Contacts of the helix formed by residues 193 - 212 (chain A) in PDB entry 2WO6
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 LYS 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A TYR* 3.4 46.9 - - + -
191A LYS 2.8 6.7 + - - -
192A ASN* 1.3 77.7 - - - +
194A LYS* 1.3 70.8 + - + +
195A ALA* 3.3 19.3 - - - +
196A PHE* 3.1 31.2 + - + -
197A LEU* 3.1 20.8 + - - +
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Residues in contact with LYS 194 (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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193A LYS* 1.3 77.0 - - + +
195A ALA* 1.3 64.4 + - - +
197A LEU* 3.2 14.1 + - + +
198A ASN* 2.9 51.0 + - - +
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Residues in contact with ALA 195 (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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170A PHE* 4.7 1.4 - - - -
193A LYS* 3.2 21.6 + - - +
194A LYS* 1.3 78.1 - - - +
196A PHE* 1.3 71.2 + - + +
198A ASN* 3.5 18.7 + - - +
199A GLN* 3.6 12.6 + - - +
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Residues in contact with PHE 196 (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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145A TYR* 4.4 7.0 - + - -
169A SER* 3.2 28.3 - - - -
170A PHE* 3.8 38.5 - + + +
190A ILE* 3.6 22.4 - - + +
191A LYS* 3.5 33.0 - - + +
193A LYS* 3.1 40.9 + - + +
195A ALA* 1.3 78.9 - - + +
197A LEU* 1.3 67.0 + - - +
199A GLN* 3.1 13.0 + - - +
200A ALA* 3.1 9.4 + - - +
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Residues in contact with LEU 197 (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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190A ILE* 3.8 9.7 - - + +
191A LYS 5.0 2.5 - - - +
193A LYS 3.1 13.3 + - - +
194A LYS* 3.5 16.6 - - + +
196A PHE* 1.3 76.8 - - - +
198A ASN* 1.3 66.7 + - - +
200A ALA* 3.1 3.8 + - - +
201A GLN* 2.9 42.7 + - - +
229A MET* 4.8 13.7 - - + -
234A LEU* 3.4 46.7 - - + +
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Residues in contact with ASN 198 (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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194A LYS* 2.9 50.9 + - - +
195A ALA* 3.5 13.6 - - - +
197A LEU* 1.3 80.1 - - - +
199A GLN* 1.3 70.3 + - - +
201A GLN* 3.4 23.0 + - - +
202A ILE* 3.4 24.0 + - + +
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Residues in contact with GLN 199 (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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170A PHE* 3.5 36.6 - - + -
195A ALA 3.6 7.1 + - - +
196A PHE 3.1 3.2 + - - +
198A ASN* 1.3 80.8 - - - +
200A ALA* 1.3 65.0 + - - +
202A ILE* 3.3 29.2 + - - +
203A GLU* 3.0 20.4 + - - +
309A GLY* 2.9 36.2 - - - +
310A SER* 4.5 5.0 - - - -
311A SER 5.4 0.3 - - - +
319A TYR* 5.5 4.8 + - - -
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Residues in contact with ALA 200 (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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170A PHE* 5.4 1.2 - - + -
190A ILE* 3.3 41.7 - - + -
196A PHE 3.1 8.1 + - - +
197A LEU 3.1 8.6 + - - +
199A GLN* 1.3 75.3 - - - +
201A GLN* 1.3 63.5 + - - +
203A GLU* 3.1 11.3 + - - +
204A VAL* 3.0 26.0 + - - +
234A LEU* 3.8 14.4 - - + -
236A LEU* 4.4 5.3 - - + +
309A GLY* 5.8 0.2 - - - -
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Residues in contact with GLN 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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197A LEU* 2.9 37.7 + - - +
198A ASN* 3.4 28.8 + - - +
199A GLN 3.2 0.2 - - - -
200A ALA* 1.3 78.1 - - - +
202A ILE* 1.3 61.3 + - + +
204A VAL* 3.3 8.0 + - - +
205A ARG* 3.2 22.3 + - - +
234A LEU* 4.0 15.0 - - + +
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Residues in contact with ILE 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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198A ASN* 3.4 10.0 + - + +
199A GLN* 3.3 40.7 + - - +
200A ALA 3.2 0.2 - - - -
201A GLN* 1.3 77.1 - - + +
203A GLU* 1.3 64.6 + - - +
205A ARG* 3.3 14.1 + - - +
206A LEU* 3.2 32.2 + - + +
308A PHE 4.6 3.8 - - - +
309A GLY 5.0 0.9 - - - +
311A SER 3.6 23.8 - - - +
312A CYS* 5.6 0.7 - - - -
316A GLN* 6.1 0.7 - - - +
