Contacts of the helix formed by residues 182 - 195 (chain i) in PDB entry 5GJQ
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 GLU 182 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120Q GLU* 3.9 17.9 - - - +
121Q LYS* 3.9 34.2 + - - +
39i ALA* 4.3 0.9 - - - -
40i ALA* 5.3 3.6 - - - +
41i ASN* 3.5 25.1 - - - +
180i ASP 3.8 8.2 + - - +
181i LEU* 1.3 80.1 - - - +
183i LEU* 1.3 65.1 + - - +
184i GLU* 2.9 22.2 + - - +
185i ASP* 3.0 17.7 + - - +
186i ALA* 3.0 10.0 + - - +
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Residues in contact with LEU 183 (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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39i ALA* 4.4 2.0 - - + -
41i ASN* 2.9 22.4 + - - +
42i GLY* 4.4 15.5 - - - -
43i VAL* 4.0 11.2 - - - +
44i VAL* 2.9 37.9 - - + -
182i GLU* 1.3 72.7 - - - +
184i GLU* 1.3 62.0 + - - +
186i ALA* 3.1 6.5 + - + -
187i ILE* 2.8 37.6 + - + +
211i ILE* 4.0 32.8 - - + -
212i CYS 4.9 0.2 - - - +
213i ASN* 4.5 22.2 - - + +
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Residues in contact with GLU 184 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82Q LYS* 3.7 19.9 + - + +
120Q GLU* 3.6 18.5 - - - +
121Q LYS 5.0 0.9 - - - +
122Q ARG* 3.3 44.3 + - + +
41i ASN* 5.2 2.3 + - - -
182i GLU* 3.2 29.5 - - - +
183i LEU* 1.3 81.1 + - + +
185i ASP* 1.3 63.9 + - - +
187i ILE* 3.1 6.7 + - + +
188i HIS* 3.0 21.0 + - - +
228i TYR* 3.6 25.7 - - - +
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Residues in contact with ASP 185 (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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121Q LYS 3.9 4.0 - - - +
122Q ARG* 3.5 18.4 + - - +
123Q THR* 3.1 32.7 + - - +
124Q PHE* 2.9 41.5 + - + +
181i LEU* 3.7 21.1 - - + +
182i GLU* 3.0 12.6 + - - +
184i GLU* 1.3 78.5 - - - +
186i ALA* 1.3 57.7 - - - +
188i HIS* 3.2 4.7 + - - +
189i THR* 2.9 30.6 + - - +
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Residues in contact with ALA 186 (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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37i ILE* 3.5 15.0 - - + +
39i ALA* 3.6 31.2 - - + -
44i VAL* 3.7 15.4 - - + +
181i LEU* 4.3 4.6 - - + +
182i GLU 3.0 5.4 + - - +
183i LEU 3.2 9.6 - - - +
185i ASP* 1.3 73.5 - - - +
187i ILE* 1.3 68.6 + - - +
189i THR* 3.2 12.4 - - - +
190i ALA* 2.9 24.1 + - - +
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Residues in contact with ILE 187 (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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44i VAL* 3.5 28.9 - - + -
183i LEU* 2.8 32.4 + - + +
184i GLU* 3.4 6.1 - - - +
186i ALA* 1.3 74.5 - - - +
188i HIS* 1.3 65.2 + - - +
190i ALA* 3.1 1.7 + - - +
191i ILE* 3.0 38.2 + - + +
209i VAL* 5.0 1.6 - - + -
211i ILE* 4.0 17.7 - - + -
220i LEU* 4.7 10.8 - - + -
228i TYR* 3.6 53.6 - - + +
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Residues in contact with HIS 188 (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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122Q ARG* 5.8 6.3 - - - +
124Q PHE* 2.8 59.1 - + + +
184i GLU 3.0 12.0 + - - +
185i ASP* 3.2 10.3 - - - +
187i ILE* 1.3 79.7 - - - +
189i THR* 1.3 58.3 + - - +
191i ILE* 3.3 5.5 + - - +
192i LEU* 2.9 41.6 + - + +
228i TYR* 4.9 16.3 - + + -
231i ALA* 3.3 36.1 + - + +
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Residues in contact with THR 189 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124Q PHE* 4.1 15.9 - - + -
