Contacts of the helix formed by residues 218 - 229 (chain I) in PDB entry 1I43
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 ASP 218 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189I VAL* 6.1 1.6 - - + -
216I CYS 4.4 0.4 + - - -
217I VAL* 1.3 69.7 - - - +
219I ILE* 1.3 63.8 + - - +
220I GLU* 3.2 11.4 + - - +
221I LEU* 2.9 42.9 + - + +
222I VAL* 3.0 23.2 + - + +
350I ILE* 3.7 28.5 - - + +
353I LYS* 3.1 28.7 + - - +
354I GLN* 3.6 7.8 - - - +
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Residues in contact with ILE 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208I SER* 4.4 6.3 - - - +
217I VAL* 2.6 18.6 + - + +
218I ASP* 1.3 70.1 - - - +
220I GLU* 1.3 60.1 + - - +
222I VAL* 4.1 3.3 - - - +
223I SER* 2.7 42.0 + - - +
233I VAL* 5.7 0.4 - - + -
235I ILE* 4.0 25.4 - - + -
245I GLN* 4.1 16.8 - - - +
247I ALA* 3.8 26.9 - - + +
250I LEU* 3.4 33.4 - - + +
252I ALA* 4.1 9.2 - - + +
354I GLN* 3.1 29.3 + - - +
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Residues in contact with GLU 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218I ASP* 3.2 8.6 + - - +
219I ILE* 1.3 79.9 - - - +
221I LEU* 1.3 63.3 + - - +
223I SER* 3.8 2.4 - - - -
224I LYS* 3.4 44.1 + - - +
250I LEU* 3.2 33.3 + - + +
353I LYS* 3.9 22.2 + - - +
354I GLN* 4.5 1.9 + - - +
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Residues in contact with LEU 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I VAL* 3.9 32.3 - - + -
218I ASP* 2.9 35.6 + - + +
220I GLU* 1.3 74.5 - - - +
222I VAL* 1.3 70.2 + - + +
224I LYS* 2.8 22.1 + - + +
225I LEU* 3.1 33.2 + - + +
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Residues in contact with VAL 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I PRO 5.9 0.7 - - - +
189I VAL* 5.5 9.6 - - + -
192I LEU* 3.6 23.3 - - + -
204I PHE* 3.2 37.7 - - + -
217I VAL* 3.6 26.2 - - + -
218I ASP* 3.0 11.4 + - + +
219I ILE* 4.1 3.4 - - - +
221I LEU* 1.3 81.3 - - + +
223I SER* 1.3 59.5 + - - +
225I LEU* 3.3 5.2 + - - +
226I CYS* 2.9 34.9 + - - -
233I VAL* 4.3 9.2 - - + -
235I ILE* 5.7 0.7 - - + -
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Residues in contact with SER 223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219I ILE* 2.7 25.4 + - - +
220I GLU 3.8 4.3 - - - -
222I VAL* 1.3 77.0 - - - +
224I LYS* 1.3 57.6 + - - +
226I CYS* 3.4 0.7 + - - +
227I HIS* 2.9 41.6 + - - -
233I VAL* 3.8 17.2 - - - +
250I LEU 4.4 0.2 - - - -
251I GLY* 3.3 21.4 - - - -
252I ALA* 3.3 24.4 + - - -
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Residues in contact with LYS 224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220I GLU* 3.4 34.6 + - - +
221I LEU* 2.8 14.9 + - + +
223I SER* 1.3 80.5 - - - +
225I LEU* 1.3 66.8 + - + +
227I HIS* 4.0 5.2 - - - +
228I GLU* 3.1 30.9 + - - +
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Residues in contact with LEU 225 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I VAL* 3.4 36.3 - - + +
192I LEU* 4.2 16.6 - - + -
193I GLU* 4.5 25.1 - - + +
196I LEU* 4.2 7.9 - - + +
221I LEU* 3.1 30.1 + - + +
222I VAL* 3.6 4.9 - - - +
224I LYS* 1.3 78.3 - - + +
226I CYS* 1.3 64.1 + - - +
228I GLU* 3.2 29.1 - - - +
229I LYS* 3.6 11.3 + - - +
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Residues in contact with CYS 226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192I LEU* 4.4 2.9 - - - -
196I LEU* 4.2 20.4 - - - -
204I PHE* 3.7 31.6 - - - -
222I VAL* 2.9 29.9 + - - +
223I SER 3.7 0.2 - - - +
225I LEU* 1.3 77.3 - - - +
227I HIS* 1.3 57.6 + - - +
229I LYS* 2.9 19.8 + - - +
231I ALA* 2.9 35.6 + - + +
233I VAL* 3.5 23.1 - - + -
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Residues in contact with HIS 227 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223I SER* 2.9 27.9 + - - +
224I LYS* 4.2 4.6 - - - +
226I CYS* 1.3 73.2 - - - +
228I GLU* 1.3 62.1 + - - +
229I LYS 3.2 0.2 - - - -
230I GLY* 3.3 11.4 + - - +
231I ALA 3.4 20.4 - - - -
232I LEU* 5.4 0.7 - - + -
233I VAL* 4.2 6.9 - - + +
251I GLY* 3.2 27.4 - - - -
253I ASP* 2.7 32.5 + - - -
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Residues in contact with GLU 228 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224I LYS* 3.1 19.5 + - - +
225I LEU* 3.2 24.3 - - - +
226I CYS 3.0 0.8 - - - -
227I HIS* 1.3 77.2 - - - +
229I LYS* 1.3 82.0 + - + +
230I GLY 3.4 0.6 + - - -
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Residues in contact with LYS 229 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196I LEU* 3.6 55.5 - - + +
197I ASN* 3.3 30.2 + - - +
200I LYS* 5.6 7.3 - - - +
201I VAL 4.8 5.0 + - - +
225I LEU 4.0 5.8 - - - +
226I CYS 2.9 2.4 + - - -
228I GLU* 1.3 98.7 + - + +
230I GLY* 1.3 61.9 + - - +
231I ALA* 3.3 2.0 + - - +
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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