Contacts of the helix formed by residues 210 - 229 (chain A) in PDB entry 4WNG
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 210 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A HIS* 2.8 43.0 + - - +
208A LEU* 3.7 25.4 - - - +
209A GLY* 1.3 74.5 - - - +
211A PHE* 1.3 58.4 + - - +
212A ARG 3.3 2.5 - - - -
213A ASP* 3.2 22.0 + - - +
214A ALA* 3.0 24.1 + - - +
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Residues in contact with PHE 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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206A TYR* 3.5 46.4 - + - -
209A GLY* 3.3 26.6 + - - -
210A ASN* 1.3 72.9 - - - +
212A ARG* 1.3 62.1 + - - +
214A ALA* 3.2 5.7 + - - +
215A VAL* 3.1 26.5 + - - +
244A ALA* 4.2 7.1 - - + +
247A PHE* 3.5 56.3 - + + -
248A LEU* 3.7 27.6 - - + -
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Residues in contact with ARG 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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210A ASN 3.3 0.6 - - - -
211A PHE* 1.3 78.2 - - - +
213A ASP* 1.3 65.7 + - - +
215A VAL* 3.4 8.2 + - - +
216A ILE* 3.2 29.0 + - + +
248A LEU* 3.9 31.0 - - + -
250A GLU* 5.9 2.7 - - - -
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Residues in contact with ASP 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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205A HIS* 3.7 31.3 - - + +
210A ASN* 3.2 23.3 + - - +
212A ARG* 1.3 76.5 - - - +
214A ALA* 1.3 60.8 + - - +
216A ILE* 3.3 19.3 + - - +
217A ALA* 2.9 29.1 + - - +
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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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202A GLY* 3.3 28.3 - - - +
205A HIS* 3.8 3.3 - - - +
206A TYR* 3.9 16.8 - - + +
210A ASN 3.0 12.1 + - - +
211A PHE* 3.2 11.4 + - - +
213A ASP* 1.3 77.6 - - - +
215A VAL* 1.3 52.6 + - - +
217A ALA* 3.1 2.4 + - - +
218A HIS* 2.7 46.3 + - + -
244A ALA* 4.4 7.6 - - + -
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Residues in contact with VAL 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 PHE 3.1 13.1 + - - +
212A ARG* 3.5 10.3 - - - +
214A ALA* 1.3 76.6 - - - +
216A ILE* 1.3 56.7 + - + +
218A HIS* 3.1 1.3 + - - -
219A GLU* 2.7 56.3 + - - +
241A LEU* 3.6 16.3 - - + +
244A ALA* 4.0 17.0 - - + +
245A TYR* 3.5 43.5 - - + +
248A LEU* 4.2 9.0 - - + -
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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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212A ARG* 3.2 17.3 + - + +
213A ASP* 3.6 21.1 - - - +
214A ALA 3.3 0.2 - - - -
215A VAL* 1.3 80.2 - - + +
217A ALA* 1.3 63.6 + - - +
219A GLU* 4.2 13.0 - - - +
220A GLN* 3.1 43.7 + - + +
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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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198A PHE* 3.4 43.0 - - + +
201A LEU* 4.4 12.8 - - + -
202A GLY* 3.5 20.9 - - - +
205A HIS* 4.8 1.1 - - + -
213A ASP 2.9 14.2 + - - +
216A ILE* 1.3 80.0 - - - +
218A HIS* 1.3 61.6 + - - +
220A GLN* 3.2 2.6 + - - +
221A ARG 3.0 17.5 + - - -
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Residues in contact with HIS 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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199A GLY* 3.2 28.1 + - - -
202A GLY* 3.4 14.4 + - - -
203A ASN* 3.1 28.5 + - - -
206A TYR* 5.5 2.0 - - - +
214A ALA* 2.7 38.9 + - + +
215A VAL* 5.0 0.4 - - - -
217A ALA* 1.3 69.9 - - - +
219A GLU* 1.3 55.8 + - - +
221A ARG* 3.5 7.2 - - - +
222A LEU* 2.7 35.7 + - - +
237A ALA* 4.1 9.0 - - - +
240A ASN* 3.4 40.2 + - + +
241A LEU* 3.7 23.8 - - + -
244A ALA* 5.4 0.9 - - + -
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Residues in contact with GLU 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 VAL* 2.7 38.1 + - - +
216A ILE* 3.6 16.6 - - - +
218A HIS* 1.3 72.3 - - - +
220A GLN* 1.3 73.5 + - - +
222A LEU* 3.4 10.7 + - + +
223A LEU* 3.1 22.0 + - - +
241A LEU* 4.0 17.0 - - + +
245A TYR* 4.1 6.9 + - - -
257A TYR* 4.9 7.4 + - - +
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Residues in contact with GLN 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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198A PHE* 3.7 39.7 - - + -
