Contacts of the helix formed by residues 188 - 209 (chain A) in PDB entry 6LGV
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A ARG 4.0 17.5 - - - -
185A ILE* 2.9 18.9 + - + +
187A PRO* 1.3 94.4 - - + +
189A LEU* 1.3 63.3 + - - +
190A PRO 3.3 2.9 - - - -
191A ALA* 3.5 10.2 + - + +
192A MET* 3.1 35.9 + - + +
405A A6L 5.4 13.9 - - + -
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE* 6.2 3.8 - - + -
44A ALA* 4.1 22.2 - - + +
47A VAL* 3.7 17.9 - - + -
48A THR* 3.4 33.0 - - + -
185A ILE* 3.3 41.2 + - + +
186A GLU* 3.3 13.6 + - + +
188A TYR* 1.3 77.2 - - - +
190A PRO* 1.3 63.8 - - + +
192A MET* 3.7 11.6 - - + +
193A SER* 2.8 35.3 + - - -
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Residues in contact with PRO 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 4.9 12.1 - - + -
109A ASN* 4.9 8.1 - - - +
110A VAL* 3.7 30.5 - - + -
186A GLU 3.4 13.5 - - - +
187A PRO* 3.8 13.9 - - + +
188A TYR 3.6 0.7 - - - -
189A LEU* 1.3 94.1 - - + +
191A ALA* 1.3 57.2 + - - +
193A SER* 3.3 6.6 + - - -
194A MET* 2.9 37.9 + - + +
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Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.4 18.8 - - + +
187A PRO 5.4 0.2 + - - -
188A TYR* 3.5 11.7 + - + +
189A LEU 3.4 0.2 - - - -
190A PRO* 1.3 75.4 - - - +
192A MET* 1.3 67.0 + - - +
194A MET* 3.2 13.1 + - - +
195A VAL* 3.1 27.3 + - + +
405A A6L 4.5 21.8 - - + -
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Residues in contact with MET 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 6.4 2.2 - - + -
185A ILE* 4.3 25.6 - - + -
188A TYR* 3.1 29.1 + - + +
189A LEU* 3.2 13.0 + - + +
191A ALA* 1.3 76.2 - - - +
193A SER* 1.3 61.2 + - - +
195A VAL* 3.1 14.4 + - - +
196A CYS* 3.1 19.7 + - - -
405A A6L 3.6 39.2 - - + +
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Residues in contact with SER 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE* 4.4 15.1 - - - +
44A ALA* 3.8 21.7 - - - +
107A ALA* 4.8 10.3 - - - -
189A LEU 2.8 22.0 + - - -
190A PRO* 3.6 6.7 - - - -
192A MET* 1.3 72.2 - - - +
194A MET* 1.3 57.7 + - - +
196A CYS* 3.3 9.8 + - - +
197A ILE* 2.9 41.6 + - - +
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Residues in contact with MET 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.6 30.5 - - + +
6A THR* 3.9 27.4 - - + +
9A PHE* 3.6 40.4 - - + -
110A VAL* 4.4 21.3 - - + -
111A MET* 5.3 4.9 - - + -
190A PRO* 2.9 21.6 + - + +
191A ALA* 3.2 9.6 + - - +
193A SER* 1.3 77.0 - - - +
195A VAL* 1.3 58.2 + - + +
197A ILE* 3.2 11.8 + - + +
198A LEU* 2.9 35.2 + - + +
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ALA 3.1 17.4 + - - +
192A MET* 3.1 8.7 + - - +
194A MET* 1.3 74.7 - - + +
196A CYS* 1.3 66.7 + - - +
198A LEU* 3.2 15.7 + - + +
199A ALA* 3.0 23.4 + - + +
405A A6L 3.6 55.2 - - + -
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Residues in contact with CYS 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.1 24.2 - - + +
40A LEU* 3.6 36.8 - - - -
41A ILE* 3.8 22.2 - - + -
192A MET 3.1 19.2 + - - -
193A SER* 3.5 8.1 - - - +
195A VAL* 1.3 80.9 - - - +
197A ILE* 1.3 56.1 + - - +
199A ALA* 3.3 4.0 + - - +
200A ILE* 3.0 31.4 + - - +
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Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PHE* 3.8 25.6 - - + -
41A ILE* 3.8 16.8 - - + -
107A ALA* 3.7 29.6 - - + +
193A SER* 2.9 32.4 + - - +
194A MET* 3.2 11.4 + - + +
196A CYS* 1.3 68.8 - - - +
198A LEU* 1.3 59.8 + - - +
200A ILE* 3.2 6.6 + - - +
201A ILE* 2.9 32.6 + - + +
287A ASN* 3.9 23.1 - - - +
401A CIT 4.2 18.8 - - + +
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PHE* 3.8 28.0 - - + +
12A TRP* 3.8 18.4 - - + -
13A ALA* 3.5 38.1 - - + +
16A LEU* 4.0 17.2 - - + +
194A MET* 2.9 18.7 + - + +
195A VAL* 3.5 16.2 - - + +
197A ILE* 1.3 77.5 - - - +
199A ALA* 1.3 59.8 + - - +
201A ILE* 3.5 6.1 + - + +
202A SER* 2.9 30.4 + - - -
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Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.9 16.8 - - + +
37A LEU* 3.6 27.8 - - + -
195A VAL* 3.0 13.8 + - + +
196A CYS* 3.6 4.5 - - - +
197A ILE 3.2 0.4 - - - -
