Contacts of the helix formed by residues 177 - 192 (chain A) in PDB entry 1R9G
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 HIS 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A HIS* 3.9 27.4 - + - -
19A ALA* 3.6 26.9 - - + +
22A ALA* 3.7 21.8 - - + +
23A CYS* 3.9 17.1 - - - -
171A PRO 5.9 1.1 - - - -
172A GLU* 5.8 2.5 - - - -
174A THR 4.4 8.4 + - - -
175A GLU* 3.2 29.0 + - + -
176A ASP* 1.3 75.4 + - - +
178A ARG* 1.3 63.2 + - - +
179A VAL 3.3 2.9 - - - -
180A THR* 3.2 10.4 + - - +
181A GLN* 3.0 21.6 + - - +
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Residues in contact with ARG 178 (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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125A LEU* 3.5 46.6 - - + +
126A ASP 4.2 1.2 - - - +
127A GLU* 2.5 39.2 + - - +
128A PRO 2.9 24.7 + - - -
129A PHE* 3.8 5.5 - - - -
176A ASP* 2.6 37.3 + - - +
177A HIS* 1.3 76.8 - - - +
179A VAL* 1.3 62.6 + - - +
181A GLN* 3.1 12.0 + - + +
182A LEU* 3.1 22.3 + - - +
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Residues in contact with VAL 179 (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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76A PHE* 4.0 26.2 - - + -
122A ILE* 3.5 35.2 - - + -
125A LEU* 4.3 3.8 - - + -
129A PHE* 3.8 24.1 - - + -
165A LEU* 4.8 5.7 - - + +
167A CYS* 5.2 0.9 - - + -
169A PHE* 4.4 8.7 - - + -
171A PRO* 4.0 17.5 - - + -
176A ASP 4.9 0.2 + - - -
177A HIS 3.3 0.6 - - - -
178A ARG* 1.3 74.4 - - - +
180A THR* 1.3 69.3 + - - +
182A LEU* 2.9 23.8 + - + +
183A PHE* 3.3 8.8 + - - +
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Residues in contact with THR 180 (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 HIS* 5.2 5.2 + - - -
19A ALA* 3.5 45.2 - - + +
20A ILE* 4.0 15.3 - - + +
23A CYS* 4.0 5.8 - - - -
43A ILE* 5.1 8.5 - - + -
76A PHE* 5.0 6.7 - - - -
171A PRO* 5.0 12.7 - - - +
172A GLU* 5.3 2.8 + - - -
177A HIS* 3.2 12.0 + - - -
179A VAL* 1.3 79.9 - - - +
181A GLN* 1.3 56.9 + - - +
183A PHE* 3.1 9.6 + - + +
184A VAL* 2.9 30.1 + - + +
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Residues in contact with GLN 181 (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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23A CYS* 3.0 42.4 + - - +
177A HIS 3.0 12.9 + - - +
178A ARG* 3.2 17.7 - - + +
179A VAL 3.0 0.2 - - - -
180A THR* 1.3 77.6 - - - +
182A LEU* 1.3 55.2 + - - +
184A VAL* 3.2 10.9 + - - +
185A GLU* 2.8 52.1 + - - +
188A GLU* 5.1 2.8 - - - +
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Residues in contact with LEU 182 (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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122A ILE* 4.1 17.9 - - + -
123A LYS 4.1 16.6 - - - +
124A GLY* 4.6 14.4 - - - +
125A LEU* 4.2 16.8 - - + -
149A LEU* 4.4 16.6 - - + -
165A LEU* 5.0 8.3 - - + -
178A ARG 3.1 14.6 + - - +
179A VAL* 2.9 18.4 + - + +
181A GLN* 1.3 76.0 - - - +
183A PHE* 1.3 63.4 + - - +
185A GLU* 3.3 22.6 + - - +
186A MSE 3.1 26.8 + - - +
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Residues in contact with PHE 183 (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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4A ILE* 3.7 20.9 - - + -
42A LEU 3.4 20.6 - - - -
43A ILE* 3.7 29.2 - - + -
74A PRO* 3.5 33.7 - - + -
75A MSE 3.6 7.9 - - - -
76A PHE* 3.5 33.2 - - + -
165A LEU* 3.8 22.6 - - + +
179A VAL 3.3 2.9 + - - +
180A THR* 3.1 11.0 + - + +
182A LEU* 1.3 78.2 - - - +
184A VAL* 1.3 67.8 + - + +
186A MSE 2.9 27.0 + - + +
187A VAL* 2.9 21.0 + - + +
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Residues in contact with VAL 184 (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* 5.1 3.6 - - + -
4A ILE* 4.4 20.9 - - + -
20A ILE* 4.9 5.8 - - + +
23A CYS* 4.1 30.7 - - + +
