Contacts of the helix formed by residues 199 - 217 (chain A) in PDB entry 1EZW
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 ASN 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ALA 3.8 0.4 - - - -
198A SER* 1.3 79.4 + - - +
200A PRO* 1.3 76.8 - - - +
201A LYS* 3.0 41.1 + - - +
202A ASP* 3.0 24.2 + - - +
203A PHE* 3.4 11.5 - - - -
264A HIS* 3.5 9.7 - - + -
296A GLU* 2.8 49.0 + - - +
297A ALA* 3.2 20.4 - - - +
314A LEU* 3.5 4.9 - - - +
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Residues in contact with PRO 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A SER 4.5 0.9 - - - +
199A ASN* 1.3 95.7 - - - +
201A LYS* 1.3 58.3 + - + +
203A PHE* 3.0 4.8 + - + +
204A GLU* 2.9 41.0 + - - +
296A GLU* 5.3 0.7 - - - +
310A LYS 5.0 0.4 - - - +
313A GLU* 3.7 45.1 - - + +
314A LEU* 3.5 14.6 - - + -
317A ALA* 3.7 11.6 - - + +
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Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASN* 3.0 23.7 + - - +
200A PRO* 1.3 77.4 - - + +
202A ASP* 1.3 63.7 + - - +
204A GLU* 3.4 21.0 + - - +
205A VAL* 3.4 25.8 + - - +
263A ARG* 3.5 35.7 - - + +
264A HIS* 3.7 23.9 + - + +
296A GLU* 4.5 8.1 + - - -
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Residues in contact with ASP 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 5.6 2.0 - - + -
197A ALA* 3.5 29.1 - - + +
198A SER 3.9 1.4 + - - -
199A ASN* 3.0 35.0 + - - +
201A LYS* 1.3 77.8 - - - +
203A PHE* 1.3 59.2 + - + +
205A VAL* 3.4 5.7 + - - +
206A ALA* 2.9 28.2 + - - +
260A VAL* 4.7 3.8 - - - +
263A ARG* 2.9 30.0 + - - +
264A HIS* 2.8 24.6 + - - -
297A ALA 4.2 2.3 - - - +
298A PHE* 5.7 1.7 - - - -
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Residues in contact with PHE 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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195A VAL* 3.6 34.5 - - + -
197A ALA* 3.8 28.5 - - + -
199A ASN 3.4 15.3 - - - -
200A PRO 3.0 6.7 + - - +
202A ASP* 1.3 73.7 - - - +
204A GLU* 1.3 59.2 + - - +
205A VAL 3.0 1.8 - - - -
206A ALA* 3.7 6.3 - - + +
207A VAL* 2.9 37.8 + - + +
226A VAL* 3.9 22.0 - - + -
227A ALA 4.6 0.2 - - - -
228A ALA* 3.5 28.3 - - + -
314A LEU* 4.0 8.7 - - + -
317A ALA* 3.7 23.4 - - + +
319A VAL* 3.5 27.8 - - + -
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Residues in contact with GLU 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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200A PRO* 2.9 30.1 + - - +
201A LYS* 3.6 24.7 - - - +
202A ASP 3.3 0.6 - - - -
203A PHE* 1.3 77.8 - - - +
205A VAL* 1.3 58.6 + - + +
208A PRO* 3.1 24.1 - - - +
317A ALA* 4.2 14.4 - - + +
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 5.1 3.3 - - + +
201A LYS 3.4 12.8 + - - +
202A ASP 3.4 7.8 + - - +
203A PHE 3.0 0.2 - - - -
204A GLU* 1.3 79.8 - - + +
206A ALA* 1.3 66.6 + - + +
208A PRO* 3.4 10.2 - - - +
209A LYS* 4.1 11.6 + - - +
263A ARG* 3.7 33.7 - - + +
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Residues in contact with ALA 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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178A GLN 5.7 0.2 - - - +
183A LEU* 3.7 32.9 - - + +
195A VAL* 4.7 14.8 - - + -
202A ASP 2.9 17.7 + - - +
203A PHE* 3.4 8.5 + - + -
205A VAL* 1.3 78.5 - - + +
207A VAL* 1.3 65.3 + - - +
209A LYS* 3.1 7.4 + - - +
210A ILE* 3.1 26.2 + - + +
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Residues in contact with VAL 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 PHE* 2.9 34.2 + - + +
206A ALA* 1.3 72.3 - - - +
208A PRO* 1.3 62.0 - - + +
210A ILE* 3.1 7.7 + - + +
211A GLU* 2.8 28.0 + - + +
221A LEU* 3.6 32.5 - - + -
226A VAL* 4.2 26.5 - - + -
317A ALA 3.5 18.8 - - - +
318A GLY* 4.3 9.9 - - - +
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Residues in contact with PRO 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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203A PHE 3.9 0.2 - - - +
204A GLU* 3.1 27.1 - - - +