198A LEU* 1.3 77.7 - - - +
200A ILE* 1.3 62.9 + - - +
202A SER* 3.4 6.8 + - - -
203A ALA* 3.0 24.8 + - - +
405A A6L 6.5 1.1 - - + -
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Residues in contact with ILE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 4.2 15.7 - - + -
37A LEU* 3.7 25.1 - - + -
38A LEU* 3.6 33.0 - - + -
41A ILE* 3.6 23.3 - - + -
196A CYS 3.0 16.9 + - - +
197A ILE* 3.2 5.1 + - - +
199A ALA* 1.3 73.7 - - - +
201A ILE* 1.3 66.7 + - - +
203A ALA* 3.2 4.9 + - - +
204A VAL* 2.8 41.3 + - + +
261A GLY* 4.4 4.5 - - - -
401A CIT 3.6 27.6 - - + +
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Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PHE* 5.0 0.4 - - + -
13A ALA* 4.3 22.4 - - + +
16A LEU* 5.4 1.6 - - + -
17A SER* 4.1 27.8 - - - +
197A ILE* 2.9 26.8 + - + +
198A LEU* 3.9 6.1 - - + +
200A ILE* 1.3 75.0 - - - +
202A SER* 1.3 67.3 + - - +
204A VAL* 3.3 8.0 - - + +
205A VAL* 2.9 30.1 + - + +
283A SER* 3.9 18.2 - - - +
284A VAL* 4.2 9.4 - - + -
287A ASN* 3.7 28.7 - - + +
401A CIT 4.2 11.2 - - - +
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Residues in contact with SER 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.6 28.5 - - - +
20A ALA* 3.6 14.7 - - - +
27A PHE* 3.7 27.2 - - - +
30A ILE* 4.7 4.0 - - - -
198A LEU 2.9 17.5 + - - -
199A ALA* 3.6 7.1 - - - -
201A ILE* 1.3 79.7 - - - +
203A ALA* 1.3 58.6 + - - +
206A ALA* 3.0 31.5 + - - +
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Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE 4.2 11.4 - - - +
28A THR* 5.5 1.2 - - - -
30A ILE* 3.7 25.3 - - + +
31A GLY* 4.1 6.6 - - - +
34A VAL* 3.6 26.9 - - + -
199A ALA 3.0 15.4 + - - +
200A ILE 3.6 0.4 - - - +
202A SER* 1.3 80.8 - - - +
204A VAL* 1.3 58.2 + - - +
206A ALA* 3.4 1.7 + - - +
207A GLY* 2.9 26.5 + - - -
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 4.4 17.3 - - + -
200A ILE* 2.8 39.5 + - + +
201A ILE* 3.3 13.0 - - - +
203A ALA* 1.3 71.2 - - - +
205A VAL* 1.3 69.1 + - + +
207A GLY* 4.1 1.5 - - - +
208A SER* 3.2 18.2 + - - -
261A GLY* 5.5 1.3 - - - -
264A ALA* 4.4 17.9 - - + -
280A ALA* 3.4 42.9 - - + +
283A SER* 4.2 10.5 - - - +
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 3.6 25.8 - - - +
20A ALA* 3.7 7.4 - - + -
21A TYR* 3.6 24.0 - - + +
201A ILE* 2.9 25.2 + - + +
204A VAL* 1.3 77.0 - - + +
206A ALA* 1.3 63.4 + - - +
208A SER* 3.3 3.1 + - - -
209A GLN* 3.0 23.1 + - + -
212A ILE* 5.3 6.9 - - + +
280A ALA* 4.5 8.7 - - + +
281A LEU* 5.8 4.0 - - + -
284A VAL* 3.3 33.4 - - + -
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA* 3.9 13.9 - - + +
24A PRO* 3.5 34.5 - - + +
27A PHE* 3.8 13.5 - - + -
28A THR* 3.9 13.4 - - + +
202A SER 3.0 19.5 + - - +
203A ALA 3.7 3.4 - - - +
205A VAL* 1.3 76.6 - - - +
207A GLY* 1.3 61.9 + - - +
209A GLN* 3.4 14.2 + - - +
210A SER 5.1 0.3 + - - -
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Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A THR* 4.5 9.2 - - - -
203A ALA 2.9 16.9 + - - -
204A VAL* 3.5 2.2 + - - -
205A VAL 3.2 0.2 - - - -
206A ALA* 1.3 78.7 - - - +
208A SER* 1.3 60.4 + - - +
209A GLN 3.4 0.2 - - - -
210A SER* 5.2 2.4 + - - -
211A HIS* 4.8 5.5 + - - -
273A PRO* 5.7 3.5 - - - +
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Residues in contact with SER 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A VAL 3.2 17.8 + - - -
205A VAL* 3.7 2.0 - - - -
207A GLY* 1.3 77.0 - - - +
209A GLN* 1.3 64.8 + - - +
210A SER 3.2 2.7 - - - -
211A HIS* 3.0 29.4 + - - +
212A ILE* 4.0 6.7 + - - +
273A PRO 4.3 4.2 + - - -
276A ALA* 4.0 10.6 - - - +
277A LEU* 3.8 40.3 + - - +
280A ALA* 3.9 7.4 - - - +
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Residues in contact with GLN 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.2 58.0 + - + +
24A PRO* 3.9 24.0 - - + +
205A VAL* 3.0 12.7 + - + +
206A ALA* 3.4 15.9 + - - +
207A GLY 3.4 0.4 - - - -
208A SER* 1.3 78.2 - - - +
210A SER* 1.3 71.7 + - - +
211A HIS 3.1 1.4 + - - -
212A ILE* 3.2 25.3 + - - +
213A ALA 4.6 0.7 + - - -
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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