Contacts of the helix formed by residues 150 - 172 (chain D) in PDB entry 3M0V
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 ASN 150 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D HIS* 4.1 9.7 + - - -
148D HIS* 2.9 22.6 + - + +
149D THR* 1.3 78.3 + - - +
151D ALA* 1.3 67.3 + - - +
152D ALA* 3.6 15.2 + - - +
153D THR* 3.0 39.9 + - - +
154D ARG* 3.1 14.5 + - - +
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Residues in contact with ALA 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D THR 3.6 2.0 + - - -
150D ASN* 1.3 73.5 + - - +
152D ALA* 1.3 57.2 + - - +
154D ARG* 3.2 32.3 + - - +
155D ALA* 2.9 29.7 + - - +
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D HIS* 3.5 29.2 - - + +
150D ASN* 3.3 13.2 + - - +
151D ALA* 1.3 77.8 - - - +
153D THR* 1.3 58.1 + - - +
155D ALA* 3.4 8.3 + - - +
156D GLN* 3.0 27.7 + - - +
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Residues in contact with THR 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D HIS* 3.4 21.5 + - + +
140D SER 3.8 13.9 + - - +
141D TYR* 3.9 19.1 - - + -
144D GLY 4.0 0.2 - - - +
145D SER 4.4 0.9 - - - +
148D HIS* 3.7 36.1 + - + -
150D ASN* 3.0 28.6 + - - +
152D ALA* 1.3 76.2 - - - +
154D ARG* 1.3 65.3 + - - +
156D GLN* 3.3 3.3 + - - +
157D ALA* 3.1 22.5 + - - +
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Residues in contact with ARG 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D SER 3.4 20.2 - - - +
146D LEU* 3.3 20.9 - - - +
148D HIS 2.9 36.1 + - - +
149D THR 3.2 20.6 + - - -
150D ASN 3.1 4.1 + - - +
151D ALA* 3.2 32.8 + - - +
153D THR* 1.3 74.8 - - - +
155D ALA* 1.3 58.3 + - - +
157D ALA* 3.2 3.3 + - - +
158D VAL* 2.9 34.6 + - + +
198D ARG* 3.8 29.9 + - - +
201D SER* 6.1 1.8 - - - -
202D ALA* 4.9 6.1 - - + +
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ALA 2.9 16.4 + - - +
152D ALA* 3.6 9.0 - - - +
153D THR 3.2 0.2 - - - -
154D ARG* 1.3 78.4 - - - +
156D GLN* 1.3 56.4 + - - +
158D VAL* 3.3 8.4 + - - +
159D GLU* 2.9 29.7 + - - +
205D GLU* 5.7 3.8 - - - +
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Residues in contact with GLN 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D GLN* 3.4 12.7 - - - +
138D ALA* 3.6 10.4 + - - +
139D HIS* 2.7 59.7 + - + +
141D TYR* 3.1 27.4 + - - +
152D ALA 3.0 16.8 + - - +
153D THR* 3.6 4.5 - - - +
154D ARG 3.2 0.2 - - - -
155D ALA* 1.3 75.2 - - - +
157D ALA* 1.3 58.8 + - - +
159D GLU* 3.3 7.0 + - - +
160D HIS* 3.0 27.6 + - + +
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Residues in contact with ALA 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D THR* 3.9 14.5 - - + +
141D TYR* 3.5 14.5 + - + +
145D SER* 3.9 18.4 - - - -
146D LEU* 3.7 16.8 - - + -
153D THR 3.1 13.2 + - - +
154D ARG 3.2 7.8 + - - +
156D GLN* 1.3 75.6 - - - +
158D VAL* 1.3 64.7 + - - +
160D HIS* 3.3 2.9 + - - +
161D ASN* 2.8 30.7 + - - -
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Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LEU* 3.8 13.0 - - + -
154D ARG* 2.9 21.6 + - + +
155D ALA* 3.6 7.4 - - - +
157D ALA* 1.3 76.8 - - - +
159D GLU* 1.3 63.4 + - - +
161D ASN 3.1 2.4 + - - -
162D LEU* 3.1 31.4 + - + +
202D ALA* 3.8 29.4 - - + +
205D GLU* 4.0 31.0 - - + +
206D ILE* 3.2 24.4 - - + +
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Residues in contact with GLU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ALA 2.9 17.0 + - - +
156D GLN* 3.6 8.3 - - - +
158D VAL* 1.3 78.0 - - - +
160D HIS* 1.3 62.1 + - - +
162D LEU* 3.1 25.8 + - - +
163D GLU* 3.0 37.5 + - + +
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Residues in contact with HIS 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE* 3.3 23.7 + - + +
103D PRO* 3.9 9.1 - - + +
128D SER* 3.7 4.9 - - - -
129D ASN 3.0 37.9 + - - -
130D THR* 3.8 16.7 - - + +
141D TYR* 4.6 4.3 - + - +
156D GLN* 3.0 15.0 + - + +
157D ALA* 3.6 10.3 - - - +
158D VAL 3.2 0.4 - - - -
159D GLU* 1.3 75.6 - - - +
161D ASN* 1.3 62.9 + - - +
163D GLU* 3.1 23.3 + - + +
164D CYS* 3.1 41.6 + - - -
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Residues in contact with ASN 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D SER* 2.9 32.9 + - - -
130D THR* 4.3 10.5 + - - +
146D LEU* 4.2 17.6 - - - +
157D ALA 2.8 24.5 + - - -
158D VAL 3.1 1.4 + - - -
160D HIS* 1.3 80.4 - - - +
162D LEU* 1.3 63.8 + - - +
164D CYS* 3.2 9.4 + - - +
165D ILE* 3.1 25.2 + - - +
176D LEU* 3.6 11.2 - - + +
178D VAL* 3.6 18.3 - - - +