205A VAL 3.4 9.4 - - - +
207A VAL* 1.3 93.9 - - + +
209A LYS* 1.3 60.0 + - + +
211A GLU* 3.4 12.3 + - + +
212A GLU* 2.9 27.8 + - - +
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Residues in contact with LYS 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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180A PRO* 4.7 30.7 - - + +
183A LEU* 4.1 22.0 - - + -
184A LYS* 3.6 16.2 - - + +
205A VAL 4.1 8.5 + - - +
206A ALA 3.1 8.6 + - - +
207A VAL 3.1 0.8 - - - -
208A PRO* 1.3 78.7 - - + +
210A ILE* 1.3 66.0 + - - +
212A GLU* 3.3 37.1 + - - +
213A GLY 3.3 15.8 + - - -
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Residues in contact with ILE 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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183A LEU* 3.6 38.4 - - + +
187A GLY* 3.4 19.9 - - - -
193A VAL* 4.0 23.3 - - + -
195A VAL* 4.7 3.6 - - + -
206A ALA* 3.1 15.8 + - + +
207A VAL* 3.1 13.4 + - + +
209A LYS* 1.3 76.2 - - - +
211A GLU* 1.3 64.4 + - - +
213A GLY 3.1 3.1 + - - -
214A ALA* 3.0 18.4 + - - +
221A LEU* 4.0 11.2 - - + -
224A ILE* 4.0 24.5 - - + -
226A VAL* 4.2 22.4 - - + -
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Residues in contact with GLU 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 VAL* 2.8 17.2 + - - +
208A PRO* 3.6 11.7 - - - +
210A ILE* 1.3 77.9 - - - +
212A GLU* 1.3 61.6 + - - +
214A ALA* 3.2 4.9 + - + +
215A LYS* 3.0 54.6 + - + +
221A LEU* 3.9 44.3 + - + +
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Residues in contact with GLU 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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184A LYS* 3.0 29.6 - - - +
208A PRO 2.9 14.5 + - - +
209A LYS* 3.4 41.5 + - - +
210A ILE 3.2 0.2 - - - -
211A GLU* 1.3 75.2 - - - +
213A GLY* 1.3 62.5 + - - +
215A LYS* 3.4 9.1 + - - +
216A GLU* 3.2 30.3 + - + +
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Residues in contact with GLY 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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184A LYS* 3.4 38.5 - - - +
187A GLY 3.7 6.7 - - - -
188A GLU* 3.5 13.6 - - - +
209A LYS 3.3 4.6 + - - -
210A ILE 3.1 5.3 + - - -
212A GLU* 1.3 76.6 - - - +
214A ALA* 1.3 65.3 + - - +
216A GLU* 3.3 4.4 + - - +
217A ALA 3.2 14.7 + - - -
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Residues in contact with ALA 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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187A GLY 3.2 19.4 + - - +
188A GLU* 4.6 0.2 - - - +
210A ILE 3.0 12.7 + - - +
211A GLU* 3.2 12.5 + - + +
213A GLY* 1.3 74.2 - - - +
215A LYS* 1.3 54.9 + - + +
217A ALA* 2.9 13.5 + - - -
219A ARG* 2.8 46.4 + - + +
220A SER 4.4 6.7 - - - +
221A LEU* 4.6 1.6 - - - +
224A ILE* 3.7 16.4 - - + -
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Residues in contact with LYS 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 GLU* 3.0 51.9 + - + +
212A GLU* 3.8 8.3 - - - +
213A GLY 3.3 0.2 - - - -
214A ALA* 1.3 75.8 - - - +
216A GLU* 1.3 58.9 + - + +
218A GLY* 2.9 19.0 + - - +
219A ARG 3.9 9.8 + - - +
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Residues in contact with GLU 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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184A LYS* 2.5 40.0 + - - +
188A GLU* 5.1 9.1 - - - +
212A GLU* 3.2 16.6 + - + +
213A GLY 3.7 8.7 - - - +
214A ALA 3.2 0.4 - - - -
215A LYS* 1.3 78.2 - - + +
217A ALA* 1.3 57.9 + - - +
218A GLY 3.3 0.8 + - - -
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Residues in contact with ALA 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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188A GLU* 3.5 35.0 - - + +
213A GLY 3.2 8.7 + - - +
214A ALA 2.9 8.9 + - - +
216A GLU* 1.3 76.9 - - - +
218A GLY* 1.3 62.7 + - - +
219A ARG* 3.4 15.7 + - - +
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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