Contacts of the helix formed by residues 208 - 222 (chain A) in PDB entry 1A16
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 GLU 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A MET 4.0 0.2 + - - -
207A PHE* 1.3 70.8 - - - +
209A TYR* 1.3 63.6 + - - +
210A HIS 3.0 1.9 + - - -
211A LEU* 3.1 11.3 + - - +
212A GLU 3.5 3.3 + - - -
233A VAL* 3.2 47.9 - - + +
235A SER* 2.7 35.5 + - - +
238A ASN* 2.8 21.9 + - - -
244A TYR* 2.7 25.1 + - - -
247A ASN* 3.6 7.6 + - - +
248A GLU 3.1 3.5 + - - -
249A CYS* 2.9 31.5 + - - +
251A MET* 3.8 12.9 - - + +
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Residues in contact with TYR 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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207A PHE* 3.4 41.4 - + + -
208A GLU* 1.3 75.2 - - - +
210A HIS* 1.3 84.3 + + - +
211A LEU 3.3 0.2 - - - -
212A GLU* 3.3 19.7 + - - +
213A GLY* 3.0 22.7 + - - -
246A GLU 5.4 0.9 - - - +
247A ASN* 2.9 34.8 + - + +
248A GLU* 4.4 7.0 - - - -
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Residues in contact with HIS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A MET* 3.8 29.1 - - + +
207A PHE* 2.9 53.6 + + + +
209A TYR* 1.3 96.9 + + - +
211A LEU* 1.3 61.5 + - - +
213A GLY* 3.2 3.1 + - - +
214A GLU* 3.0 32.0 + - + +
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Residues in contact with LEU 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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198A ALA* 3.7 24.0 - - + +
201A LYS* 4.5 4.5 - - + -
202A CYS* 4.0 20.2 - - + +
206A MET* 3.6 24.2 - - + -
208A GLU 3.1 8.4 + - - +
210A HIS* 1.3 73.0 - - - +
212A GLU* 1.3 60.2 + - - +
214A GLU* 3.2 5.8 + - + +
215A ILE* 2.9 36.9 + - - +
233A VAL* 4.2 6.3 - - + -
251A MET* 3.8 33.0 - - + -
257A VAL* 4.5 1.8 - - + -
259A ILE* 3.5 33.2 - - + -
276A PHE* 4.4 3.1 - - + -
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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 GLU 3.5 2.2 + - - -
209A TYR* 3.3 20.0 + - - +
210A HIS 3.2 0.2 - - - -
211A LEU* 1.3 78.9 - - - +
213A GLY* 1.3 57.0 + - - +
215A ILE* 3.4 2.0 + - - -
216A HIS* 3.0 61.0 + - + +
231A THR* 4.0 23.5 - - + +
233A VAL* 4.1 2.8 - - + +
245A THR 5.0 1.0 - - - +
247A ASN* 2.8 31.2 + - - +
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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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209A TYR 3.0 14.1 + - - -
210A HIS* 3.2 4.7 + - - -
211A LEU 3.2 0.6 - - - -
212A GLU* 1.3 78.1 - - - +
214A GLU* 1.3 62.1 + - - +
216A HIS* 3.6 4.6 + - - +
217A HIS* 3.1 24.1 + - - +
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Residues in contact with GLU 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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197A ARG* 2.8 61.2 + - + +
198A ALA* 5.0 6.1 - - - -
201A LYS* 3.2 41.6 + - + +
206A MET* 5.4 2.7 - - + -
210A HIS 3.0 20.3 + - - +
211A LEU* 3.2 11.6 + - + +
213A GLY* 1.3 75.9 - - - +
215A ILE* 1.3 61.9 + - + +
217A HIS 3.2 1.7 + - - -
218A GLU* 3.0 19.4 + - - +
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Residues in contact with ILE 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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194A ALA* 3.9 29.4 - - + +
195A HIS* 5.2 2.7 - - + +
198A ALA* 4.0 12.8 - - + -
211A LEU 2.9 24.5 + - - +
212A GLU* 3.7 7.4 - - - +
