Contacts of the helix formed by residues 154 - 175 (chain A) in PDB entry 2I10
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 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLY 3.3 6.0 + - - +
153A THR* 1.3 72.0 - - - +
155A CYS* 1.3 56.7 + - - +
156A THR* 3.3 10.9 + - - -
157A ALA* 2.9 34.3 + - + +
158A LEU* 2.9 30.7 + - - +
184B ALA* 4.9 5.0 - - - +
188B LEU* 5.1 1.7 - - + +
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Residues in contact with CYS 155 (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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137A LEU* 3.5 9.9 - - + +
140A PHE* 3.7 31.0 - - + -
141A GLU* 3.2 29.6 - - - +
144A LEU* 4.0 20.6 - - - -
149A LEU* 4.1 11.7 - - - -
153A THR* 3.2 16.7 + - - -
154A ASP* 1.3 71.0 + - - +
156A THR* 1.3 60.4 + - - +
158A LEU* 4.2 6.1 - - - -
159A ALA* 2.9 30.8 + - - +
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Residues in contact with THR 156 (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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133A ARG* 4.6 11.8 + - - +
137A LEU* 3.9 18.2 - - - +
141A GLU* 5.6 0.9 + - - -
154A ASP* 3.3 8.0 + - - -
155A CYS* 1.3 79.8 - - - +
157A ALA* 1.3 61.7 + - - +
159A ALA* 3.4 2.6 + - - +
160A ARG* 3.1 22.0 + - - +
181B GLU* 3.2 32.4 - - + +
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Residues in contact with ALA 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASP* 2.9 32.0 + - + +
156A THR* 1.3 73.9 - - - +
158A LEU* 1.3 57.1 + - - +
160A ARG* 3.4 7.7 + - - +
161A TYR* 2.9 28.1 + - - +
181B GLU* 4.5 8.5 - - + +
184B ALA* 3.6 31.6 - - + -
185B ALA* 4.0 3.1 - - - +
188B LEU* 3.8 12.4 - - + +
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Residues in contact with LEU 158 (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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140A PHE* 3.6 27.1 - - + -
149A LEU* 4.3 17.5 - - + -
153A THR* 4.0 22.0 - - + -
154A ASP 2.9 18.1 + - - +
155A CYS* 3.9 4.9 - - - +
157A ALA* 1.3 77.4 - - - +
159A ALA* 1.3 55.5 + - - +
161A TYR* 3.3 5.5 + - + +
162A VAL* 3.1 26.9 + - - +
192A VAL* 3.8 36.6 - - + +
193A VAL* 4.3 13.5 - - + -
194A PRO* 4.3 4.5 - - + -
188B LEU* 3.8 17.4 - - + +
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ARG* 4.5 13.9 - - + +
136A VAL* 3.9 21.5 - - + +
137A LEU* 4.2 18.6 - - + +
140A PHE* 3.5 11.1 - - + -
155A CYS 2.9 21.8 + - - +
156A THR* 3.9 3.6 - - - +
158A LEU* 1.3 69.6 - - - +
160A ARG* 1.3 66.1 + - - +
162A VAL* 3.1 4.0 + - - +
163A MSE 3.0 30.0 + - + +
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Residues in contact with ARG 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG* 4.0 11.9 - - - +
133A ARG* 3.7 33.9 - - - +
156A THR 3.1 13.2 + - - +
157A ALA 3.6 7.9 - - - +
159A ALA* 1.3 75.2 - - - +
161A TYR* 1.3 62.9 + - - +
163A MSE 3.4 7.3 + - - +
164A ALA* 3.1 21.1 + - - +
172B GLU* 2.8 37.6 + - - -
177B ALA* 3.6 25.9 - - - +
178B PRO* 3.9 12.5 - - - +
181B GLU* 2.7 41.9 + - + +
182B LEU* 3.7 22.7 - - + -
185B ALA* 4.1 7.0 - - + -
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Residues in contact with TYR 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 5.6 1.6 - - + -
157A ALA 2.9 14.5 + - - +
158A LEU* 3.5 12.8 - - + +
159A ALA 3.2 0.4 - - - -
160A ARG* 1.3 76.0 - - - +
162A VAL* 1.3 70.6 + - + +
164A ALA* 3.1 8.2 + - + +
165A ALA* 2.9 39.9 + - + +
189A ALA* 2.8 47.6 + - - +
192A VAL* 3.4 31.6 - - + +
193A VAL* 5.3 2.2 - - + -
161B TYR* 3.4 22.9 + + - -
165B ALA* 5.8 1.3 - - + -
