Contacts of the helix formed by residues 203 - 223 (chain A) in PDB entry 1NUA
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 SER 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ALA 3.0 13.4 + - - +
202A SER* 1.3 84.4 + - - +
204A GLU* 1.3 62.1 + - - +
205A GLU* 3.4 14.6 + - - +
206A GLU* 2.9 37.5 + - - +
207A PHE* 3.1 9.0 + - - +
372A GLY* 3.9 1.9 - - - -
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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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203A SER* 1.3 71.8 - - - +
205A GLU* 1.3 65.0 + - + +
207A PHE* 3.6 1.9 + - - +
208A THR* 2.8 36.2 + - - -
315A ARG* 2.8 32.0 + - - +
371A ILE* 3.2 44.2 - - + +
372A GLY* 3.9 5.4 - - - -
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Residues in contact with GLU 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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203A SER* 3.0 9.6 + - - +
204A GLU* 1.3 85.2 - - + +
206A GLU* 1.3 60.0 + - - +
208A THR* 3.3 8.0 + - - +
209A ALA* 3.1 24.9 + - - +
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Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ALA* 3.9 18.8 - - + -
203A SER* 2.9 27.6 + - - +
205A GLU* 1.3 73.8 - - - +
207A PHE* 1.3 63.6 + - - +
209A ALA* 3.3 3.5 + - - +
210A LEU* 3.1 26.4 + - + +
242A ARG* 2.6 50.5 + - - +
245A ALA* 3.5 32.4 - - + +
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Residues in contact with PHE 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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196A ILE* 3.9 22.2 - - + -
199A ALA* 3.9 7.1 - - + +
200A ALA* 3.7 34.8 - - + -
203A SER 3.1 10.4 + - - +
204A GLU 3.8 8.1 - - - +
206A GLU* 1.3 73.2 - - - +
208A THR* 1.3 59.8 + - - +
210A LEU* 3.2 12.2 + - + +
211A GLU* 2.9 64.6 + - + +
315A ARG* 3.7 18.8 - - - -
316A ILE* 4.0 15.3 - - + -
319A CYS* 3.6 20.4 - - + -
371A ILE* 3.8 30.1 - - + -
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Residues in contact with THR 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 GLU* 2.8 26.4 + - - -
205A GLU* 3.4 13.2 - - - +
207A PHE* 1.3 78.6 - - - +
209A ALA* 1.3 56.1 + - - +
211A GLU* 3.2 14.8 + - - +
212A GLU* 3.0 49.2 + - + +
315A ARG* 3.3 14.4 + - - -
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Residues in contact with ALA 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 GLU 3.1 13.0 + - - +
206A GLU* 3.6 5.8 - - - +
207A PHE 3.3 0.2 - - - -
208A THR* 1.3 73.4 - - - +
210A LEU* 1.3 60.2 + - - +
212A GLU* 3.8 12.7 - - - +
213A ASN* 3.0 37.9 + - - +
242A ARG* 3.3 38.1 - - - +
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Residues in contact with LEU 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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192A MET* 3.7 24.5 - - + -
195A VAL* 4.1 13.2 - - + +
196A ILE* 4.1 17.3 - - + -
199A ALA* 3.4 33.2 - - + -
206A GLU* 3.1 18.0 + - + +
207A PHE* 3.3 11.2 - - + +
209A ALA* 1.3 76.8 - - - +
211A GLU* 1.3 65.5 + - - +
214A ALA 2.9 10.2 + - - -
217A ILE* 5.6 0.2 - - + -
242A ARG* 4.0 22.0 - - + +
319A CYS* 4.5 5.8 - - - -
323A TYR* 2.6 42.4 + - + +
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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 PHE* 2.9 45.7 + - + +
208A THR* 3.2 14.1 + - - +
210A LEU* 1.3 76.2 - - - +
212A GLU* 1.3 64.6 + - + +
214A ALA* 3.4 15.8 - - - +
315A ARG* 3.2 41.9 + - - +
318A LYS* 6.0 0.2 - - - +
319A CYS* 4.2 15.0 - - + +
322A ALA* 5.5 1.4 - - - +
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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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208A THR* 3.0 30.3 + - + +
209A ALA* 3.8 13.4 - - - +
211A GLU* 1.3 80.5 - - + +
213A ASN* 1.3 68.5 + - - +
214A ALA 3.3 1.4 + - - -
215A GLU* 4.3 7.4 + - - +
216A THR* 4.4 5.4 + - - -
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Residues in contact with ASN 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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209A ALA* 3.0 22.2 + - - +
212A GLU* 1.3 82.0 - - - +
214A ALA* 1.3 64.2 + - - +
215A GLU 3.5 0.7 - - - -
216A THR* 3.3 9.8 + - - +
217A ILE* 2.8 34.8 + - + +
238A ILE* 3.4 43.6 - - + +
242A ARG* 3.0 33.5 - - - +
323A TYR* 3.7 4.0 - - - +
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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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210A LEU 2.9 11.1 + - - +
