Contacts of the helix formed by residues 144 - 165 (chain A) in PDB entry 2VXX
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 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.8 18.0 - - + +
25A THR* 4.7 1.1 - - + +
29A ILE* 3.5 32.7 - - + +
83A ARG* 2.9 24.9 + - - -
87A LEU* 3.8 12.6 - - - +
139A ALA* 2.8 15.4 + - + +
140A GLU* 4.9 0.4 - - - -
142A LEU 3.5 1.8 + - - -
143A GLY* 1.3 74.1 - - - +
145A ARG* 1.3 61.6 + - - +
146A ALA* 3.6 2.8 + - - +
147A THR* 2.6 30.0 + - - -
148A ALA* 3.2 16.6 + - - +
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Residues in contact with ARG 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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140A GLU* 5.6 4.7 - - - +
143A GLY* 3.3 15.7 + - - +
144A ASP* 1.3 71.3 - - - +
146A ALA* 1.3 57.9 + - - +
148A ALA* 3.4 7.8 + - - +
149A TYR* 2.9 29.7 + - - +
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Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 3.7 24.9 - - - +
144A ASP* 3.3 1.9 + - - +
145A ARG* 1.3 76.4 - - - +
147A THR* 1.3 60.4 + - - +
149A TYR* 3.3 11.2 + - + +
150A LEU* 2.9 29.3 + - - +
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Residues in contact with THR 147 (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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29A ILE* 4.0 7.6 - - + -
33A MET* 3.8 14.1 - - + -
83A ARG* 2.7 26.1 + - - +
87A LEU* 4.0 5.5 - - - +
139A ALA* 3.7 9.9 - - + -
144A ASP* 2.6 34.0 + - - -
146A ALA* 1.3 73.5 - - - +
148A ALA* 1.3 55.3 + - - +
150A LEU* 3.2 5.4 + - + +
151A TYR* 2.8 62.4 + - + -
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Residues in contact with ALA 148 (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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136A ALA* 3.8 14.0 - - - +
139A ALA* 3.7 4.7 - - - +
140A GLU* 3.7 33.9 - - + +
144A ASP 3.2 11.6 + - - +
145A ARG* 3.6 9.4 - - - +
147A THR* 1.3 78.3 - - - +
149A TYR* 1.3 57.6 + - - +
151A TYR* 3.4 6.3 + - - +
152A ASP* 2.9 37.0 + - - +
145C ARG* 4.6 3.4 - - - +
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Residues in contact with TYR 149 (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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145A ARG 2.9 13.9 + - - +
146A ALA* 3.4 13.2 - - + +
148A ALA* 1.3 76.3 - - - +
150A LEU* 1.3 67.1 + - + +
152A ASP* 3.3 9.1 + - - +
153A GLN* 3.0 52.7 + - - +
149C TYR* 3.5 28.7 + + - -
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Residues in contact with LEU 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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33A MET* 5.5 1.3 - - + -
79A ALA* 4.2 25.6 - - + +
80A LEU* 4.1 19.3 - - + -
83A ARG* 3.8 26.7 - - + -
146A ALA 2.9 19.5 + - - +
147A THR* 3.6 6.5 - - - +
149A TYR* 1.3 79.4 - - + +
151A TYR* 1.3 63.5 + - + +
153A GLN* 3.3 21.6 + - - +
154A ILE* 3.0 45.5 + - + +
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Residues in contact with TYR 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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29A ILE* 4.2 4.6 + - + -
33A MET* 3.3 46.0 + - + +
36A LEU* 3.5 20.7 - - + +
80A LEU* 3.7 26.5 - - + -
132A LEU* 3.8 22.0 - - + +
135A GLN* 3.5 22.7 - - + +
136A ALA* 3.6 33.0 - - + -
139A ALA* 4.9 0.2 - - + -
147A THR* 2.8 39.8 + - + +
148A ALA 3.7 4.3 - - - +
150A LEU* 1.3 73.9 - - + +
152A ASP* 1.3 53.8 + - - +
154A ILE* 3.3 5.0 + - + +
155A LEU* 2.7 37.1 + - - +
