Contacts of the helix formed by residues 189 - 209 (chain A) in PDB entry 3LOC
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 ASP 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A GLY 4.9 1.1 - - - +
185A ALA* 3.8 8.6 - - + -
186A THR* 3.0 39.9 + - - +
187A LEU 4.1 0.7 - - - -
188A ARG* 1.3 73.6 - - - +
190A GLU* 1.3 58.9 + - - +
191A VAL* 3.3 2.7 - - + +
192A PHE* 2.9 31.6 + - + +
193A PHE* 2.9 10.7 + - - +
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Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU 5.1 0.2 - - - -
188A ARG 3.2 8.6 + - - +
189A ASP* 1.3 70.7 - - - +
191A VAL* 1.3 64.3 + - + +
193A PHE* 3.3 9.4 + - - +
194A ASN* 3.1 33.9 + - - +
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ASP* 3.3 1.0 - - + -
190A GLU* 1.3 78.8 - - + +
192A PHE* 1.3 57.5 + - - +
194A ASN* 4.1 5.8 - - - +
195A GLN* 3.1 26.8 + - + +
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Residues in contact with PHE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR* 4.3 8.5 - + - -
179A VAL* 3.6 32.1 - - + -
183A THR* 3.0 25.8 - - + -
185A ALA* 3.3 25.8 - - + -
186A THR 3.5 22.7 - - - +
187A LEU* 4.2 8.1 - - + -
189A ASP* 2.9 13.7 + - + +
191A VAL* 1.3 79.4 - - - +
193A PHE* 1.3 55.3 + - - +
195A GLN* 3.2 6.4 + - + +
196A THR* 2.8 49.1 + - - -
160B HIS* 3.7 28.5 - + - -
163B PHE* 5.1 0.2 - + - -
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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
----------------------------------------------------------
98A ARG* 5.6 3.4 - - + -
101A LEU* 3.7 23.6 - - + -
102A GLU* 3.9 26.2 - - + -
105A ARG* 3.6 35.2 - - + -
187A LEU* 3.5 45.5 - - + +
189A ASP 2.9 6.7 + - - +
190A GLU* 3.3 12.3 + - - +
192A PHE* 1.3 79.0 - - - +
194A ASN* 1.3 72.0 + - - +
196A THR* 3.3 3.8 + - - -
197A VAL* 3.0 48.8 + - + +
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Residues in contact with ASN 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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190A GLU* 3.1 19.4 + - - +
191A VAL* 4.2 5.2 - - - +
193A PHE* 1.3 92.7 - - - +
195A GLN* 1.3 65.6 + - - +
197A VAL* 3.3 5.0 + - - +
198A GLU* 3.0 28.2 + - - +
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Residues in contact with GLN 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A VAL* 3.1 22.1 + - + +
192A PHE* 3.2 10.7 + - + +
194A ASN* 1.3 77.4 - - - +
196A THR* 1.3 60.1 + - - +
198A GLU* 4.2 2.6 - - - +
199A ASN* 2.7 36.7 + - - +
160B HIS* 3.8 11.8 + - + +
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Residues in contact with THR 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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101A LEU* 4.0 15.7 - - + -
172A TYR* 3.4 45.3 - - + +
187A LEU* 3.9 6.9 - - + +
192A PHE* 2.8 36.1 + - - -
193A PHE 3.5 5.4 - - - -
194A ASN 3.1 0.2 - - - -
195A GLN* 1.3 75.4 - - - +
197A VAL* 1.3 60.8 - - - +
199A ASN* 3.2 1.4 + - - +
200A VAL* 2.8 30.6 + - + +
160B HIS* 3.1 19.2 - - - -
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Residues in contact with VAL 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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98A ARG* 4.3 20.2 - - + -
101A LEU* 3.7 24.7 - - + -
193A PHE* 3.0 42.8 + - + +
194A ASN* 3.3 5.8 + - - +
196A THR* 1.3 73.5 - - - +
198A GLU* 1.3 69.6 + - - +
200A VAL* 4.3 0.2 - - - +
201A GLN* 3.0 57.7 + - + +
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Residues in contact with GLU 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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194A ASN 3.0 17.8 + - - +
195A GLN* 4.2 4.7 - - - +
197A VAL* 1.3 77.3 - - - +
199A ASN* 1.3 56.8 + - - +
201A GLN* 3.4 9.8 - - - +
202A ARG* 2.6 40.5 + - + +
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Residues in contact with ASN 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 GLN* 2.7 30.9 + - - +
196A THR 3.2 1.7 + - - +
197A VAL 3.1 0.8 - - - -
198A GLU* 1.3 80.3 - - - +
200A VAL* 1.3 66.4 + - - +
202A ARG* 3.7 5.0 - - - +
203A ILE* 3.0 30.9 + - + +
156B ILE* 3.3 13.2 - - + +
157B ASP* 3.1 39.3 + - - +
160B HIS* 3.6 29.2 - - + -
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Residues in contact with VAL 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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97A ILE* 3.5 29.8 - - + -
101A LEU* 4.3 4.5 - - + -
168A SER* 3.9 30.1 - - - +