216A ILE* 3.1 36.4 + - + +
217A ALA 3.2 6.1 + - - +
219A GLU* 1.3 87.6 + - - +
221A ARG* 1.3 66.0 + - - +
223A LEU* 3.4 12.3 + - - +
224A ILE* 3.3 26.9 + - + +
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Residues in contact with ARG 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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192A ALA 5.5 0.4 + - - -
195A GLY* 3.1 42.1 - - - +
196A ARG* 4.4 3.8 - - - +
198A PHE* 3.9 9.8 - - + +
199A GLY* 3.6 15.3 - - - +
217A ALA 3.0 13.7 + - - +
218A HIS* 3.5 13.5 - - - +
220A GLN* 1.3 77.5 - - - +
222A LEU* 1.3 64.6 + - - +
224A ILE* 3.3 8.3 + - - +
225A ALA* 3.0 36.1 + - - +
228A PHE* 6.1 0.2 - - - -
230A ASP* 5.2 2.0 + - - -
233A ALA* 3.7 25.8 - - - +
236A ARG* 3.7 2.4 - - - +
237A ALA* 4.3 16.4 - - + +
998B GLU* 2.8 37.0 + - - -
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Residues in contact with LEU 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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218A HIS 2.7 19.7 + - - +
219A GLU* 3.5 10.1 - - + +
220A GLN 3.3 0.2 - - - -
221A ARG* 1.3 73.3 - - - +
223A LEU* 1.3 62.1 + - - +
225A ALA* 3.1 6.2 + - - +
226A LYS* 3.0 42.6 + - - +
234A GLU* 3.7 24.2 - - + +
237A ALA* 3.8 12.5 - - + +
238A TYR* 3.5 47.8 - - + -
241A LEU* 4.1 13.0 - - + -
257A TYR* 5.1 3.8 - - + +
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Residues in contact with LEU 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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191A ARG* 3.7 24.0 - - - +
219A GLU 3.1 10.1 + - - +
220A GLN* 3.6 16.6 - - - +
221A ARG 3.3 0.2 - - - -
222A LEU* 1.3 80.2 - - - +
224A ILE* 1.3 61.1 + - + +
226A LYS* 3.3 17.7 + - + +
227A GLU* 3.0 28.1 + - + +
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Residues in contact with ILE 224 (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 ARG* 3.5 52.5 - - + +
192A ALA* 4.9 0.7 - - - -
194A GLN* 3.9 16.2 - - + -
195A GLY* 3.7 27.8 - - - +
198A PHE* 3.9 13.7 - - + -
220A GLN* 3.3 15.8 + - + +
221A ARG* 3.8 11.4 - - - +
223A LEU* 1.3 76.1 - - + +
225A ALA* 1.3 66.1 + - - +
227A GLU* 3.1 8.3 + - + +
228A PHE* 3.1 39.0 + - + -
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Residues in contact with ALA 225 (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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221A ARG* 3.0 20.6 + - - +
222A LEU* 3.1 10.1 + - - +
224A ILE* 1.3 77.7 - - - +
226A LYS* 1.3 56.3 + - - +
228A PHE* 3.3 1.6 + - - -
229A GLY 3.0 6.9 + - - -
230A ASP* 2.8 36.3 + - - +
233A ALA* 3.7 15.0 - - + +
234A GLU* 3.5 35.8 - - - +
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Residues in contact with LYS 226 (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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222A LEU* 3.0 39.6 + - - +
223A LEU* 3.5 18.5 - - + +
225A ALA* 1.3 72.5 - - - +
227A GLU* 1.3 66.0 + - - +
229A GLY* 3.0 14.6 + - - +
234A GLU* 4.0 21.5 - - - +
238A TYR* 3.6 23.0 + - - -
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Residues in contact with GLU 227 (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 ARG* 2.9 56.4 + - - +
223A LEU* 3.0 17.5 + - + +
224A ILE* 3.3 11.2 - - - +
226A LYS* 1.3 78.7 - - - +
228A PHE* 1.3 66.5 + - + +
229A GLY 3.5 0.2 + - - -
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Residues in contact with PHE 228 (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 ARG* 3.8 12.8 - - + -
192A ALA* 3.6 44.6 - - + -
221A ARG* 6.1 0.2 - - - -
224A ILE* 3.1 36.2 + - + +
225A ALA* 3.9 4.0 - - - +
227A GLU* 1.3 87.6 - - + +
229A GLY* 1.3 60.7 + - - +
230A ASP* 4.2 12.2 - - + +
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Residues in contact with GLY 229 (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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225A ALA 3.0 5.2 + - - -
226A LYS* 3.0 13.6 + - - -
227A GLU 3.3 0.8 + - - -
228A PHE* 1.3 78.9 - - - +
230A ASP* 1.3 58.4 + - - +
231A LYS* 3.2 16.7 + - - +
234A GLU* 5.8 1.1 - - - -
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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