Contacts of the helix formed by residues 186 - 203 (chain A) in PDB entry 4MBS
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 GLN 186 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A PRO* 3.3 34.0 - - - +
184A TYR 4.4 7.5 + - - -
185A SER* 1.3 78.3 + - - +
187A TYR* 1.4 65.5 + - - +
188A GLN 3.5 2.2 - - - -
189A PHE* 3.2 16.4 + - + +
190A TRP* 3.1 38.4 + - + +
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Residues in contact with TYR 187 (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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19A PRO* 6.1 6.8 - - + +
182A PHE* 3.9 41.3 - + + -
183A PRO 3.1 10.9 + - - +
184A TYR* 4.4 20.6 - + + -
185A SER* 4.5 2.4 - - - +
186A GLN* 1.4 75.2 - - - +
188A GLN* 1.3 61.9 + - + +
190A TRP* 3.3 3.3 + - - +
191A LYS* 2.9 44.8 + - + +
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Residues in contact with GLN 188 (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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186A GLN 3.5 0.8 - - - -
187A TYR* 1.3 79.6 - - + +
189A PHE* 1.4 65.5 + - - +
191A LYS* 3.7 10.9 - - - +
192A ASN* 2.9 57.3 + - - +
259A THR* 4.3 12.2 - - - +
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Residues in contact with PHE 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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186A GLN* 3.2 19.2 + - + +
188A GLN* 1.4 79.3 - - - +
190A TRP* 1.4 99.8 + + - +
192A ASN* 3.4 8.2 + - + +
193A PHE* 2.8 57.4 + + + +
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Residues in contact with TRP 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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162A PRO* 5.3 5.4 - - + -
166A PHE* 3.5 32.3 - + - -
182A PHE* 3.7 26.7 - - + -
183A PRO* 3.5 36.2 - - + +
186A GLN* 3.1 34.1 + - - +
187A TYR 3.3 1.7 + - - +
189A PHE* 1.4 102.2 - + - +
191A LYS* 1.4 61.5 + - - +
193A PHE* 4.3 16.8 - + + -
194A GLN* 2.8 50.8 + - - +
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Residues in contact with LYS 191 (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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182A PHE* 4.2 3.1 - - + -
187A TYR* 2.9 50.5 + - + +
188A GLN* 3.7 12.8 - - - +
190A TRP* 1.4 71.9 - - - +
192A ASN* 1.4 54.6 + - - +
195A THR* 2.7 38.4 + - - -
259A THR* 3.9 9.9 - - + -
1101A MRV 3.8 32.5 - - - +
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Residues in contact with ASN 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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188A GLN* 2.9 50.4 + - - +
189A PHE* 3.5 7.4 - - + +
191A LYS* 1.4 74.9 - - - +
193A PHE* 1.4 55.3 + - - +
195A THR* 3.5 2.4 + - - -
196A LEU* 3.1 37.5 + - + +
259A THR* 3.6 11.3 - - - +
260A PHE* 3.5 32.0 - - + -
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Residues in contact with PHE 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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162A PRO* 5.7 2.5 - - + -
189A PHE* 2.8 49.4 + + + +
190A TRP* 3.9 17.0 - + + +
192A ASN* 1.4 69.9 - - - +
194A GLN* 1.4 77.3 + - - +
196A LEU* 3.3 7.8 + - - +
197A LYS* 3.0 50.1 + - + +
1103A OLC 4.9 14.8 - - - -
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Residues in contact with GLN 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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109A PHE* 5.3 1.2 - - - -
162A PRO* 3.9 14.2 - - - +
163A ASN* 2.6 30.6 + - - +
166A PHE* 4.3 1.8 - - - -
182A PHE* 4.0 22.4 - - + -
190A TRP* 2.8 32.7 + - + +
193A PHE* 1.4 86.8 - - - +
195A THR* 1.4 65.4 + - - +
197A LYS* 3.3 32.3 + - - +
198A ILE* 3.4 30.7 + - + +
1101A MRV 3.8 21.5 - - + -
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Residues in contact with THR 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 LYS 2.7 22.9 + - - -
192A ASN 3.6 4.3 - - - -
194A GLN* 1.4 75.9 - - - +
