.3 - - + +
171A TYR* 4.1 15.3 - - + -
172A CYS* 4.2 4.9 - - - -
212A GLN* 2.9 43.2 + - + +
213A LYS* 3.7 4.9 - - - +
215A ASN* 1.3 75.2 - - - +
217A ILE* 1.3 62.4 + - - +
219A ASP* 3.9 3.7 - - - -
220A TYR* 3.5 12.3 + - - -
223A ASP* 4.7 6.3 - - - +
230A PHE* 3.8 32.5 - - + -
231A TRP* 2.9 40.3 + - + -
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A TRP* 4.1 12.8 - - + -
213A LYS 2.9 26.0 + - - +
214A THR* 3.6 4.0 - - - +
216A ILE* 1.3 79.2 - - - +
218A ARG* 1.3 63.1 + - - +
220A TYR* 3.4 10.0 + - - +
231A TRP* 3.6 19.5 - - + +
259A LEU* 3.4 32.8 - - + +
262A LEU* 3.8 42.8 - - + +
263A ILE* 3.9 16.4 - - + +
266A ALA* 4.5 3.6 - - + -
300A LEU* 4.3 10.1 - - + -
303A CYS* 5.0 6.3 - - + -
309A VAL* 4.0 6.6 - - - +
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Residues in contact with ARG 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A THR 2.9 17.7 + - - +
215A ASN* 2.9 28.3 + - - +
217A ILE* 1.3 77.3 - - - +
219A ASP* 1.3 106.0 + - - +
220A TYR 3.3 3.9 + - - -
221A LEU 4.9 0.7 + - - -
299A THR* 4.1 31.4 + - + +
303A CYS* 4.2 17.5 - - - -
309A VAL* 4.6 14.0 - - + +
312A GLY 4.8 5.5 - - - +
313A ALA* 5.4 9.5 - - - -
314A VAL* 5.3 16.2 + - + +
316A ILE* 6.3 0.4 - - - +
991A IN0 5.3 11.7 + - - +
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Residues in contact with ASP 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ASN* 2.7 28.5 + - - +
216A ILE 3.9 3.1 - - - +
217A ILE 3.3 0.2 - - - -
218A ARG* 1.3 112.6 + - - +
220A TYR* 1.3 63.5 + - - +
221A LEU 3.4 2.5 - - - -
222A GLU* 3.3 29.5 + - + +
223A ASP* 2.9 36.6 + - - +
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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
------------------------------------------------------------
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