Contacts of the helix formed by residues 191 - 212 (chain A) in PDB entry 3RAW
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 VAL 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A GLU 3.9 22.2 - - - +
142A GLY* 4.3 3.4 - - - -
189A ARG* 2.8 27.4 + - + +
190A ASN* 1.3 77.7 - - - +
192A GLY* 1.3 69.7 + - - +
193A LYS* 4.1 11.0 - - + +
194A TYR* 3.1 21.4 + - + -
195A ARG* 2.9 25.6 + - - +
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Residues in contact with GLY 192 (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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191A VAL* 1.3 74.2 - - - +
193A LYS* 1.3 59.7 - - - +
195A ARG* 3.3 19.4 + - - +
196A GLU* 3.0 26.1 + - - +
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Residues in contact with LYS 193 (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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191A VAL* 3.2 7.9 + - + +
192A GLY* 1.3 75.0 - - - +
194A TYR* 1.3 72.4 + - + +
196A GLU* 3.4 6.5 - - - +
197A ALA* 3.0 27.3 + - - +
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Residues in contact with TYR 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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166A THR* 3.5 35.9 + - - -
167A PHE* 3.6 26.0 - - + +
188A ILE* 3.6 20.1 - - + +
189A ARG* 3.3 31.2 + - + +
191A VAL* 3.1 26.0 + - + +
193A LYS* 1.3 83.1 - - + +
195A ARG* 1.3 66.3 + - - +
197A ALA* 3.2 9.4 + - + +
198A ALA* 2.9 24.4 + - - +
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Residues in contact with ARG 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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188A ILE* 4.1 5.8 - - - +
189A ARG 4.3 2.2 + - - +
190A ASN* 2.6 42.4 + - - -
191A VAL* 2.9 11.3 + - - +
192A GLY* 3.6 22.7 - - - +
194A TYR* 1.3 75.5 - - - +
196A GLU* 1.3 57.1 + - - +
198A ALA* 3.1 5.0 + - - +
199A ARG* 2.9 58.8 + - - +
227A ASN* 4.8 3.6 - - - +
230A GLY* 3.0 21.3 + - - +
232A MET* 3.5 29.1 - - + +
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Residues in contact with GLU 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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192A GLY 3.0 17.6 + - - +
193A LYS* 3.4 7.0 - - - +
195A ARG* 1.3 75.8 - - - +
197A ALA* 1.3 63.2 + - - +
199A ARG* 3.2 22.5 + - - +
200A LEU* 3.0 41.5 + - + +
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Residues in contact with ALA 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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193A LYS 3.0 17.9 + - - +
194A TYR* 3.2 12.5 + - + +
196A GLU* 1.3 75.6 - - - +
198A ALA* 1.3 57.4 + - - +
200A LEU* 3.5 10.3 + - - +
201A GLU* 2.9 26.5 + - - +
322A GLY* 3.7 26.2 - - - +
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Residues in contact with ALA 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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188A ILE* 3.7 30.3 - - + -
194A TYR 2.9 13.0 + - - +
195A ARG 3.5 7.4 - - - +
197A ALA* 1.3 76.1 - - - +
199A ARG* 1.3 63.8 + - - +
201A GLU* 3.2 9.4 + - - +
202A ILE* 2.9 30.1 + - - +
232A MET* 3.8 15.3 - - + -
234A ILE* 4.2 8.0 - - + +
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Residues in contact with ARG 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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195A ARG* 2.9 43.6 + - - +
196A GLU* 3.2 20.0 + - - +
198A ALA* 1.3 73.9 - - - +
200A LEU* 1.3 64.6 + - + +
202A ILE* 3.2 11.6 + - + +
203A ASN* 3.1 21.7 + - - +
227A ASN* 4.0 20.6 - - - +
232A MET* 4.2 20.2 - - + +
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Residues in contact with LEU 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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196A GLU* 3.0 35.1 + - + +
197A ALA* 3.5 11.7 - - - +
199A ARG* 1.3 77.8 - - + +
201A GLU* 1.3 62.4 + - - +
203A ASN* 3.2 9.7 + - + +
204A VAL* 3.0 28.6 + - + +
321A PHE 4.8 1.1 - - - +
322A GLY 4.6 12.6 - - - +
323A SER* 6.2 0.7 - - - -
324A ALA 5.4 8.3 - - - +
329A GLU* 5.0 14.8 - - - +
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Residues in contact with GLU 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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1A 3RA 3.7 4.2 - - - +
186A LYS* 2.5 34.1 + - - -
188A ILE* 5.3 0.5 - - - +
197A ALA 2.9 17.5 + - - +
198A ALA* 3.2 10.9 + - - +
200A LEU* 1.3 76.3 - - - +
202A ILE* 1.3 57.8 + - - +
204A VAL* 3.2 3.2 + - - +
205A LEU* 2.8 47.6 + - + +
234A ILE* 3.5 17.1 - - + +