169A THR* 4.4 5.2 - - + -
172A TYR* 4.1 31.6 - - + +
196A THR* 2.8 24.5 + - + +
197A VAL 4.3 0.2 - - - +
199A ASN* 1.3 75.2 - - + +
201A GLN* 1.3 58.3 + - - +
203A ILE* 3.4 1.2 + - - +
204A ILE* 3.1 32.7 + - + +
160B HIS* 5.7 3.1 - - + +
164B MSE 4.4 11.2 - - + -
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Residues in contact with GLN 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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94A LYS* 2.8 48.0 + - + +
95A GLU* 4.9 0.2 - - - +
97A ILE* 3.8 26.7 - - + -
98A ARG* 3.9 11.1 - - - +
197A VAL* 3.0 41.1 + - - +
198A GLU* 3.4 7.1 - - - +
200A VAL* 1.3 73.9 - - - +
202A ARG* 1.3 67.0 + - - +
205A ILE* 2.9 34.9 + - + +
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Residues in contact with ARG 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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198A GLU* 2.6 24.4 + - + +
199A ASN* 3.3 5.6 + - - +
201A GLN* 1.3 71.9 - - - +
203A ILE* 1.3 65.1 + - - +
205A ILE* 5.0 1.3 - - - -
206A GLU* 3.0 44.5 + - + +
154B ALA* 5.5 3.8 - - - -
155B PRO* 3.0 33.7 - - - -
156B ILE* 3.2 20.0 - - + -
207B GLY 4.9 6.3 - - - -
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Residues in contact with ILE 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 ASN 3.0 16.4 + - - +
202A ARG* 1.3 76.8 - - - +
204A ILE* 1.3 64.2 + - + +
207A GLY* 2.9 19.9 + - - -
156B ILE* 3.8 23.3 - - + -
160B HIS* 4.8 2.2 - - + +
161B LEU* 4.0 39.0 - - + +
164B MSE 3.4 31.0 - - + -
203B ILE* 3.8 1.8 - - + +
204B ILE* 4.0 34.3 - - + +
207B GLY* 3.4 8.2 - - - -
208B ILE* 4.2 8.5 - - + -
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Residues in contact with ILE 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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93A ILE* 4.5 5.2 - - + -
97A ILE* 3.9 26.9 - - + -
161A LEU* 3.5 28.3 - - + -
164A MSE 4.1 18.8 - - + -
165A ILE* 4.0 16.2 - - + -
168A SER* 3.7 23.6 - - - +
200A VAL* 3.1 15.9 + - + +
203A ILE* 1.3 75.6 - - - +
205A ILE* 1.3 65.4 + - - +
207A GLY* 3.1 2.8 + - - -
208A ILE* 3.0 30.1 + - + +
164B MSE 4.1 11.9 - - + -
203B ILE* 4.0 11.1 - - + +
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Residues in contact with ILE 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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90A LEU* 3.8 26.0 - - + +
93A ILE* 3.8 19.3 - - + -
94A LYS* 3.8 43.1 - - + +
97A ILE* 4.7 2.9 - - + -
201A GLN* 2.9 30.7 + - - +
202A ARG* 4.4 1.1 - - - +
204A ILE* 1.3 75.0 - - - +
206A GLU* 1.3 65.5 + - - +
207A GLY 3.1 0.5 + - - -
208A ILE* 3.1 11.1 + - + +
209A ARG* 3.1 42.1 + - - +
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Residues in contact with GLU 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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202A ARG* 3.0 40.1 + - + +
205A ILE* 1.3 76.8 - - + +
207A GLY* 1.3 60.6 + - - +
208A ILE 3.4 1.0 + - - -
209A ARG* 3.3 35.3 + - - -
211A ARG* 2.8 44.3 + - - +
206B GLU* 3.8 4.8 - - - +
207B GLY* 3.9 18.4 - - - +
211B ARG* 5.0 3.6 + - - +
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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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203A ILE 2.9 10.9 + - - -
204A ILE 3.4 5.2 - - - -
205A ILE 3.0 0.4 - - - -
206A GLU* 1.3 78.3 - - - +
208A ILE* 1.3 59.1 + - - +
209A ARG 3.5 0.2 - - - -
202B ARG* 2.6 30.8 + - - -
203B ILE* 3.2 32.8 - - - +
206B GLU 4.0 2.0 - - - -
207B GLY* 3.5 8.0 - - - -
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Residues in contact with ILE 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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90A LEU* 4.1 4.3 - - + -
93A ILE* 3.7 41.5 - - + -
153A LEU* 3.4 21.9 - - + +
154A ALA* 3.0 25.0 + - + +
156A ILE* 4.3 10.8 - - + -
161A LEU* 3.8 34.1 - - + -
204A ILE* 3.0 20.3 + - + +
205A ILE* 3.1 12.5 + - + +
207A GLY* 1.3 79.7 - - - +
209A ARG* 1.3 66.8 + - - +
210A PRO 3.4 0.5 - - - -
203B ILE* 4.1 15.0 - - + -
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Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 3.5 32.0 - - + +
154A ALA* 3.4 9.2 - - - +
205A ILE* 3.1 23.0 + - - +
206A GLU* 3.3 27.2 + - - +
208A ILE* 1.3 80.0 - - - +
210A PRO* 1.3 84.9 - - + +
211A ARG* 3.2 47.8 + - - +
202B ARG* 4.2 2.1 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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