211A GLU* 3.4 17.0 - - - +
212A GLU 3.2 1.0 - - - -
213A ASN* 1.3 75.0 - - - +
215A GLU* 1.3 59.4 + - - +
217A ILE* 3.9 0.9 - - - +
218A LEU* 2.8 35.9 + - - +
322A ALA* 3.7 32.8 - - + +
323A TYR* 3.4 23.1 - - + -
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Residues in contact with GLU 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 4.9 0.2 + - - -
212A GLU 4.3 5.6 + - - +
213A ASN 3.5 0.6 - - - -
214A ALA* 1.3 77.9 - - - +
216A THR* 1.3 56.8 + - - +
218A LEU* 3.6 4.1 - - - +
219A LYS* 2.7 43.8 + - + +
322A ALA 4.9 1.5 + - - -
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Residues in contact with THR 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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212A GLU 4.4 3.8 + - - -
213A ASN* 3.6 17.5 + - - -
215A GLU* 1.3 80.2 - - - +
217A ILE* 1.3 67.3 + - - +
219A LYS* 2.8 20.8 + - + +
220A ALA* 2.9 14.0 + - - +
235A THR* 3.2 33.0 - - + -
238A ILE* 5.2 7.0 - - + +
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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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188A PHE* 3.8 34.1 - - + -
192A MET* 5.2 4.0 - - + -
213A ASN* 2.8 37.4 + - + +
214A ALA 3.9 1.8 - - - +
216A THR* 1.3 72.7 - - - +
218A LEU* 1.3 59.6 + - - +
220A ALA* 3.1 8.4 + - - +
221A VAL* 2.9 31.7 + - + +
232A PHE* 5.6 1.6 - - + -
235A THR* 5.6 5.6 - - - +
238A ILE* 4.2 12.6 - - + -
239A LEU* 4.3 18.6 - - + -
242A ARG* 4.2 21.1 - - + -
243A ILE* 6.0 0.2 - - + -
323A TYR* 3.8 27.8 - - + +
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Residues in contact with LEU 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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188A PHE* 5.7 2.7 - - + -
189A ILE* 4.2 26.7 - - + -
214A ALA 2.8 22.6 + - - +
215A GLU* 3.8 4.3 - - - +
217A ILE* 1.3 75.0 - - - +
219A LYS* 1.3 61.9 + - - +
221A VAL* 3.5 11.4 + - + -
222A ARG* 3.1 59.2 + - - +
321A ALA 5.1 0.2 - - - +
322A ALA 3.1 23.6 - - - +
323A TYR* 3.9 10.3 - - + +
324A GLY* 3.8 15.0 - - - +
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Residues in contact with LYS 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 GLU* 2.7 28.7 + - + +
216A THR* 2.8 10.7 + - + +
218A LEU* 1.3 71.8 - - - +
220A ALA* 1.3 60.7 + - - +
222A ARG* 3.4 4.4 + - - +
223A ARG* 2.8 37.6 + - + +
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Residues in contact with ALA 220 (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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216A THR* 2.9 10.7 + - + +
217A ILE* 3.5 10.8 - - - +
219A LYS* 1.3 74.0 - - - +
221A VAL* 1.3 67.6 + - - +
222A ARG 3.1 1.2 + - - -
223A ARG* 3.1 24.6 + - - +
231A ARG* 3.1 28.2 - - - +
232A PHE* 3.7 23.8 - - + -
235A THR* 4.6 10.3 - - + +
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Residues in contact with VAL 221 (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 5.7 1.6 - - - +
185A VAL* 3.7 36.9 - - + +
188A PHE* 3.6 57.7 - - + -
189A ILE* 4.5 5.2 - - + -
217A ILE* 2.9 25.0 + - + +
218A LEU* 3.7 10.8 - - + +
219A LYS 3.4 0.2 - - - -
220A ALA* 1.3 78.1 - - - +
222A ARG* 1.3 57.5 + - - +
231A ARG* 3.4 21.5 + - - +
232A PHE* 4.1 8.3 - - + -
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Residues in contact with ARG 222 (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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185A VAL* 4.1 27.7 - - + +
189A ILE* 4.6 5.9 - - - +
218A LEU* 3.1 52.7 + - + +
219A LYS* 4.0 3.6 - - - +
220A ALA 3.1 0.4 - - - -
221A VAL* 1.3 76.0 - - - +
223A ARG* 1.3 67.2 + - - +
224A GLU* 3.7 3.6 + - - +
231A ARG* 4.4 0.4 - - - -
324A GLY* 4.3 15.0 + - - -
333A ARG* 5.5 4.2 - - - +
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Residues in contact with ARG 223 (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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219A LYS* 2.8 26.0 + - + +
220A ALA* 3.1 18.4 + - - +
222A ARG* 1.3 78.5 - - - +
224A GLU* 1.3 75.5 + - - +
225A VAL* 3.3 20.6 + - + +
226A THR* 4.2 1.0 + - - +
229A GLU* 3.6 31.5 + - - +
230A HIS 3.7 19.2 + - - -
231A ARG* 2.7 47.3 + - - -
233A GLU* 4.8 8.1 + - - +
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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