169B LEU* 6.5 0.4 - - + -
185B ALA* 3.8 19.8 - - + +
188B LEU* 4.2 10.1 - - + -
189B ALA* 3.6 25.1 - - + -
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Residues in contact with VAL 162 (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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85A VAL* 4.0 29.6 - - + -
88A PHE* 4.3 15.9 - - + -
89A LEU* 4.4 3.3 - - + +
136A VAL* 4.3 12.8 - - + -
140A PHE* 3.8 20.9 - - + -
158A LEU 3.1 18.3 + - - +
159A ALA 3.1 7.8 + - - +
161A TYR* 1.3 88.5 - - + +
163A MSE 1.3 73.9 + - + +
165A ALA* 3.3 4.8 + - - +
166A VAL* 3.0 28.2 + - - +
193A VAL* 4.3 4.5 - - + -
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Residues in contact with MSE 163 (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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88A PHE* 4.2 3.4 - - + -
129A ARG* 4.9 2.5 - - - +
132A MSE 3.1 56.5 - - + -
133A ARG* 4.1 25.1 - - + -
136A VAL* 4.0 12.8 - - + -
159A ALA* 3.0 16.7 + - + +
160A ARG* 3.6 10.3 - - - +
162A VAL* 1.3 97.4 - - + +
164A ALA* 1.3 62.9 + - - +
166A VAL* 3.2 6.3 + - + +
167A TYR* 2.9 31.7 + - + -
172B GLU* 3.5 22.2 - - - +
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Residues in contact with ALA 164 (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 ARG 3.1 10.8 + - - +
161A TYR* 3.4 14.8 - - + +
163A MSE 1.3 78.2 - - - +
165A ALA* 1.3 57.9 + - - +
167A TYR* 4.8 0.2 - - - -
168A GLY* 2.8 27.5 + - - -
164B ALA 4.2 0.8 - - - +
165B ALA* 5.0 3.6 - - - +
168B GLY* 3.0 36.9 - - - +
169B LEU* 3.8 18.8 - - + +
172B GLU* 3.9 7.7 - - + +
182B LEU* 5.5 0.4 - - + -
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 4.4 9.0 - - + -
161A TYR* 2.9 28.2 + - + +
162A VAL* 3.7 8.5 - - - +
163A MSE 3.3 0.2 - - - -
164A ALA* 1.3 73.9 - - - +
166A VAL* 1.3 65.1 + - - +
168A GLY* 3.2 0.6 + - - -
169A LEU* 2.8 34.7 + - + +
189A ALA* 4.1 26.0 - - + -
161B TYR* 5.6 2.2 - - + -
164B ALA* 5.4 4.9 - - - -
165B ALA* 5.8 2.5 - - - +
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Residues in contact with VAL 166 (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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66A CYS* 6.0 2.0 - - + +
88A PHE* 3.5 30.1 - - + -
89A LEU* 4.0 14.1 - - + +
92A ARG* 3.7 27.4 - - + -
96A PHE* 4.2 3.7 - - + -
132A MSE 4.1 25.1 - - + -
162A VAL 3.0 15.1 + - - +
163A MSE 3.3 15.5 - - + +
165A ALA* 1.3 77.5 - - - +
167A TYR* 1.3 73.6 + - + +
169A LEU* 3.6 5.6 + - + +
170A SER* 3.1 20.6 + - - -
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Residues in contact with TYR 167 (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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66A CYS* 3.8 21.3 - - + -
67A GLU* 2.4 32.9 + - - -
107A THR* 4.0 25.2 - - + +
129A ARG* 3.4 24.4 - - - +
132A MSE 2.6 29.7 - - + +
163A MSE 2.9 30.7 + - + +
164A ALA* 4.1 1.8 - - - +
166A VAL* 1.3 79.1 - - + +
168A GLY* 1.3 59.1 + - - +
170A SER* 3.1 7.6 - - - -
171A VAL* 2.9 32.7 + - - +
168B GLY* 4.4 1.8 - - - -
171B VAL* 3.7 26.5 - - + -
172B GLU* 3.1 26.0 - - + -
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Residues in contact with GLY 168 (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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164A ALA 2.8 17.8 + - - -
165A ALA 3.8 0.2 - - - -
167A TYR* 1.3 69.5 - - - +
169A LEU* 1.3 60.9 + - - +
171A VAL* 3.2 3.5 + - - +
172A GLU* 2.9 28.6 + - - +
164B ALA* 3.1 34.0 - - - -
167B TYR* 4.3 5.3 - - - +
168B GLY* 3.5 10.0 - - - -