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Residues in contact with ASP 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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136A ALA* 3.8 4.2 - - - +
148A ALA 2.9 19.3 + - - +
149A TYR* 3.3 6.2 + - - +
151A TYR* 1.3 74.8 - - - +
153A GLN* 1.3 57.9 + - - +
155A LEU* 3.2 7.6 + - - +
156A LEU* 2.9 30.7 + - - +
145C ARG* 2.8 62.1 + - - +
146C ALA* 4.7 2.6 - - - +
149C TYR* 3.7 28.2 - - + +
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Residues in contact with GLN 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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149A TYR* 3.0 39.9 + - - +
150A LEU* 3.4 24.5 - - + +
152A ASP* 1.3 78.2 - - - +
154A ILE* 1.3 61.0 + - + +
156A LEU* 3.6 4.3 + - - +
157A LYS* 3.5 45.2 + - - +
149C TYR* 3.1 34.8 + - + +
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Residues in contact with ILE 154 (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 PHE* 3.6 32.5 - - + -
76A HIS* 3.7 35.8 + - + +
79A ALA* 4.8 2.7 - - + -
80A LEU* 3.8 34.3 - - + -
132A LEU* 3.9 9.2 - - + -
150A LEU* 3.0 37.2 + - + +
151A TYR* 3.7 6.7 - - + +
153A GLN* 1.3 74.4 - - + +
155A LEU* 1.3 61.1 + - - +
157A LYS* 3.3 5.2 + - + +
158A THR* 2.8 34.3 + - - +
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Residues in contact with LEU 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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129A ILE* 3.8 23.3 - - + +
132A LEU* 3.8 35.2 - - + +
133A ARG* 4.1 15.9 - - + +
136A ALA* 6.1 0.2 - - + -
151A TYR 2.7 22.3 + - - +
152A ASP* 3.2 9.6 + - - +
154A ILE* 1.3 74.0 - - - +
156A LEU* 1.3 56.9 + - - +
158A THR* 3.7 0.4 - - - -
159A GLU* 2.8 63.1 + - + +
145C ARG* 3.8 31.4 - - + +
146C ALA* 4.0 8.7 - - + +
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Residues in contact with LEU 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 ASP 2.9 16.4 + - - +
153A GLN 3.8 6.3 - - - +
154A ILE 3.3 0.4 - - - -
155A LEU* 1.3 74.9 - - - +
157A LYS* 1.3 64.8 + - + +
159A GLU* 4.0 2.9 - - - +
160A GLU* 3.2 22.7 + - - +
163A TYR* 6.1 0.9 - - - +
83C ARG* 4.0 24.9 + - - +
146C ALA* 3.9 31.1 - - + +
149C TYR* 3.9 26.9 - - + -
150C LEU* 4.3 24.7 - - + -
153C GLN* 5.0 3.8 - - - +
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Residues in contact with LYS 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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72A GLN* 3.7 29.2 - - + +
75A ASP* 4.6 11.9 + - - +
76A HIS* 3.8 24.0 - - + -
153A GLN* 3.5 38.2 + - - +
154A ILE* 3.3 7.8 + - - +
156A LEU* 1.3 78.0 - - + +
158A THR* 1.3 58.6 - - - +
160A GLU* 3.3 13.2 - - - +
161A ARG* 3.0 32.8 - - - +
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Residues in contact with THR 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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40A PHE* 3.7 4.0 - - - -
125A GLU* 3.2 28.8 - - - +
128A ILE* 4.3 6.7 - - + -
129A ILE* 3.8 21.3 - - + -
132A LEU* 3.9 14.3 - - + +
154A ILE* 2.8 34.2 + - - +
155A LEU 3.7 3.8 - - - -
157A LYS* 1.3 73.8 + - - +
159A GLU* 1.3 65.0 + - - +
161A ARG* 3.1 24.7 + - - +
162A ALA* 3.0 21.5 + - - +
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Residues in contact with GLU 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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129A ILE* 3.8 27.4 - - + -
133A ARG* 2.9 21.7 + - - -
155A LEU* 2.8 42.0 + - + +
156A LEU 4.0 3.6 - - - +
158A THR* 1.3 72.4 - - - +
