Contacts of the helix formed by residues 144 - 166 (chain A) in PDB entry 2B69
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 ARG 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PRO* 4.2 17.2 - - - +
84A TYR* 3.5 27.0 + - - +
85A MSE 4.3 13.6 - - - +
120A GLU* 3.0 33.5 + - - -
142A GLY 3.3 0.8 - - - -
143A PRO* 1.3 75.9 - - + +
145A ALA* 1.3 64.1 + - - +
146A CYS* 3.3 4.0 - - - -
147A TYR* 3.1 8.9 + - - +
148A ASP* 3.1 33.0 + - - +
270A ALA* 5.0 7.5 - - - +
271A GLN 3.8 16.8 + - - +
272A ASP* 3.6 25.7 + - + -
273A ASP* 4.1 13.5 + - - +
274A PRO* 3.7 15.9 - - - +
900A UDP 3.1 24.7 + - - -
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Residues in contact with ALA 145 (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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92A LEU* 4.7 0.5 - - - +
139A ASN 3.4 20.3 + - - +
140A PRO* 3.3 28.3 - - + +
141A ILE* 4.3 0.9 - - - -
142A GLY 3.2 16.5 + - - +
144A ARG* 1.3 75.7 - - - +
146A CYS* 1.3 66.4 + - - +
148A ASP* 4.2 8.0 + - - +
149A GLU* 2.9 31.8 + - + +
150A GLY 3.8 0.2 + - - -
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Residues in contact with CYS 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 3.4 33.4 - - - -
85A MSE 4.5 2.0 - - - -
88A PRO* 3.7 40.8 - - + +
91A THR* 3.6 12.5 - - + +
92A LEU* 3.5 33.3 - - + +
95A ASN* 4.9 0.3 + - - -
142A GLY 4.7 1.0 + - - -
143A PRO 4.0 17.9 + - - -
144A ARG 4.6 0.4 - - - -
145A ALA* 1.3 77.2 - - - +
147A TYR* 1.3 62.3 + - - +
150A GLY* 3.7 8.1 + - - -
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Residues in contact with TYR 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A SER* 3.9 6.1 - - - -
78A PRO 3.3 27.1 - - - -
79A ALA* 4.3 7.5 + - - -
84A TYR* 3.5 52.7 - + + -
91A THR* 4.0 7.2 - - + -
95A ASN* 4.8 2.0 + - - +
118A THR* 3.8 14.9 + - + -
120A GLU* 3.9 19.5 - - + -
144A ARG 3.1 2.4 + - - +
145A ALA 3.1 0.2 - - - -
146A CYS* 1.3 79.8 - - - +
148A ASP* 1.3 78.8 + - - +
149A GLU 3.4 0.2 - - - -
150A GLY* 3.3 0.5 + - - -
151A LYS* 3.0 45.3 + - + +
800A NAD 2.8 43.4 + - - -
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Residues in contact with ASP 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 2.5 53.8 - - - +
121A VAL* 4.9 1.6 - - - +
123A GLY* 5.5 2.4 - - - -
138A VAL* 3.8 25.8 - - + +
139A ASN 5.2 1.7 + - - +
144A ARG* 3.1 31.3 + - - +
145A ALA* 3.3 4.3 + - - -
147A TYR* 1.3 82.4 - - - +
149A GLU* 1.3 58.7 + - - +
151A LYS* 3.5 3.8 + - - +
152A ARG* 3.1 34.2 + - - +
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Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 5.3 5.8 - - + -
138A VAL* 3.5 22.8 - - + +
140A PRO* 4.0 37.0 - - + +
145A ALA* 2.9 18.3 + - + +
148A ASP* 1.3 76.2 - - - +
150A GLY* 1.3 65.7 + - - +
152A ARG* 4.0 19.3 + - - +
153A VAL* 3.1 28.5 + - - +
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Residues in contact with GLY 150 (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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92A LEU* 4.5 10.1 - - - +
95A ASN* 3.7 24.2 - - - +
96A THR* 4.8 2.7 - - - -
146A CYS 3.7 15.6 + - - -
147A TYR 3.3 6.1 + - - -
149A GLU* 1.3 79.4 - - - +
151A LYS* 1.3 56.1 + - - +
153A VAL* 3.5 10.4 - - - +
154A ALA* 3.1 26.3 + - - +