236A PHE* 4.2 3.4 - - - -
320A ASP* 3.4 5.9 + - - -
321A PHE* 3.1 36.5 + - + +
322A GLY* 3.7 16.8 + - - +
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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 ALA 2.9 20.7 + - - +
199A ARG* 3.2 8.5 + - + +
201A GLU* 1.3 76.3 - - - +
203A ASN* 1.3 57.6 + - - +
205A LEU* 4.5 5.8 - - - -
206A LYS* 3.0 30.8 + - + +
222A MET* 4.0 7.6 - - + +
225A TRP* 3.5 54.3 - - + +
232A MET* 3.7 31.9 - - + -
233A CYS 5.1 0.2 - - - +
234A ILE* 3.7 24.5 - - + -
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Residues in contact with ASN 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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199A ARG 3.1 11.5 + - - +
200A LEU* 3.6 12.3 + - + +
201A GLU 3.2 0.2 - - - -
202A ILE* 1.3 76.2 - - - +
204A VAL* 1.3 66.6 + - - +
206A LYS* 3.5 13.7 + - - +
207A LYS* 3.0 30.8 + - - +
326A PHE* 4.2 20.2 - - - -
329A GLU* 5.5 3.4 + - - -
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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 LEU* 3.0 19.6 + - + +
201A GLU 3.6 5.6 - - - +
203A ASN* 1.3 78.8 - - - +
205A LEU* 1.3 57.5 + - - +
207A LYS* 3.1 6.3 + - - +
208A ILE* 2.8 46.3 + - + +
279A LEU* 4.1 14.8 - - + -
321A PHE* 3.7 30.3 - - + +
324A ALA* 4.0 26.7 - - + +
326A PHE* 4.3 19.5 - - + -
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Residues in contact with LEU 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 GLU* 2.8 44.6 + - + +
204A VAL* 1.3 73.2 - - - +
206A LYS* 1.3 58.1 + - - +
208A ILE* 3.3 10.0 + - + +
209A LYS* 2.9 30.7 + - - +
220A VAL* 4.0 28.5 - - + +
222A MET* 3.8 33.0 - - + +
234A ILE* 4.2 4.0 - - + -
236A PHE* 3.8 24.9 - - + -
321A PHE* 3.7 27.8 - - + -
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Residues in contact with LYS 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* 3.0 19.8 + - + +
203A ASN* 3.8 17.5 - - - +
205A LEU* 1.3 78.3 - - - +
207A LYS* 1.3 64.3 + - + +
209A LYS* 3.3 15.1 + - - +
210A GLU* 3.0 60.9 + - + +
222A MET* 3.8 12.8 - - + +
225A TRP* 6.2 0.4 - - - +
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Residues in contact with LYS 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 ASN* 3.0 26.6 + - - +
204A VAL* 3.6 5.4 - - - +
206A LYS* 1.3 78.8 - - + +
208A ILE* 1.3 56.9 + - + +
210A GLU* 3.3 17.5 + - + +
211A LYS* 2.9 39.7 + - + +
279A LEU* 6.0 1.6 - - + -
326A PHE* 3.8 32.8 - - + -
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Residues in contact with ILE 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* 2.8 42.0 + - + +
205A LEU* 3.6 12.6 - - + +
207A LYS* 1.3 73.4 - - - +
209A LYS* 1.3 58.7 + - - +
211A LYS* 3.2 5.9 + - - +
212A ASP* 2.9 32.9 + - + +
219A CYS* 4.1 18.8 - - + -
220A VAL 5.9 0.9 - - - +
273A PHE* 4.1 19.1 - - + -
274A LEU* 4.0 16.6 - - + -
279A LEU* 4.7 6.1 - - + -
321A PHE* 3.9 32.5 - - + -
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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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205A LEU 2.9 21.2 + - - +
206A LYS* 3.7 12.8 - - - +
208A ILE* 1.3 77.8 - - + +
210A GLU* 1.3 62.4 + - + +
212A ASP 3.4 7.2 - - - +
213A LYS* 3.4 24.9 + - - +
221A LEU* 4.4 19.0 - - + +
222A MET* 3.1 51.1 + - + +
223A SER* 4.7 8.7 + - - +
224A ASP* 5.9 0.2 - - - +
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Residues in contact with GLU 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 LYS* 3.0 55.6 + - + +
207A LYS* 3.6 15.8 + - + +
208A ILE 3.2 0.2 - - - -
209A LYS* 1.3 80.4 - - + +
211A LYS* 1.3 61.4 + - + +
212A ASP 3.3 0.2 - - - -
213A LYS* 4.6 5.1 + - - +
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Residues in contact with LYS 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 LYS* 2.9 28.6 + - + +
208A ILE* 3.2 2.9 + - - +
210A GLU* 1.3 76.7 - - + +
212A ASP* 1.3 58.9 + - - +
213A LYS 4.0 0.7 - - - -
217A PHE* 5.5 1.4 - - - -
273A PHE* 3.9 27.2 - - + -
277A ASN* 3.7 22.9 - - + +
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Residues in contact with ASP 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 ILE* 2.9 18.1 + - + +
209A LYS* 3.4 10.4 - - - +
211A LYS* 1.3 80.1 - - - +
213A LYS* 1.3 65.4 + - - +
214A GLU* 3.9 4.0 + - - +
215A ASN* 3.1 13.2 + - - -
216A LYS* 3.0 25.8 + - - +
217A PHE* 3.0 43.3 + - + +
218A LEU 4.5 0.3 + - - -
219A CYS* 5.4 2.1 + - - +
273A PHE* 3.8 15.4 - - + -
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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