Contacts of the helix formed by residues 188 - 204 (chain Q) 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 TYR 188 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20Q TYR* 3.8 1.1 - + - -
21Q VAL* 6.1 0.9 - - + -
107Q LEU* 5.4 6.2 - - + +
110Q MET* 4.5 17.3 - - + -
114Q ILE* 4.6 11.9 - - + -
184Q ILE* 3.1 36.6 + - + +
185Q GLU* 3.6 0.4 + - - -
186Q PRO 3.1 0.2 - - - -
187Q ILE* 1.3 79.6 - - + +
189Q ALA* 1.3 60.3 + - - +
190Q LEU 3.5 2.0 - - - -
191Q LEU* 3.3 29.4 + - + +
192Q ARG* 3.1 37.5 + - + +
210R PHE* 1.5 72.7 - + + -
211R SER* 2.4 29.9 + - - -
218R LYS* 4.1 4.2 + - - -
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Residues in contact with ALA 189 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185Q GLU 3.3 5.4 + - - +
186Q PRO* 3.0 22.1 + - + +
188Q TYR* 1.3 74.8 - - - +
190Q LEU* 1.3 61.3 + - - +
192Q ARG* 3.1 33.0 + - - +
193Q GLU* 2.9 26.3 + - - +
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Residues in contact with LEU 190 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186Q PRO 4.2 2.5 + - - +
187Q ILE 5.4 1.3 - - - +
189Q ALA* 1.3 78.4 - - - +
191Q LEU* 1.3 59.9 + - + +
193Q GLU* 3.1 29.0 + - + +
194Q THR* 2.7 42.7 + - - +
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Residues in contact with LEU 191 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q LEU* 3.4 35.9 - - + +
20Q TYR* 3.6 27.8 - - + -
21Q VAL* 4.6 5.8 - - + -
107Q LEU* 4.8 11.0 - - + -
110Q MET* 6.4 0.4 - - + -
187Q ILE 3.1 27.1 - - - +
188Q TYR* 3.4 36.6 - - + +
189Q ALA 3.2 0.2 - - - -
190Q LEU* 1.3 81.9 - - + +
192Q ARG* 1.3 54.5 + - - +
194Q THR* 3.2 9.8 + - - -
195Q GLU* 2.7 34.0 + - - +
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Residues in contact with ARG 192 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Q LEU* 4.2 19.7 - - + +
111Q ARG* 4.1 33.7 - - + +
185Q GLU* 2.6 60.3 + - - +
188Q TYR* 3.1 24.8 + - + +
189Q ALA* 3.3 25.3 + - - +
191Q LEU* 1.3 75.4 - - - +
193Q GLU* 1.3 52.2 + - - +
195Q GLU* 3.0 12.2 + - - +
196Q ASP* 2.6 36.3 + - - +
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Residues in contact with GLU 193 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Q ALA 2.9 12.8 + - - +
190Q LEU* 3.3 31.4 - - + +
192Q ARG* 1.3 72.9 - - - +
194Q THR* 1.3 64.9 + - - +
196Q ASP* 3.3 11.2 + - + +
197Q VAL* 3.0 30.2 + - + +
426W PRO* 4.7 17.3 - - - +
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Residues in contact with THR 194 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Q ALA* 3.8 39.5 + - + +
14Q LEU* 4.2 7.0 - - + +
17Q LEU* 3.6 21.5 - - + +
190Q LEU* 2.7 28.9 + - - +
191Q LEU* 3.2 9.6 - - - -
193Q GLU* 1.3 72.5 - - - +
195Q GLU* 1.3 51.7 + - - -
197Q VAL* 3.3 7.1 + - + +
198Q ASN* 2.8 34.3 + - + +
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Residues in contact with GLU 195 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q LEU* 6.4 0.2 - - - -
17Q LEU* 4.3 6.9 - - + +
103Q VAL* 6.0 3.8 - - + -
104Q LYS* 4.5 22.2 - - + +
107Q LEU* 3.6 30.6 - - + +
111Q ARG* 5.9 1.2 + - - -
191Q LEU 2.7 16.4 + - - +