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Residues in contact with LEU 169 (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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89A LEU* 4.3 18.6 - - + +
92A ARG* 6.2 0.9 - - + -
93A VAL* 4.2 15.5 - - + -
96A PHE* 4.2 6.9 - - + -
165A ALA* 2.8 28.7 + - + +
166A VAL* 3.9 5.2 - - + +
168A GLY* 1.3 76.1 - - - +
170A SER* 1.3 56.7 + - - +
172A GLU* 4.4 2.2 - - - -
173A ALA* 3.0 30.0 + - - +
182A LEU* 3.8 23.6 - - + +
185A ALA* 3.9 30.1 - - + +
186A ALA* 4.0 25.8 - - + +
189A ALA* 4.9 3.8 - - + -
161B TYR* 6.0 0.7 - - + -
164B ALA* 3.9 16.1 - - + +
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Residues in contact with SER 170 (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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66A CYS* 5.2 1.6 - - - -
96A PHE* 3.3 33.3 - - - -
104A GLY* 5.6 0.2 - - - -
105A CYS* 3.0 34.1 + - - -
107A THR* 4.2 3.5 - - - +
166A VAL 3.1 11.3 + - - -
167A TYR* 3.1 15.0 - - - -
168A GLY 3.1 0.8 - - - -
169A LEU* 1.3 73.2 - - - +
171A VAL* 1.3 58.7 + - - +
173A ALA* 3.4 2.6 + - - +
174A ALA* 2.9 30.1 + - - +
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Residues in contact with VAL 171 (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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107A THR* 4.4 11.0 - - + +
167A TYR 2.9 21.5 + - - +
168A GLY 3.6 5.8 - - - +
170A SER* 1.3 71.8 - - - +
172A GLU* 1.3 58.9 + - - +
174A ALA* 3.2 7.9 + - - +
175A SER* 2.8 34.7 + - - +
107B THR* 4.0 29.8 - - + +
108B VAL* 4.0 25.8 - - + +
111B GLY* 5.7 3.1 - - - -
167B TYR* 3.9 28.9 - - + -
171B VAL* 4.2 9.4 - - + -
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Residues in contact with GLU 172 (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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168A GLY 2.9 17.5 + - - +
169A LEU* 3.8 1.1 - - - +
171A VAL* 1.3 72.5 - - - +
173A ALA* 1.3 62.2 + - - +
175A SER* 3.2 10.2 + - - -
176A GLY 3.3 0.5 + - - -
177A ALA* 3.1 26.0 + - + +
182A LEU* 3.6 20.6 - - + -
129B ARG* 2.1 39.2 + - - +
160B ARG* 2.6 34.8 + - - +
163B MSE 3.5 7.6 - - - +
164B ALA* 4.0 24.7 - - + +
167B TYR* 3.2 26.1 - - + -
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Residues in contact with ALA 173 (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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96A PHE* 3.6 37.6 - - + +
97A THR* 4.7 2.2 - - + -
169A LEU 3.0 19.0 + - - +
170A SER 3.7 3.8 - - - +
172A GLU* 1.3 76.6 - - - +
174A ALA* 1.3 60.7 + - - +
176A GLY* 3.3 13.7 + - - -
177A ALA 4.2 2.9 + - - +
182A LEU* 3.6 21.9 - - + +
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Residues in contact with ALA 174 (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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104A GLY* 3.8 32.8 - - - +
105A CYS 5.3 0.2 - - - +
170A SER 2.9 17.6 + - - +
171A VAL* 3.2 8.9 + - - +
173A ALA* 1.3 76.1 - - - +
175A SER* 1.3 58.6 + - - +
176A GLY* 3.6 0.7 + - - -
111B GLY* 3.9 19.6 - - - +
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Residues in contact with SER 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL* 2.8 18.9 + - - +
172A GLU 3.2 3.5 + - - -
174A ALA* 1.3 76.3 - - - +
176A GLY* 1.3 58.0 + - - +
107B THR* 3.8 21.8 + - - +
111B GLY* 5.4 3.7 - - - -
129B ARG* 3.5 31.8 + - - -
201B NPO 2.8 17.1 + - - -
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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
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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