24A GLY 5.2 0.7 - - - +
25A ALA* 4.7 11.9 - - + -
180A THR* 2.9 26.7 + - + +
181A GLN* 3.2 16.4 + - - +
183A PHE* 1.3 78.6 - - + +
185A GLU* 1.3 61.9 + - - +
187A VAL* 3.2 8.8 + - - +
188A GLU* 3.1 39.3 + - + +
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Residues in contact with GLU 185 (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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181A GLN* 2.8 48.4 + - - +
182A LEU* 3.5 25.6 - - - +
183A PHE 3.2 0.2 - - - -
184A VAL* 1.3 76.1 - - - +
186A MSE 1.3 57.0 + - - +
188A GLU* 3.4 14.3 + - - +
189A GLU* 3.0 30.5 + - - +
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Residues in contact with MSE 186 (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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74A PRO* 3.9 8.0 - - + +
160A LYS* 4.2 26.0 - - + +
162A GLY 3.7 9.9 - - - +
163A GLN* 3.2 36.8 - - - +
164A PHE 3.5 20.6 - - - +
165A LEU* 3.6 33.0 - - + -
182A LEU* 3.1 18.2 + - - +
183A PHE* 2.9 18.0 + - + +
185A GLU* 1.3 77.4 - - - +
187A VAL* 1.3 57.5 + - - +
189A GLU* 3.4 15.8 + - - +
190A TYR* 3.1 24.6 + - - +
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Residues in contact with VAL 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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2A LEU* 4.4 9.0 - - + -
4A ILE* 3.7 28.5 - - + -
40A ASP* 3.4 40.2 - - + +
41A GLY* 4.2 3.1 - - - -
74A PRO* 3.7 26.2 - - + -
183A PHE* 2.9 29.5 + - + +
184A VAL 3.2 6.7 + - - +
186A MSE 1.3 76.1 - - - +
188A GLU* 1.3 59.7 + - - +
190A TYR* 3.1 4.7 + - - +
191A LYS* 2.9 23.9 + - - +
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Residues in contact with GLU 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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2A LEU* 3.3 41.3 - - + +
181A GLN* 5.1 2.4 - - - +
184A VAL* 3.1 26.3 + - + +
185A GLU* 3.8 16.0 - - - +
186A MSE 3.3 0.2 - - - -
187A VAL* 1.3 71.8 - - - +
189A GLU* 1.3 66.8 + - - +
190A TYR 3.0 1.6 - - - -
191A LYS* 3.0 4.4 + - - +
192A GLN* 2.9 31.7 + - - +
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Residues in contact with GLU 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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160A LYS* 5.3 5.2 + - - -
185A GLU 3.0 16.2 + - - +
186A MSE 3.4 19.9 - - - +
188A GLU* 1.3 77.8 - - - +
190A TYR* 1.3 60.5 + - - +
192A GLN* 3.5 14.2 + - - +
193A LYS* 3.8 23.2 + - - +
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Residues in contact with TYR 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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40A ASP* 3.8 31.4 - - + -
71A GLN* 3.6 19.3 + - - +
72A GLY* 3.1 27.6 - - - +
73A LYS* 3.5 26.5 - - + +
74A PRO* 3.6 14.6 - - + -
186A MSE 3.1 12.5 + - - +
187A VAL 3.2 11.0 - - - +
188A GLU 3.0 0.2 - - - -
189A GLU* 1.3 76.0 - - - +
191A LYS* 1.3 75.5 + - + +
192A GLN 3.2 0.2 - - - -
193A LYS* 3.2 6.3 + - + +
194A ALA* 3.0 47.0 + - + +
196A VAL* 5.4 2.6 - - - +
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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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1A MSE 4.2 11.7 + - - +
2A LEU* 3.4 28.6 - - + +
40A ASP* 2.9 37.1 + - - +
187A VAL 2.9 10.2 + - - +
188A GLU* 3.0 8.9 + - - +
190A TYR* 1.3 87.5 - - + +
192A GLN* 1.3 65.2 + - - +
193A LYS 3.1 5.2 + - - -
194A ALA* 3.7 16.1 + - + +
196A VAL* 6.6 0.2 - - + -
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Residues in contact with GLN 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 GLU* 2.9 23.8 + - - +
189A GLU* 3.9 9.6 - - + +
190A TYR 3.2 0.6 - - - -
191A LYS* 1.3 83.3 - - - +
193A LYS* 1.3 58.8 + - - +
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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