214A GLU* 1.3 75.7 - - - +
216A HIS* 1.3 63.1 + - + +
218A GLU* 3.1 4.2 + - - +
219A PHE* 2.9 60.6 + - + -
231A THR* 4.6 2.9 - - + -
233A VAL* 5.0 0.4 - - + -
259A ILE* 3.5 33.4 - - + -
261A ALA* 3.9 15.0 - - + -
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Residues in contact with HIS 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* 3.0 45.7 + - + +
213A GLY* 4.3 4.9 - - - +
215A ILE* 1.3 84.0 - - + +
217A HIS* 1.3 63.7 + - - +
219A PHE* 3.8 12.4 - + + +
220A ASN* 3.1 23.0 + - - +
225A ARG 5.0 5.2 - - - +
227A PRO* 3.4 29.1 - - + +
231A THR* 2.4 34.2 + - - -
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Residues in contact with HIS 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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197A ARG* 2.8 35.5 + - - +
213A GLY 3.1 18.4 + - - +
214A GLU 3.6 4.0 - - - +
215A ILE 3.2 0.2 - - - -
216A HIS* 1.3 75.8 - - - +
218A GLU* 1.3 61.5 + - - +
220A ASN* 3.4 10.3 + - + +
221A ARG* 3.0 43.0 + - + +
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Residues in contact with GLU 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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190A ILE* 4.7 2.0 - - - +
193A MET* 3.9 13.6 - - + +
194A ALA* 3.7 33.4 - - + +
197A ARG* 3.0 32.0 + - - +
214A GLU 3.0 12.6 + - - +
215A ILE 3.5 7.6 - - - +
217A HIS* 1.3 75.8 - - - +
219A PHE* 1.3 66.7 + - - +
221A ARG* 3.1 35.4 + - - +
222A HIS* 2.9 49.3 + - + +
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Residues in contact with PHE 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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190A ILE* 4.1 12.5 - - + +
191A THR* 4.0 11.2 - - + -
194A ALA* 3.5 25.8 - - + -
215A ILE* 2.9 32.6 + - + -
216A HIS* 3.8 28.3 - + - +
218A GLU* 1.3 76.1 - - - +
220A ASN* 1.3 63.5 + - - +
222A HIS* 3.2 8.1 + - - +
223A GLY 3.6 0.2 + - - -
224A ALA* 3.1 33.8 + - - +
225A ARG 5.2 2.2 - - - +
226A TYR 4.5 0.7 - - - -
227A PRO* 4.0 15.7 - - + -
261A ALA* 4.1 3.1 - - + -
262A GLY* 3.3 41.5 - - - -
263A CYS* 3.6 24.9 - - + -
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Residues in contact with ASN 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 HIS 3.1 15.9 + - - +
217A HIS* 3.6 12.9 + - + +
219A PHE* 1.3 80.8 - - - +
221A ARG* 1.3 62.1 + - - +
223A GLY* 2.9 21.5 + - - -
224A ALA 3.3 9.8 + - - +
225A ARG* 4.1 27.9 + - - +
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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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193A MET* 5.3 3.0 - - - -
197A ARG* 4.9 0.6 - - - +
217A HIS* 3.0 33.4 + - + +
218A GLU* 3.1 46.2 + - - +
219A PHE 3.4 0.4 - - - -
220A ASN* 1.3 80.5 + - - +
222A HIS* 1.3 77.4 + - + +
223A GLY 3.3 0.9 + - - -
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Residues in contact with HIS 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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186A ARG* 3.6 25.9 + - - +
190A ILE* 3.8 29.1 - - + +
193A MET* 3.6 26.3 - - + +
218A GLU* 2.9 48.9 + - + +
219A PHE 3.2 5.7 + - - +
220A ASN 3.1 1.2 - - - -
221A ARG* 1.3 101.2 + - + +
223A GLY* 1.3 60.4 + - - +
224A ALA 3.5 1.6 - - - -
265A TYR* 4.0 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
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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