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Residues in contact with LYS 151 (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 HIS 5.6 0.8 + - - -
75A LEU 5.5 0.6 - - - -
76A ALA 5.1 1.2 + - - -
77A SER* 3.8 5.4 - - - -
95A ASN* 3.4 22.2 + - - +
115A LEU* 4.8 6.6 - - + +
116A ALA* 2.9 29.2 + - - +
117A SER* 4.3 6.4 + - - +
118A THR* 3.7 30.7 - - + -
121A VAL* 4.5 5.2 - - + -
147A TYR* 3.0 38.0 + - + +
148A ASP 3.9 3.1 - - - +
150A GLY* 1.3 73.7 - - - +
152A ARG* 1.3 66.7 + - - +
154A ALA* 3.3 10.1 + - + +
155A GLU* 3.2 24.8 + - - +
800A NAD 2.9 37.8 + - - -
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Residues in contact with ARG 152 (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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121A VAL* 2.9 56.3 + - + +
135A TRP* 2.9 24.0 + - - +
136A GLY* 4.4 2.6 + - - -
138A VAL* 4.1 20.3 - - - +
148A ASP 3.1 21.8 + - - +
149A GLU* 3.4 29.6 + - - +
151A LYS* 1.3 75.3 - - - +
153A VAL* 1.3 61.3 + - - +
155A GLU* 3.2 17.4 + - - +
156A THR* 3.1 15.2 + - - -
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Residues in contact with VAL 153 (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 THR* 3.8 26.2 - - + -
149A GLU* 3.1 17.4 + - - +
150A GLY* 3.5 11.9 - - - +
152A ARG* 1.3 73.8 - - - +
154A ALA* 1.3 68.0 + - - +
156A THR* 3.2 15.3 + - + +
157A MSE 2.9 43.1 + - + +
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASN* 3.8 18.8 - - - +
99A THR* 3.9 13.2 - - + +
115A LEU* 3.8 18.4 - - + -
150A GLY 3.1 18.4 + - - +
151A LYS* 3.3 10.7 + - + +
153A VAL* 1.3 77.4 - - - +
155A GLU* 1.3 60.7 + - - +
157A MSE 3.4 14.8 + - - +
158A CYS* 3.2 26.5 + - - -
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 3.9 14.6 - - + -
117A SER* 2.7 32.0 + - - +
121A VAL* 3.9 10.7 - - - +
151A LYS 3.2 9.2 + - - +
152A ARG* 3.2 7.8 + - - +
154A ALA* 1.3 73.9 - - - +
156A THR* 1.3 66.6 + - - +
158A CYS* 3.2 13.2 + - - +
159A TYR* 3.2 29.0 + - + -
171A VAL* 4.0 12.1 - - + -
173A ARG* 2.8 45.0 + - - +
236A PRO* 4.5 3.7 - - - +
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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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152A ARG 3.1 13.9 + - - -
153A VAL* 3.2 20.0 + - + +
155A GLU* 1.3 77.6 - - - +
157A MSE 1.3 63.3 + - - +
159A TYR* 3.3 6.8 + - - +
160A ALA* 3.0 23.8 + - + +
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Residues in contact with MSE 157 (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 THR* 3.6 43.7 - - + +
99A THR* 4.1 14.4 - - + -
100A LEU* 3.8 38.1 - - + -
103A LEU* 3.8 15.0 - - + -
153A VAL* 2.9 32.1 + - + +
154A ALA* 3.5 10.8 - - - +
155A GLU 3.2 0.2 - - - -
156A THR* 1.3 74.1 - - - +
158A CYS* 1.3 65.7 + - - +
160A ALA* 3.3 7.1 + - - +
161A TYR* 3.0 29.6 + - + -
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Residues in contact with CYS 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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99A THR* 4.7 4.5 - - - -
103A LEU* 4.0 18.2 - - - -
113A LEU* 4.0 19.1 - - - -
115A LEU* 4.0 28.9 - - - -
154A ALA 3.2 15.1 + - - -
155A GLU 3.2 9.2 + - - +
157A MSE 1.3 79.0 - - - +
159A TYR* 1.3 59.4 + - + +
161A TYR* 3.3 1.2 + - - -
