Contacts of the helix formed by residues 214 - 226 (chain W) in PDB entry 5IY8
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 214 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210W HIS* 3.8 12.2 + - - +
211W TYR 3.8 12.6 - - - +
212W LEU 3.7 1.0 - - - +
213W LEU* 1.4 71.6 - - - +
215W PRO* 1.4 72.2 - - - +
216W LYS* 3.2 13.2 + - - +
217W ILE* 3.1 30.0 + - + +
218W ALA* 2.8 22.0 + - - +
246W SER* 3.4 32.8 + - - +
247W MET* 5.1 1.3 - - - -
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Residues in contact with PRO 215 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213W LEU 3.3 9.6 - - - +
214W ASP* 1.4 84.2 - - - +
216W LYS* 1.3 59.8 + - - +
218W ALA* 3.2 8.7 + - + +
219W ASP* 3.1 22.9 + - - +
243W CYS* 5.4 0.4 - - - -
247W MET* 3.8 33.7 - - + -
443W ALA* 3.6 21.5 - - - +
446W PRO* 4.2 23.3 - - + -
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Residues in contact with LYS 216 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214W ASP* 3.3 9.2 + - - +
215W PRO* 1.3 73.7 - - - +
217W ILE* 1.4 68.6 + - + +
219W ASP* 3.4 22.8 - - - +
220W LEU* 3.5 8.0 + - - +
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Residues in contact with ILE 217 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210W HIS 5.5 0.2 - - - +
211W TYR* 3.2 52.3 - - + +
214W ASP* 3.1 24.7 + - + +
216W LYS* 1.4 77.8 - - + +
218W ALA* 1.4 48.5 + - - +
220W LEU* 2.9 22.2 + - + +
221W VAL* 2.8 39.6 + - + -
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Residues in contact with ALA 218 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211W TYR 4.1 1.6 + - - -
212W LEU* 3.5 25.8 - - + +
214W ASP 2.8 14.5 + - - +
215W PRO* 3.4 13.2 - - + +
217W ILE* 1.4 73.7 - - - +
219W ASP* 1.3 50.7 + - - +
221W VAL* 3.3 8.8 + - - +
222W SER* 2.8 44.0 + - - +
446W PRO* 6.0 4.7 - - + -
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Residues in contact with ASP 219 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215W PRO 3.1 10.8 + - - +
216W LYS* 3.4 16.8 - - - +
218W ALA* 1.3 75.2 - - - +
220W LEU* 1.4 63.8 + - - +
222W SER* 3.6 6.0 + - - -
223W LYS* 3.1 19.9 + - - +
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Residues in contact with LEU 220 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192W TYR* 5.7 4.5 - - - +
196W ARG* 6.3 1.8 - - + -
207W TYR* 6.1 1.3 - - - +
216W LYS 3.5 7.2 + - - +
217W ILE* 2.9 27.4 + - + +
219W ASP* 1.4 76.3 + - - +
221W VAL* 1.4 69.0 + - + +
223W LYS* 3.0 37.1 + - + +
224W GLU* 3.2 29.1 + - + +
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Residues in contact with VAL 221 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71W ILE* 4.2 23.8 - - + -
199W ILE* 6.5 0.2 - - + -
207W TYR* 4.3 27.1 - - + +
211W TYR* 5.2 6.3 - - + +
212W LEU* 4.5 16.2 - - + -
217W ILE* 2.8 33.2 + - + +
218W ALA* 3.3 10.3 + - - +
220W LEU* 1.4 75.6 - - + +
222W SER* 1.3 62.6 + - - +
224W GLU* 3.2 10.2 + - - +
225W LEU* 3.2 33.0 + - + +
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Residues in contact with SER 222 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212W LEU* 6.1 1.0 - - - +
218W ALA* 2.8 23.3 + - - +
219W ASP* 3.8 6.5 - - - -
221W VAL* 1.3 76.4 - - - +
223W LYS* 1.3 55.6 + - - +
225W LEU* 3.4 13.2 + - - +
226W ALA* 3.1 27.7 + - - -
227W ARG 4.6 3.0 + - - +
451W PHE* 5.8 8.3 - - - +
452W GLN* 5.1 6.4 + - - -
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Residues in contact with LYS 223 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219W ASP 3.1 13.3 + - - +
220W LEU* 3.0 31.9 + - + +
222W SER* 1.3 75.3 - - - +
224W GLU* 1.3 64.8 + - + +
226W ALA* 3.4 15.8 + - - +
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Residues in contact with GLU 224 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196W ARG* 2.7 59.0 + - + +
199W ILE* 3.8 32.5 - - + -
200W LEU* 3.3 30.0 + - - +
220W LEU* 3.2 33.5 + - + +
221W VAL* 3.2 9.2 + - - +
223W LYS* 1.3 79.7 - - - +
225W LEU* 1.3 64.8 + - - +
226W ALA 3.3 0.3 + - - -
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Residues in contact with LEU 225 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69W LYS* 2.9 43.6 + - + +
70W LEU 6.3 0.2 - - - -
71W ILE* 5.0 19.1 - - + -
199W ILE* 4.0 19.7 - - + +
200W LEU* 4.4 1.3 - - - +
205W VAL* 4.8 13.5 - - + -
221W VAL* 3.2 30.9 + - + +
222W SER* 3.4 15.0 + - - +
224W GLU* 1.3 76.3 - - - +
226W ALA* 1.3 60.6 + - - +
227W ARG* 3.1 21.1 + - - +
229W ALA* 3.8 28.7 - - + -
452W GLN* 5.8 2.2 - - - +
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Residues in contact with ALA 226 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200W LEU* 4.5 17.7 - - + -
222W SER 3.1 12.1 + - - -
223W LYS* 3.4 14.8 + - - +
224W GLU 3.2 4.8 - - - +
225W LEU* 1.3 76.7 - - - +
227W ARG* 1.3 58.8 + - - +
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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