160A GLU* 1.3 56.5 + - - +
162A ALA* 3.2 2.8 + - - +
163A TYR* 3.0 34.8 + - + -
19C ILE* 3.5 22.6 - - + +
83C ARG* 2.6 38.5 + - - +
144C ASP* 4.8 2.1 - - - +
145C ARG 5.8 0.2 + - - -
146C ALA* 3.3 10.1 + - - +
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Residues in contact with GLU 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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72A GLN* 5.0 8.0 + - - +
156A LEU 3.2 12.4 + - - +
157A LYS* 3.4 16.4 - - - +
158A THR 3.2 0.8 - - - -
159A GLU* 1.3 77.2 - - - +
161A ARG* 1.3 63.6 + - + +
163A TYR* 3.4 29.1 + - + +
164A HIS* 2.7 53.4 + - + -
82C GLU* 4.3 9.5 - - - +
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Residues in contact with ARG 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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40A PHE* 3.7 15.6 - - - -
47A TYR* 4.4 2.9 - - - +
65A PHE* 4.3 3.0 - - + -
69A CYS* 4.0 37.5 - - - +
72A GLN* 3.1 34.1 + - - +
73A VAL* 3.7 12.7 - - - +
76A HIS* 2.9 26.1 + - - -
125A GLU* 2.8 45.3 + - - +
157A LYS 3.0 17.7 - - - +
158A THR* 3.1 27.0 + - - +
160A GLU* 1.3 75.2 - - + +
162A ALA* 1.3 64.6 + - - +
164A HIS* 3.2 8.3 + - - +
165A ILE* 3.0 29.0 + - - +
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Residues in contact with ALA 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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122A LEU* 3.3 29.9 - - + +
125A GLU* 4.0 9.8 - - + +
126A GLN* 5.3 0.4 - - + +
129A ILE* 3.9 20.0 - - + -
158A THR 3.0 13.7 + - - +
159A GLU 3.2 8.5 + - - +
161A ARG* 1.3 76.0 - - - +
163A TYR* 1.3 58.3 + - - +
165A ILE* 3.2 7.8 + - - +
166A GLY 3.0 21.5 + - - -
18C VAL* 3.4 5.2 - - + +
19C ILE* 4.2 6.3 - - + -
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Residues in contact with TYR 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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156A LEU* 6.1 0.3 - - - +
159A GLU 3.0 29.7 + - - -
160A GLU* 3.4 24.4 + - + +
162A ALA* 1.3 73.5 - - - +
164A HIS* 1.3 86.9 + + - +
166A GLY* 3.4 1.3 + - - -
167A HIS* 3.1 45.6 + + + +
18C VAL* 3.6 16.8 - - + +
19C ILE* 4.0 9.6 - - + -
82C GLU* 4.0 22.4 - - + +
83C ARG* 3.7 40.3 + - - +
86C GLY* 3.5 39.3 - - - +
87C LEU* 6.1 0.4 - - + -
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Residues in contact with HIS 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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65A PHE* 4.0 17.7 - + + -
160A GLU* 2.7 49.5 + - + +
161A ARG* 3.2 6.9 + - - +
163A TYR* 1.3 87.0 - + - +
165A ILE* 1.3 64.3 + - - +
167A HIS* 3.3 4.8 + + - -
168A PHE* 3.2 18.0 + - - +
82C GLU* 3.1 17.7 + - + -
59D PHE* 3.4 38.8 - + + -
60D TYR* 4.4 12.1 - + - -
63D HIS* 3.5 1.9 + + - -
201D ZN 2.3 28.0 - - - -
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Residues in contact with ILE 165 (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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47A TYR* 3.1 26.7 - - + +
65A PHE* 3.7 22.0 - - + -
118A LEU* 3.2 40.4 - - + +
121A ASP* 3.9 6.3 - - + -
122A LEU* 3.8 29.8 - - + +
125A GLU* 3.9 9.0 - - + -
161A ARG 3.0 22.7 + - - +
162A ALA* 3.5 6.5 - - - +
164A HIS* 1.3 74.6 - - - +
166A GLY* 1.3 64.3 + - - +
168A PHE* 3.1 9.8 + - - +
169A LEU* 3.1 23.1 + - + +
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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
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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