162A MSE 3.1 23.0 + - - +
169A VAL* 3.7 27.7 - - + +
170A ARG 5.4 0.2 - - - -
171A VAL* 4.4 10.8 - - + -
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Residues in contact with TYR 159 (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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155A GLU* 3.2 30.1 + - + -
156A THR* 4.0 6.3 - - - +
158A CYS* 1.3 74.2 - - - +
160A ALA* 1.3 65.0 + - - +
162A MSE 3.7 19.3 - - - +
163A LYS* 3.1 32.1 + - + +
169A VAL* 4.1 11.2 - - + -
171A VAL* 3.3 26.7 - - + +
234A SER* 2.7 32.1 + - - -
235A SER* 4.5 2.2 - - - -
236A PRO* 3.2 33.9 - - + +
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Residues in contact with ALA 160 (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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156A THR* 3.0 16.1 + - + +
157A MSE 3.3 12.3 + - - +
159A TYR* 1.3 77.5 - - - +
161A TYR* 1.3 60.4 + - + +
163A LYS* 4.0 3.6 - - - +
164A GLN* 3.0 34.2 + - + +
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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
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100A LEU* 4.0 29.9 + - + +
103A LEU* 3.7 48.9 - - + -
104A GLY* 4.3 2.0 - - - -
107A LYS* 4.7 9.2 - - + -
157A MSE 3.0 27.4 + - + +
158A CYS 3.3 3.5 + - - +
160A ALA* 1.3 76.6 - - + +
162A MSE 1.3 60.7 + - - +
164A GLN* 5.1 0.7 - - - -
165A GLU* 3.0 38.7 + - + +
166A GLY 3.2 6.4 + - - -
167A VAL* 3.3 23.5 + - + -
901A UDP 2.7 37.9 + - - -
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Residues in contact with MSE 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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158A CYS 3.1 16.5 + - - +
159A TYR* 3.7 19.5 - - - +
161A TYR* 1.3 77.0 - - - +
163A LYS* 1.3 68.4 - - + +
166A GLY* 3.2 20.4 + - - -
167A VAL* 3.4 25.6 + - - +
168A GLU* 4.7 2.9 - - - -
169A VAL* 3.7 25.4 - - + +
170A ARG* 5.1 1.3 - - - +
234A SER* 3.5 37.0 - - - +
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Residues in contact with LYS 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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159A TYR* 3.1 20.5 + - + +
160A ALA* 4.1 3.8 - - - +
162A MSE 1.3 89.6 - - + +
164A GLN* 1.3 60.6 + - + +
166A GLY 4.8 0.7 + - - -
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Residues in contact with GLN 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 ALA* 3.0 18.5 + - + +
161A TYR* 5.1 0.2 - - - -
163A LYS* 1.3 78.9 - - + +
165A GLU* 1.3 84.5 + - + +
166A GLY 3.8 0.4 - - - -
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Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 3.9 46.1 + - + +
161A TYR* 3.0 23.4 + - + +
164A GLN* 1.3 103.9 + - + +
166A GLY* 1.3 64.0 + - - +
167A VAL* 3.3 8.6 + - + +
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Residues in contact with GLY 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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161A TYR 3.2 0.2 + - - -
162A MSE 3.2 16.2 + - - -
163A LYS 4.7 0.6 + - - -
164A GLN 3.8 0.8 - - - -
165A GLU* 1.3 77.4 - - - +
167A VAL* 1.3 65.2 + - - +
168A GLU* 3.5 8.5 + - - +
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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