37i ILE* 3.5 15.3 - - + +
172i PHE* 4.3 6.8 - - - -
173i LEU* 4.2 6.2 - - - +
176i ARG* 3.6 17.0 + - - +
177i TYR* 4.2 7.4 - - + +
181i LEU* 4.2 15.3 - - + -
185i ASP 2.9 18.2 + - - +
186i ALA* 3.2 20.4 - - - +
188i HIS* 1.3 75.8 - - - +
190i ALA* 1.3 56.4 + - - +
192i LEU* 3.3 11.0 - - - +
193i THR* 2.9 27.6 + - - +
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Residues in contact with ALA 190 (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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35i VAL* 4.4 8.0 - - + +
37i ILE* 3.7 14.4 - - + -
44i VAL* 4.0 20.0 - - + -
46i ALA* 4.7 11.7 - - + -
186i ALA 2.9 18.0 + - - +
187i ILE 3.4 6.3 - - - +
188i HIS 3.1 0.2 - - - -
189i THR* 1.3 74.9 - - - +
191i ILE* 1.3 62.5 + - + +
192i LEU 3.1 0.9 - - - -
193i THR* 3.0 12.4 - - - +
194i LEU* 2.9 30.4 + - - +
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Residues in contact with ILE 191 (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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46i ALA* 5.5 3.4 - - + -
187i ILE* 3.0 24.8 + - + +
188i HIS* 3.8 4.5 - - - +
190i ALA* 1.3 77.3 - - + +
192i LEU* 1.3 61.3 + - - +
194i LEU* 3.8 7.4 - - - +
195i LYS* 3.0 23.9 + - - +
202i MET* 3.4 17.8 - - + +
207i ILE* 4.0 13.9 - - + -
209i VAL* 5.0 13.2 - - + -
225i VAL* 4.8 2.5 - - + +
228i TYR* 4.0 29.2 - - + +
229i LEU* 3.2 38.4 - - + -
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Residues in contact with LEU 192 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124Q PHE* 3.9 30.5 - - + -
172i PHE* 4.0 22.8 - - + -
176i ARG* 5.4 4.3 - - + -
188i HIS* 2.9 25.8 + - + +
189i THR* 3.3 12.3 - - - +
191i ILE* 1.3 78.6 - - - +
193i THR* 1.3 57.4 + - - +
195i LYS* 3.2 40.2 + - + +
196i GLU* 3.4 14.3 + - - +
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Residues in contact with THR 193 (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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35i VAL* 3.7 18.8 - - + +
161i ALA* 5.1 2.3 - - - +
169i GLY* 3.7 26.9 + - - -
172i PHE* 3.6 22.5 - - - -
173i LEU* 3.5 19.5 - - + +
189i THR 2.9 16.2 + - - +
190i ALA* 3.0 22.2 - - - +
192i LEU* 1.3 73.1 - - - +
194i LEU* 1.3 63.6 + - - +
196i GLU* 3.4 17.6 - - - +
197i SER* 4.6 3.5 + - - -
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Residues in contact with LEU 194 (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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33i PRO* 3.6 41.1 - - + +
34i SER 4.5 2.2 - - - +
35i VAL* 5.0 5.8 - - + +
46i ALA* 3.9 15.3 - - + +
47i THR* 3.5 38.8 - - - +
48i GLU* 3.9 7.0 - - + +
190i ALA 2.9 16.1 + - - +
191i ILE* 3.8 8.7 - - - +
192i LEU 3.3 0.2 - - - -
193i THR* 1.3 77.5 - - - +
195i LYS* 1.3 56.4 + - - +
196i GLU 3.1 2.8 + - - -
197i SER* 3.4 4.8 + - - -
198i PHE* 3.1 27.3 + - + +
202i MET* 4.8 5.8 - - - -
207i ILE* 4.1 17.7 - - + -
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Residues in contact with LYS 195 (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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191i ILE* 3.0 17.8 + - - +
192i LEU* 3.2 33.0 + - + +
194i LEU* 1.3 72.6 - - - +
196i GLU* 1.3 57.4 + - - +
197i SER 2.9 11.3 + - - -
198i PHE* 3.9 19.4 + - + +
202i MET* 3.5 31.6 - - + +
231i ALA 4.8 14.6 + - - -
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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