Contacts of the helix formed by residues 218 - 229 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217H VAL* 1.3 71.7 - - - +
219H ILE* 1.3 61.4 + - - +
220H GLU* 3.4 9.9 + - - +
221H LEU* 3.0 41.6 + - + +
222H VAL* 2.8 23.8 + - + +
350H ILE* 3.7 34.5 - - + +
353H LYS* 3.1 29.6 + - - +
354H GLN* 3.8 2.8 - - - +
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Residues in contact with ILE 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208H SER* 4.9 4.5 - - - +
217H VAL* 2.6 18.0 + - + +
218H ASP* 1.3 70.0 - - - +
220H GLU* 1.3 64.1 + - - +
222H VAL* 3.9 6.0 - - - +
223H SER* 2.8 38.2 + - - +
235H ILE* 4.3 23.8 - - + -
245H GLN* 4.3 15.9 - - - +
247H ALA* 3.9 28.7 - - + +
250H LEU* 3.4 37.9 - - + +
252H ALA* 4.1 8.5 - - + +
354H GLN* 3.2 22.9 + - - +
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Residues in contact with GLU 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H ASP* 3.3 8.4 + - - +
219H ILE* 1.3 79.9 - - - +
221H LEU* 1.3 63.3 + - - +
223H SER* 3.7 2.6 - - - -
224H LYS* 3.3 46.4 + - - +
250H LEU* 3.1 32.8 + - + +
353H LYS* 3.9 22.9 + - - +
354H GLN* 4.5 1.6 + - - +
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Residues in contact with LEU 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H VAL* 4.0 35.4 - - + -
218H ASP* 3.0 34.6 + - + +
220H GLU* 1.3 74.6 - - - +
222H VAL* 1.3 68.7 + - + +
224H LYS* 2.9 23.9 + - + +
225H LEU* 3.2 30.7 + - + +
353H LYS* 5.7 0.2 - - - +
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Residues in contact with VAL 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186H PRO 5.9 1.1 - - - +
189H VAL* 5.6 8.7 - - + -
192H LEU* 3.6 23.8 - - + -
204H PHE* 3.3 37.2 - - + -
217H VAL* 3.5 26.0 - - + -
218H ASP* 2.8 18.7 + - + +
219H ILE* 3.9 4.0 - - - +
221H LEU* 1.3 76.5 - - + +
223H SER* 1.3 65.9 + - - +
225H LEU* 3.5 3.1 + - - +
226H CYS* 3.1 25.7 + - - -
233H VAL* 4.1 10.8 - - + -
235H ILE* 5.5 0.9 - - + -
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Residues in contact with SER 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H ILE* 2.8 27.7 + - - +
220H GLU 3.7 4.7 - - - -
222H VAL* 1.3 76.4 - - - +
224H LYS* 1.3 58.7 + - - +
226H CYS* 3.3 0.9 + - - +
227H HIS* 2.9 40.8 + - - -
233H VAL* 3.9 19.5 - - - +
251H GLY* 3.4 37.8 - - - -
252H ALA* 3.5 7.4 + - - -
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Residues in contact with LYS 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220H GLU* 3.3 37.3 + - - +
221H LEU* 2.9 17.1 + - + +
223H SER* 1.3 80.8 - - - +
225H LEU* 1.3 67.2 + - + +
227H HIS* 4.0 3.7 - - - +
228H GLU* 3.1 29.8 + - - +
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Residues in contact with LEU 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H VAL* 3.5 32.5 - - + -
192H LEU* 4.1 17.5 - - + -
193H GLU* 4.5 30.7 - - + +
196H LEU* 4.0 8.3 - - + +
221H LEU* 3.2 28.6 + - + +
222H VAL* 3.8 5.4 - - - +
224H LYS* 1.3 78.7 - - + +
226H CYS* 1.3 66.0 + - - +
228H GLU* 3.3 27.3 - - - +
229H LYS* 3.5 11.6 + - - +
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Residues in contact with CYS 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H LEU* 4.2 5.2 - - - -
196H LEU* 4.0 20.9 - - - -
201H VAL* 5.9 0.2 - - - -
204H PHE* 3.7 35.9 - - - -
222H VAL 3.1 22.5 + - - +
223H SER 3.7 0.2 - - - +
225H LEU* 1.3 78.8 - - - +
227H HIS* 1.3 58.2 + - - +
229H LYS* 2.9 20.4 + - - +
231H ALA* 3.0 34.5 + - + +
233H VAL* 3.5 21.3 - - + -
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Residues in contact with HIS 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223H SER* 2.9 28.2 + - - +
224H LYS* 4.0 4.4 - - - +
226H CYS* 1.3 72.1 - - - +
228H GLU* 1.3 62.8 + - - +
230H GLY* 3.1 12.9 + - - +
231H ALA 3.4 20.2 - - - +
232H LEU* 5.3 1.3 - - + -
233H VAL* 4.2 6.9 - - + +
251H GLY* 3.3 24.8 + - - -
253H ASP* 2.8 33.9 + - - -
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Residues in contact with GLU 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193H GLU* 5.8 0.3 - - - +
224H LYS* 3.1 18.6 + - - +
225H LEU* 3.3 22.9 - - - +
226H CYS 3.0 0.4 + - - -
227H HIS* 1.3 78.1 - - - +
229H LYS* 1.3 80.5 + - + +
230H GLY 3.4 0.6 + - - -
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Residues in contact with LYS 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196H LEU* 3.5 50.3 - - + +
197H ASN* 3.5 30.8 + - - +
200H LYS* 5.6 7.8 - - - +
201H VAL 4.8 4.9 + - - +
225H LEU 3.9 7.2 - - - +
226H CYS 2.9 2.6 + - - -
228H GLU* 1.3 102.5 + - + +
230H GLY* 1.3 60.8 + - - +
231H ALA 3.3 1.6 + - - -
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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