192Q ARG* 3.2 10.9 - - - +
194Q THR* 1.3 74.3 - - - +
196Q ASP* 1.3 57.4 + - - +
198Q ASN* 3.3 9.4 + - + +
199Q LEU* 2.8 55.9 + - - +
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Residues in contact with ASP 196 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192Q ARG 2.6 20.4 + - - +
193Q GLU* 3.4 13.2 - - + +
194Q THR 3.3 0.2 - - - -
195Q GLU* 1.3 78.3 + - - +
197Q VAL* 1.3 62.7 + - - +
199Q LEU* 3.5 10.3 + - - +
200Q ALA* 3.1 21.8 + - - +
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Residues in contact with VAL 197 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193Q GLU* 3.0 20.0 + - + +
194Q THR* 3.7 8.5 - - - +
196Q ASP* 1.3 75.3 - - + +
198Q ASN* 1.3 61.2 + - - +
200Q ALA* 3.2 9.4 + - + +
201Q TYR* 3.0 27.1 + - + +
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Residues in contact with ASN 198 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Q PRO* 4.9 6.2 - - - +
14Q LEU* 3.9 36.1 - - + +
101Q ASN* 5.1 2.6 + - - -
104Q LYS* 6.0 4.2 - - - +
194Q THR* 2.8 21.7 + - + +
195Q GLU* 3.3 11.9 + - - +
197Q VAL* 1.3 75.8 - - - +
199Q LEU* 1.3 56.7 + - - +
201Q TYR* 3.2 18.5 + - - +
202Q GLU* 3.1 49.8 + - - +
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Residues in contact with LEU 199 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q LYS* 6.0 3.1 - - + -
195Q GLU* 2.8 38.1 + - - +
196Q ASP* 3.7 11.0 - - - +
198Q ASN* 1.3 74.6 - - - +
200Q ALA* 1.3 56.2 + - - +
202Q GLU* 3.2 23.0 + - + +
203Q ILE* 3.0 35.1 + - + +
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Residues in contact with ALA 200 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196Q ASP* 3.1 13.7 + - - +
197Q VAL* 3.2 14.3 + - + +
199Q LEU* 1.3 72.8 - - - +
201Q TYR* 1.3 59.0 + - - +
202Q GLU 3.0 4.5 - - - -
203Q ILE* 3.2 30.4 + - + +
204Q LEU* 3.5 9.0 + - - +
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Residues in contact with TYR 201 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Q PRO* 4.7 24.4 - - + +
197Q VAL* 3.0 14.1 + - + +
198Q ASN* 3.2 24.4 + - - +
200Q ALA* 1.3 75.0 - - - +
202Q GLU* 1.3 63.0 + - + +
203Q ILE 3.5 0.2 - - - -
204Q LEU* 4.0 24.3 + - + +
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Residues in contact with GLU 202 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q ASN* 3.3 33.0 + - - +
104Q LYS* 4.1 20.5 + - - +
198Q ASN* 3.1 32.4 + - - +
199Q LEU* 3.5 26.5 - - + +
200Q ALA 3.0 1.0 - - - -
201Q TYR* 1.3 81.9 - - + +
203Q ILE* 1.3 65.2 + - - +
204Q LEU 3.2 3.6 - - - -
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Residues in contact with ILE 203 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199Q LEU* 3.0 27.6 + - + +
200Q ALA* 3.2 19.9 + - + +
202Q GLU* 1.3 80.0 - - - +
204Q LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 204 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200Q ALA 3.5 7.0 + - - +
201Q TYR* 4.0 23.8 + - + +
202Q GLU 3.2 4.4 - - - -
203Q ILE* 1.3 85.8 - - - +
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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