Contacts of the helix formed by residues 190 - 199 (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 CYS 190 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112W ARG* 4.6 9.6 - - - -
116W CYS* 3.6 23.3 - - - -
119W PRO* 5.6 2.0 - - - -
137W LEU* 3.8 24.0 - - + -
156W ARG* 2.9 30.7 + - + +
188W GLY 4.3 0.2 - - - -
189W TRP* 1.4 84.6 - - + +
191W PRO* 1.4 68.8 - - - +
192W TYR* 4.1 4.9 - - - -
193W PHE* 3.4 30.6 + - + -
194W LEU 3.4 8.8 + - - -
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Residues in contact with PRO 191 (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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115W LEU* 3.5 25.8 - - + +
116W CYS* 3.3 23.6 - - - -
180W LEU* 4.0 37.6 - - + +
181W LYS* 5.1 0.9 - - - -
184W GLY* 4.3 17.5 - - - -
189W TRP* 2.9 12.7 - - + +
190W CYS* 1.4 81.0 - - - +
192W TYR* 1.3 62.1 + - - +
194W LEU* 3.2 10.4 + - + +
195W ALA* 3.0 23.0 + - - +
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Residues in contact with TYR 192 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109W LEU* 3.9 14.7 - - + +
110W SER 3.5 26.0 - - - -
111W SER* 3.9 2.0 - - - -
112W ARG* 3.5 51.8 - - + -
115W LEU* 3.9 13.1 - - + +
116W CYS* 4.4 3.6 - - - -
134W CYS* 5.2 3.6 - - - -
190W CYS* 3.3 5.8 - - - -
191W PRO* 1.3 78.5 - - - +
193W PHE* 1.3 75.5 + + - +
195W ALA* 3.1 5.7 + - - +
196W ARG* 2.9 40.4 + - + +
207W TYR* 3.1 25.7 + - - -
211W TYR* 3.9 10.9 + - - -
220W LEU* 5.7 4.3 - - - +
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Residues in contact with PHE 193 (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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134W CYS* 3.8 36.3 - - + -
137W LEU* 3.9 20.6 - - + -
138W THR* 3.7 18.2 - - - -
157W PHE* 3.7 43.3 - + - -
161W PHE* 4.4 7.2 - - + -
189W TRP* 3.7 15.9 - + + -
190W CYS* 3.4 13.9 + - + +
192W TYR* 1.3 89.3 - + - +
194W LEU* 1.3 65.8 + - - +
196W ARG* 3.2 15.4 + - + +
197W TYR* 2.8 26.9 + - - +
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Residues in contact with LEU 194 (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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161W PHE 3.8 22.4 - - - +
166W ARG* 4.0 32.1 - - + +
167W GLU* 5.2 3.4 - - - +
170W LEU* 3.9 27.4 - - + -
180W LEU* 5.4 6.7 - - + -
183W LEU* 6.1 3.4 - - + -
187W GLN* 5.5 0.9 - - - +
189W TRP* 3.6 35.8 - - + +
190W CYS 3.4 4.1 + - - +
191W PRO* 3.2 12.0 + - + +
193W PHE* 1.3 78.8 - - - +
195W ALA* 1.3 53.3 + - - +
197W TYR* 3.5 10.3 + - + +
198W SER* 2.8 43.5 + - - +
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Residues in contact with ALA 195 (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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107W LEU* 5.6 0.4 - - + -
108W ALA 5.0 0.4 - - - +
109W LEU* 4.2 24.0 - - + -
170W LEU* 4.7 2.9 - - - +
175W TYR* 3.8 32.7 + - + +
180W LEU* 4.2 7.2 - - + +
191W PRO 3.0 13.3 + - - +
192W TYR* 3.6 6.7 - - - +
194W LEU* 1.3 73.7 - - - +
196W ARG* 1.3 52.9 - - - +
198W SER* 3.0 6.8 + - - -
199W ILE* 2.9 38.5 + - + +
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Residues in contact with ARG 196 (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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109W LEU* 5.2 2.8 - - + +
161W PHE* 4.7 8.8 - - - -
192W TYR* 2.9 33.0 + - + +
193W PHE* 3.6 15.9 - - + +
195W ALA* 1.3 78.1 - - - +
197W TYR* 1.3 88.2 + - - +
199W ILE* 3.6 21.7 + - + +
200W LEU* 5.2 4.5 + - - +
220W LEU* 6.3 2.0 - - + -
224W GLU* 2.7 54.8 + - + +
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Residues in contact with TYR 197 (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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161W PHE* 3.5 64.1 - + + -
162W ASP* 2.7 27.7 + - - -
193W PHE 2.8 20.2 + - - +
194W LEU* 3.6 10.5 - - + +
196W ARG* 1.3 91.9 + - - +
198W SER* 1.3 62.6 + - - +
200W LEU* 3.4 20.6 - - + +
201W HIS* 4.3 4.9 + - - -
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Residues in contact with SER 198 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107W LEU* 4.5 4.0 - - - +
167W GLU* 5.8 2.6 + - - +
170W LEU* 3.6 26.9 - - - +
175W TYR* 3.9 8.1 - - - -
194W LEU* 2.8 25.2 + - - +
195W ALA 3.0 5.1 + - - -
197W TYR* 1.3 79.6 - - - +
199W ILE* 1.3 61.9 + - - +
200W LEU 3.3 2.0 + - - -
201W HIS* 3.7 27.6 + - - +
202W ALA* 4.4 2.6 + - - +
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Residues in contact with ILE 199 (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* 4.6 1.4 + - - -
107W LEU* 4.0 15.9 - - + -
109W LEU* 3.7 28.0 - - + -
195W ALA 2.9 21.4 + - - +
196W ARG* 3.6 19.9 + - + +
197W TYR 3.5 2.6 - - - -
198W SER* 1.3 72.8 - - - +
200W LEU* 1.4 60.5 + - - +
202W ALA* 3.3 21.5 + - - +
205W VAL* 4.6 13.9 - - + +
207W TYR* 5.1 6.5 - - + -
221W VAL* 6.5 0.4 - - + -
224W GLU* 3.8 33.0 - - + -
225W LEU* 4.0 23.9 - - + +
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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