196A LEU* 1.4 64.2 + - - +
198A ILE* 3.3 4.7 + - - +
199A VAL* 3.1 23.4 + - + +
255A LEU* 3.8 33.7 - - + +
256A LEU* 4.3 10.1 - - + -
259A THR* 2.7 21.6 + - - +
260A PHE* 3.7 21.5 - - + -
1101A MRV 3.3 13.2 - - - +
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Residues in contact with LEU 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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192A ASN* 3.1 24.2 + - + +
193A PHE* 3.3 5.6 + - - +
195A THR* 1.4 75.3 - - - +
197A LYS* 1.4 53.3 + - - +
199A VAL* 4.3 7.0 - - + -
200A ILE* 2.8 55.7 + - + +
256A LEU* 4.7 12.6 - - + -
260A PHE* 3.7 28.7 - - + -
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Residues in contact with LYS 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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113A PHE* 4.3 13.7 - - + -
159A ALA* 2.8 29.8 + - + +
162A PRO* 3.5 19.0 - - - +
163A ASN* 3.2 18.1 - - - +
193A PHE* 3.0 38.2 + - + +
194A GLN* 3.3 23.2 - - - +
196A LEU* 1.4 76.3 - - - +
198A ILE* 1.4 58.0 + - + +
200A ILE* 5.0 2.7 - - - -
201A LEU* 3.1 49.6 + - + +
1103A OLC 4.5 19.0 - - - +
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Residues in contact with ILE 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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109A PHE* 4.4 8.5 - - + -
112A PHE* 4.2 18.6 - - + -
113A PHE* 4.4 21.5 - - + -
194A GLN* 3.4 20.6 + - + +
195A THR 3.3 5.1 + - - +
197A LYS* 1.4 74.6 - - + +
199A VAL* 1.3 56.3 + - - +
202A GLY* 2.8 31.5 + - - -
251A TYR* 4.5 10.5 - - + -
252A ASN* 3.3 12.3 - - - +
255A LEU* 4.0 16.4 - - + -
1101A MRV 3.8 53.4 - - + +
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Residues in contact with VAL 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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195A THR* 3.1 23.2 + - + +
196A LEU* 4.0 9.9 - - + +
198A ILE* 1.3 74.8 - - - +
200A ILE* 1.3 63.8 + - + +
203A LEU* 3.2 13.3 + - + +
204A VAL* 2.9 36.3 + - + +
252A ASN* 3.7 34.5 - - + +
255A LEU* 4.5 6.7 - - + -
256A LEU* 3.8 34.1 - - + -
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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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196A LEU* 2.8 40.8 + - + +
197A LYS* 4.3 3.1 - - - +
199A VAL* 1.3 79.4 - - + +
201A LEU* 1.4 66.4 + - + +
204A VAL* 3.3 22.1 + - + -
205A LEU* 2.6 38.1 + - + +
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Residues in contact with LEU 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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113A PHE* 3.6 37.2 - - + -
116A ILE* 3.8 15.0 - - - +
117A PHE* 4.5 9.4 - - + -
159A ALA* 4.4 14.6 - - + -
197A LYS* 3.1 31.9 + - + +
200A ILE* 1.4 84.0 - - + +
202A GLY* 1.3 56.7 + - - +
205A LEU* 4.1 22.6 - - + +
206A PRO* 3.4 14.1 - - - +
1103A OLC 3.9 40.8 - - + +
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Residues in contact with GLY 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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112A PHE* 4.2 13.6 - - - -
116A ILE* 4.5 3.1 - - - -
198A ILE 2.8 23.1 + - - -
201A LEU* 1.3 73.6 - - - +
203A LEU* 1.3 59.3 + - - +
206A PRO* 3.6 12.0 - - - +
244A TYR* 3.2 31.6 + - - -
245A PHE* 4.6 1.2 - - - -
252A ASN* 4.0 9.3 + - - +
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Residues in contact with LEU 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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199A VAL* 3.2 20.5 + - + +
201A LEU 3.6 0.8 - - - -
202A GLY* 1.3 79.8 - - - +
204A VAL* 1.3 67.8 + - + +
205A LEU 3.5 0.9 - - - -
206A PRO* 3.5 4.2 - - - +
207A LEU* 3.1 50.2 + - + +
245A PHE* 4.2 12.0 - - + -
249A ALA* 4.3 24.2 - - + -
252A ASN* 3.8 30.1 - - + +
253A ILE* 4.6 16.2 - - + -
256A LEU* 5.7 5.2 - - + -
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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