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Residues in contact with GLU 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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188A LYS* 2.5 34.2 + - - +
199A GLN 3.0 13.2 + - - +
200A ALA* 3.1 12.1 + - - +
202A ILE* 1.3 75.0 - - - +
204A VAL* 1.3 57.5 + - - +
206A LEU* 3.4 2.1 + - - +
207A LEU* 2.9 59.5 + - + +
222A VAL* 5.4 0.5 - - - +
236A LEU* 3.4 14.6 - - + +
238A PHE* 3.8 7.6 - - - -
307A ASP* 3.4 6.9 + - - -
308A PHE* 2.9 50.3 + - + +
309A GLY* 4.2 4.1 - - - -
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Residues in contact with VAL 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 ALA 3.0 20.7 + - - +
201A GLN* 3.6 10.1 - - - +
202A ILE 3.3 0.4 - - - -
203A GLU* 1.3 76.0 - - - +
205A ARG* 1.3 63.4 + - - +
207A LEU* 3.8 0.5 - - - +
208A GLU* 2.9 39.5 + - + +
224A LEU* 4.2 11.4 - - + -
227A HIS* 3.6 36.1 - - + +
234A LEU* 4.6 5.4 - - + -
236A LEU* 3.8 31.0 - - + -
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Residues in contact with ARG 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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201A GLN 3.2 13.0 + - - +
202A ILE* 3.3 14.4 + - - +
204A VAL* 1.3 78.1 - - - +
206A LEU* 1.3 76.5 + - - +
208A GLU* 3.5 7.4 + - - +
209A LEU* 3.0 39.5 + - + +
313A GLN* 3.0 31.3 + - - -
316A GLN* 3.7 26.5 + - - +
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Residues in contact with LEU 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 ILE* 3.2 23.9 + - + +
203A GLU* 3.9 3.6 - - - +
205A ARG* 1.3 93.0 - - - +
207A LEU* 1.3 59.6 + - - +
209A LEU* 3.3 6.8 + - + +
210A MET* 3.0 40.6 + - + +
283A ILE* 4.1 22.0 - - + +
308A PHE* 4.3 6.5 - - + +
311A SER* 3.6 44.4 - - - +
312A CYS* 4.1 3.8 - - - +
313A GLN* 3.8 31.9 - - + +
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Residues in contact with LEU 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 GLU* 2.9 44.2 + - + +
204A VAL 3.9 2.7 - - - +
206A LEU* 1.3 74.5 - - - +
208A GLU* 1.3 57.9 + - - +
210A MET* 3.2 26.5 + - + +
211A ASN* 3.0 33.9 + - - +
221A ILE* 4.3 3.1 - - + -
222A VAL* 3.9 24.7 - - + +
224A LEU* 3.9 26.0 - - + +
236A LEU* 4.7 0.7 - - + -
238A PHE* 3.6 27.1 - - + -
308A PHE* 4.2 13.7 - - + -
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Residues in contact with GLU 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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204A VAL* 2.9 36.8 + - + +
205A ARG* 3.9 6.0 - - - +
207A LEU* 1.3 75.5 - - - +
209A LEU* 1.3 60.8 + - - +
211A ASN* 3.4 22.8 + - - +
212A LYS* 3.6 13.3 + - - +
224A LEU* 4.4 9.1 - - + +
227A HIS* 3.0 28.6 + - - -
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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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205A ARG* 3.0 29.4 + - + +
206A LEU* 3.5 11.9 - - + +
207A LEU 3.2 0.2 - - - -
208A GLU* 1.3 74.3 - - - +
210A MET* 1.3 63.1 + - - +
212A LYS* 3.3 30.2 + - + +
213A HIS* 3.3 18.2 - - - +
280A GLU 4.3 5.8 - - - +
281A LEU* 3.8 19.7 - - + -
283A ILE* 4.8 1.1 - - + -
313A GLN* 3.6 35.7 - - - +
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Residues in contact with MET 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 LEU* 3.0 27.8 + - + +
207A LEU* 3.2 37.0 + - + +
209A LEU* 1.3 77.2 - - - +
211A ASN* 1.3 57.8 - - - +
213A HIS* 2.9 25.8 + - - +
218A LYS* 3.6 10.8 - - + +
221A ILE* 3.7 21.3 - - + -
275A PHE* 3.7 21.6 - - + -
276A LEU* 3.9 21.1 - - - -
281A LEU* 4.1 10.3 - - + -
283A ILE* 3.8 17.9 - - + -
308A PHE* 3.9 24.9 - - + -
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Residues in contact with ASN 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 LEU 3.0 21.8 + - - +
208A GLU* 3.4 27.4 + - - +
209A LEU 3.3 0.4 - - - -
210A MET* 1.3 75.6 - - - +
212A LYS* 1.3 59.2 + - - +
213A HIS 3.2 1.7 + - - -
218A LYS* 3.8 30.8 + - + -
223A HIS* 3.6 30.8 + - + +
224A LEU* 3.8 13.4 + - - +
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Residues in contact with LYS 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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208A GLU 3.6 9.7 + - - +
209A LEU* 3.3 29.2 + - + +
210A MET 3.1 2.0 + - - -
211A ASN* 1.3 77.3 - - - +
213A HIS* 1.3 66.2 + - + +
214A ASP* 3.9 2.3 + - - +
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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