180D ILE* 6.2 0.2 - - - +
206D ILE* 3.4 26.2 - - + -
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Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D VAL* 3.1 27.8 + - + +
159D GLU* 3.1 26.4 + - - +
161D ASN* 1.3 77.6 - - - +
163D GLU* 1.3 62.3 + - + +
165D ILE* 3.2 17.0 + - + +
166D GLU* 3.0 27.1 + - + +
205D GLU 4.6 3.1 - - - +
206D ILE* 4.4 19.5 - - + +
209D GLY* 4.2 26.0 - - - +
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Residues in contact with GLU 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE* 6.0 3.4 - - + -
106D LYS* 6.0 0.5 + - - -
159D GLU* 3.0 32.6 + - - +
160D HIS* 3.1 27.1 + - + +
162D LEU* 1.3 75.3 - - - +
164D CYS* 1.3 65.6 + - - +
166D GLU* 3.2 9.8 + - - +
167D ILE* 3.0 29.7 + - + +
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Residues in contact with CYS 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE* 3.7 25.1 - - + -
126D MET* 3.6 18.7 - - + +
127D ASN 4.2 0.9 - - - -
128D SER* 3.8 15.5 - - - -
160D HIS* 3.1 43.3 + - - -
161D ASN 3.2 8.2 + - - +
163D GLU* 1.3 76.9 - - - +
165D ILE* 1.3 58.1 + - - +
167D ILE* 3.3 9.2 + - - +
168D GLY 2.9 22.9 + - - -
176D LEU* 4.0 16.2 - - + -
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Residues in contact with ILE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ASN 3.1 14.8 + - - +
162D LEU* 3.4 20.9 - - + +
163D GLU 3.2 0.2 - - - -
164D CYS* 1.3 77.6 - - - +
166D GLU* 1.3 59.4 + - - +
169D LYS* 2.9 35.7 + - + +
176D LEU* 3.9 16.6 - - + -
206D ILE* 4.6 5.4 - - + -
209D GLY 4.1 17.0 - - - +
210D LEU* 4.0 24.7 - - + -
211D PRO* 3.6 29.2 - - + -
214D TRP* 3.5 23.4 - - + -
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Residues in contact with GLU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D LEU 3.0 16.6 + - - +
163D GLU* 3.2 11.4 + - - +
165D ILE* 1.3 77.9 - - - +
167D ILE* 1.3 66.7 + - + +
169D LYS* 3.0 37.5 + - - +
170D ALA* 3.4 19.8 + - - +
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Residues in contact with ILE 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LEU* 5.4 0.4 - - + -
102D ILE* 4.6 18.4 - - + -
106D LYS* 6.2 4.7 - - + -
107D ALA 4.9 3.4 - - - +
109D PRO* 3.3 35.7 - - + -
112D LEU* 4.8 10.1 - - + -
126D MET* 3.8 18.8 - - + -
163D GLU* 3.0 22.4 + - + +
164D CYS* 3.6 7.9 - - - +
166D GLU* 1.3 79.4 - - + +
168D GLY* 1.3 64.1 + - - +
170D ALA* 3.1 13.7 + - - +
171D ILE* 3.3 20.5 + - + +
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Residues in contact with GLY 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D MET* 3.7 29.8 - - - -
164D CYS 2.9 10.9 + - - -
165D ILE 3.6 3.4 - - - -
167D ILE* 1.3 78.7 - - - +
169D LYS* 1.3 61.2 + - - +
171D ILE* 3.2 2.9 + - - -
172D GLY 3.0 5.9 + - - -
173D SER* 2.9 25.9 + - - -
214D TRP* 3.6 9.9 - - - -
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Residues in contact with LYS 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D ILE* 2.9 21.1 + - + +
166D GLU* 3.0 38.6 + - - +
167D ILE 3.3 0.4 - - - -
168D GLY* 1.3 77.4 - - - +
170D ALA* 1.3 59.3 + - - +
171D ILE 3.6 0.3 + - - -
172D GLY* 4.1 5.8 + - - +
173D SER 4.7 2.7 - - - -
174D LYS* 5.8 3.9 + - - +
211D PRO* 3.6 27.1 - - + +
213D ASP* 5.7 0.2 - - - +
214D TRP* 3.7 19.5 - - + +
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Residues in contact with ALA 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D PRO* 3.6 25.8 - - + +
110D LYS* 5.3 5.5 - - + +
113D LYS* 4.2 12.5 - - - +
166D GLU 3.4 9.7 + - - +
167D ILE 3.1 10.6 + - - +
169D LYS* 1.3 80.5 - - - +
171D ILE* 1.3 59.6 + - - +
172D GLY 3.7 0.2 - - - -
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Residues in contact with ILE 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LEU* 3.5 30.5 - - + -
109D PRO* 3.4 34.1 - - + +
112D LEU* 4.2 6.7 - - + -
113D LYS* 3.3 35.4 - - + +
123D PHE* 3.5 36.0 + - + -
126D MET* 3.9 19.1 - - - -
167D ILE* 3.6 14.4 - - + +
168D GLY* 3.5 11.2 - - - +
170D ALA* 1.3 80.2 - - - +
172D GLY* 1.3 57.6 + - - +
173D SER* 4.1 4.3 - - - +
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Residues in contact with GLY 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LYS* 5.3 2.5 - - - -
123D PHE* 4.0 10.0 + - - +
168D GLY 3.0 4.0 + - - -
169D LYS* 4.1 5.1 + - - -
170D ALA 3.7 2.2 - - - -
171D ILE* 1.3 79.7 - - - +
173D SER* 1.3 66.2 + - - +
174D LYS* 3.8 20.8 + - - +
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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