Contacts of the helix formed by residues 218 - 232 (chain A) in PDB entry 4I2C
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 GLY 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A CYS 3.8 3.8 + - - -
217A LEU* 1.3 76.8 - - - +
219A ASP* 1.3 61.8 + - - -
220A LYS 3.4 3.1 - - - -
221A VAL* 3.3 11.5 + - - +
222A LYS* 3.0 26.6 + - - +
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Residues in contact with ASP 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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218A GLY* 1.3 71.4 - - - -
220A LYS* 1.4 61.5 + - - +
222A LYS* 3.4 12.4 + - - +
223A SER* 2.9 28.6 + - - -
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Residues in contact with LYS 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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191A PHE* 4.2 22.2 - - + -
218A GLY 3.4 0.8 - - - -
219A ASP* 1.4 75.7 - - - +
221A VAL* 1.3 64.6 + - + +
223A SER* 3.2 26.0 + - - -
224A ILE* 3.3 23.1 + - - +
236A GLU* 4.9 11.1 + - - -
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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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172A LEU* 4.3 10.3 - - + -
190A ALA* 4.5 9.9 - - + +
191A PHE* 3.9 23.8 - - + -
194A ALA* 3.7 34.1 - - + -
216A CYS 4.8 0.7 - - - +
217A LEU* 3.9 11.0 - - + -
218A GLY* 3.3 18.0 + - - +
220A LYS* 1.3 75.9 - - + +
222A LYS* 1.3 59.1 + - - +
224A ILE* 3.1 12.3 + - - +
225A ILE* 3.0 44.4 + - + +
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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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208A MET* 3.8 25.6 - - + +
211A THR* 3.7 26.4 + - - +
212A GLU* 5.8 1.6 - - - +
214A ILE 5.3 3.0 + - - -
217A LEU* 3.5 37.0 + - + +
218A GLY 3.0 18.8 + - - +
219A ASP* 3.4 12.3 + - - +
221A VAL* 1.3 74.8 - - - +
223A SER* 1.4 55.4 + - - +
225A ILE* 3.4 9.7 + - + +
226A GLU* 2.9 30.0 + - - +
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Residues in contact with SER 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 ASP 2.9 17.4 + - - -
220A LYS* 3.4 22.4 + - - -
221A VAL 3.2 0.2 - - - -
222A LYS* 1.4 74.8 - - - +
224A ILE* 1.3 63.2 + - - +
226A GLU* 3.4 15.4 + - - +
227A GLY* 3.1 19.4 + - - -
236A GLU* 4.8 5.6 - - - +
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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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171A ALA* 4.8 2.5 - - + -
172A LEU* 4.1 18.8 - - + -
175A LEU* 3.8 15.3 - - + -
191A PHE* 3.5 34.1 - - + -
220A LYS* 3.3 30.9 + - - +
221A VAL* 3.1 8.1 + - - +
223A SER* 1.3 73.6 - - - +
225A ILE* 1.3 64.4 - - + +
227A GLY* 3.3 2.8 + - - -
228A ILE* 3.2 39.7 + - + +
234A SER* 4.1 10.9 - - - +
236A GLU* 3.8 31.2 - - + +
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Residues in contact with ILE 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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168A PHE* 3.6 33.8 - - + -
172A LEU* 5.2 3.6 - - + -
198A LEU* 4.1 22.7 - - + -
205A ILE* 4.3 4.9 - - + -
208A MET* 3.8 16.6 - - - -
211A THR* 4.2 16.8 - - + -
217A LEU* 4.2 19.3 - - + -
221A VAL* 3.0 38.1 + - + +
222A LYS* 3.7 10.1 - - + +
224A ILE* 1.3 76.4 - - + +
226A GLU* 1.4 57.7 + - - +
228A ILE 3.2 2.6 + - - -
229A ILE* 3.0 35.1 + - + +
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Residues in contact with GLU 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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208A MET* 3.8 24.9 - - + +
222A LYS 2.9 17.7 + - - +
223A SER* 3.5 13.1 - - - +
225A ILE* 1.4 77.7 - - - +
227A GLY* 1.3 55.8 + - - +
229A ILE* 3.4 7.9 + - - +
230A GLU* 3.0 36.1 + - + +
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Residues in contact with GLY 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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223A SER 3.1 14.1 + - - -
224A ILE 3.3 4.2 + - - -
225A ILE 3.3 0.2 - - - -
226A GLU* 1.3 75.7 + - - +
228A ILE* 1.3 62.4 + - - +
230A GLU* 3.3 22.3 - - - +
231A ASP* 3.2 20.1 - - - +
233A GLU 3.3 6.0 - - - +
234A SER* 5.4 1.6 - - - -
236A GLU* 5.8 4.0 - - - -
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Residues in contact with ILE 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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167A LEU* 3.7 41.3 - - + +
168A PHE* 3.7 31.6 - - + -
171A ALA* 3.8 29.4 - - + -
224A ILE* 3.2 24.4 + - + +
225A ILE* 3.2 6.5 + - + +
227A GLY* 1.3 71.5 - - - +
229A ILE* 1.4 61.4 + - - +
232A GLY* 2.8 36.5 + - - -
233A GLU 3.4 17.0 - - - +
234A SER* 3.7 12.8 - - - -
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Residues in contact with ILE 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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168A PHE* 3.9 17.3 - - + -
205A ILE* 4.1 3.1 - - + +
206A THR* 4.0 20.0 - - - +
207A SER* 3.6 33.0 - - - +
208A MET* 3.8 13.9 - - + +
225A ILE* 3.0 34.5 + - + +
226A GLU* 3.4 7.6 + - - +
228A ILE* 1.4 76.2 - - - +
230A GLU* 1.4 63.4 + - - +
231A ASP 3.7 0.2 + - - -
232A GLY 4.4 1.2 + - - -
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Residues in contact with GLU 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 GLU* 3.0 21.3 + - + +
227A GLY* 3.3 20.1 - - - +
228A ILE 3.2 0.2 - - - -
229A ILE* 1.4 79.7 - - - +
231A ASP* 1.4 62.7 + - + +
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Residues in contact with ASP 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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227A GLY 3.2 6.1 + - - +
230A GLU* 1.4 78.4 - - + +
232A GLY* 1.3 60.3 + - - +
233A GLU* 3.2 43.9 + - - +
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Residues in contact with GLY 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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167A LEU* 3.7 34.2 - - - +
228A ILE* 2.8 28.3 + - - -
229A ILE 4.4 1.6 + - - -
230A GLU 3.9 0.4 - - - -
231A ASP* 1.3 70.3 - - - +
233A GLU* 1.3 60.7 + - - +
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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