Contacts of the helix formed by residues 219 - 232 (chain A) in PDB entry 2GH1
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 HIS 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A MSE 3.8 18.3 + - + +
218A HIS* 1.3 77.0 - - - +
220A ASN* 1.3 77.8 + - + +
221A ASP* 2.8 53.4 + - + +
222A LYS* 3.0 13.8 + - - +
223A ASN* 3.4 15.9 + - - +
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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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219A HIS* 1.3 85.1 + - + +
221A ASP* 1.3 59.8 + - - +
223A ASN* 3.2 18.7 + - + +
224A ASP* 2.7 41.6 + - - +
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Residues in contact with ASP 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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217A MSE 4.9 9.0 - - - -
219A HIS* 2.8 32.6 + - + +
220A ASN* 1.3 80.7 - - - +
222A LYS* 1.3 62.0 + - - +
224A ASP* 3.3 11.7 + - - +
225A LEU* 2.9 24.6 + - - +
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Residues in contact with LYS 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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212A PHE 5.6 0.4 - - - +
213A LEU* 3.6 22.8 - - + +
214A ASP 3.0 33.2 + - - +
215A SER* 4.1 9.9 + - - +
217A MSE 2.7 54.5 + - + +
218A HIS* 4.4 7.4 + - - +
219A HIS 3.0 10.4 + - - +
221A ASP* 1.3 78.3 - - - +
223A ASN* 1.3 77.5 + - - +
225A LEU* 3.2 9.0 + - + +
226A TYR* 3.1 17.7 + - - +
274A LEU* 3.7 25.2 + - + +
275A HIS* 5.4 1.8 - - - +
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Residues in contact with ASN 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 HIS 3.7 14.9 + - - +
220A ASN* 3.2 22.2 + - + +
222A LYS* 1.3 84.7 - - - +
224A ASP* 1.3 65.3 + - - +
226A TYR* 3.2 5.7 + - - +
227A GLN* 3.1 22.1 + - - +
274A LEU* 3.8 30.2 - - + +
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Residues in contact with ASP 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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220A ASN* 2.7 32.8 + - - +
221A ASP* 3.3 11.7 + - - +
223A ASN* 1.3 77.3 - - - +
225A LEU* 1.3 60.1 + - - +
227A GLN* 3.4 20.0 + - - +
228A SER* 3.0 27.2 + - - -
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Residues in contact with LEU 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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20A LEU* 3.7 15.3 - - + -
211A ASN* 4.1 11.2 - - + +
212A PHE 3.4 39.7 - - - +
213A LEU* 3.7 17.0 - - + +
221A ASP 2.9 13.4 + - - +
222A LYS* 3.5 11.4 - - + +
224A ASP* 1.3 73.9 - - - +
226A TYR* 1.3 62.6 + - - +
228A SER* 3.0 6.0 + - - -
229A LEU* 2.8 50.9 + - + +
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Residues in contact with TYR 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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213A LEU* 3.9 21.9 - - + +
222A LYS 3.1 6.5 + - - +
223A ASN 3.2 8.7 + - - +
225A LEU* 1.3 78.1 - - - +
227A GLN* 1.3 60.1 + - + +
229A LEU* 3.3 9.2 + - + +
230A LYS* 3.0 73.9 + - + +
272A LEU* 3.8 15.2 + - + -
273A HIS* 3.4 30.1 - - - +
274A LEU* 3.5 47.3 + - + -
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Residues in contact with GLN 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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16A ASN* 5.3 2.6 - - - +
223A ASN 3.1 9.8 + - - +
224A ASP* 3.6 24.2 - - - +
226A TYR* 1.3 83.1 - - - +
228A SER* 1.3 57.9 + - - +
230A LYS* 3.3 5.1 + - - +
231A GLU* 2.9 58.3 + - + +
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Residues in contact with SER 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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15A LYS 3.9 8.0 + - - -
16A ASN* 2.9 33.1 + - - +
20A LEU* 4.2 19.1 - - - -
224A ASP* 3.0 15.6 + - - +
225A LEU* 3.4 9.6 - - - -
227A GLN* 1.3 75.3 + - - +
229A LEU* 1.3 64.3 + - - +
231A GLU* 3.2 12.4 + - - +
232A GLU* 3.2 26.3 + - - +
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Residues in contact with LEU 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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20A LEU* 3.4 36.3 - - + -
211A ASN* 4.7 10.1 - - + -
213A LEU* 4.5 19.5 - - + +
225A LEU* 2.8 34.3 + - + +
226A TYR* 3.4 12.8 - - + +
228A SER* 1.3 73.3 - - - +
230A LYS* 1.3 63.3 + - + +
232A GLU* 3.3 8.3 + - - +
234A ILE* 3.1 39.5 + - + +
272A LEU* 5.3 2.9 - - + -
278A LEU* 3.9 28.9 - - + -
280A TYR* 4.7 10.1 - - + -
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Residues in contact with LYS 230 (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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226A TYR* 3.0 62.0 + - + +
227A GLN* 3.8 4.9 - - - +
229A LEU* 1.3 72.8 - - - +
231A GLU* 1.3 59.0 + - + +
232A GLU 3.0 5.2 - - - -
233A GLY* 2.9 20.7 + - - +
234A ILE 3.0 24.3 + - - +
235A ALA* 3.3 22.2 + - - +
236A GLY* 4.8 2.6 - - - -
269A PHE* 4.9 8.2 + - - -
272A LEU* 4.4 13.2 + - + +
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Residues in contact with GLU 231 (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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16A ASN* 3.2 30.0 + - + +
227A GLN* 2.9 44.9 + - + +
228A SER* 3.2 5.3 + - - +
230A LYS* 1.3 76.3 - - + +
232A GLU* 1.3 62.0 + - - +
233A GLY 3.7 0.2 + - - -
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Residues in contact with GLU 232 (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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16A ASN* 5.6 2.0 - - + +
17A THR* 3.1 28.4 + - - +
20A LEU* 3.3 29.4 - - + -
21A TYR* 2.8 32.5 + - - +
228A SER 3.2 7.7 + - - +
229A LEU 3.5 10.3 - - - +
230A LYS 3.0 0.6 - - - -
231A GLU* 1.3 81.4 - - - +
233A GLY* 1.3 59.8 + - - +
234A ILE* 3.5 11.9 - - + +
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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