Contacts of the helix formed by residues 145 - 161 (chain B) in PDB entry 1MPX
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 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ARG* 3.9 13.2 - - - +
134B PRO 3.6 22.7 - - - +
135B LEU* 3.5 14.1 - - + +
136B ARG* 2.9 31.6 + - - +
140B ASN* 3.6 3.1 - - - +
144B VAL* 1.3 76.5 - - - +
146B HIS* 1.3 59.9 + - - +
147B ALA* 2.9 20.5 + - - +
148B THR* 2.9 19.7 + - - +
149B ASP* 3.0 32.9 + - - -
182B MSE 6.1 0.2 - - - -
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Residues in contact with HIS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 3.1 25.4 + - - +
119B VAL* 3.9 32.3 - - + -
120B ARG* 5.2 6.3 - - + -
129B TYR* 5.9 1.1 - + - -
130B VAL 5.0 0.4 + - - -
133B ARG* 3.5 50.1 + - + +
145B ASP* 1.3 74.3 - - - +
147B ALA* 1.3 60.2 + - - +
149B ASP* 3.9 6.6 + - - -
150B ALA* 3.1 28.8 + - - +
175B TYR* 4.4 7.2 + + - -
178B PHE* 3.6 21.9 - + - -
179B THR* 4.2 9.5 - - + +
182B MSE 3.5 25.8 - - + +
183B ALA 4.8 0.2 + - - -
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 4.1 6.5 - - + +
145B ASP* 2.9 13.7 + - - +
146B HIS* 1.3 77.8 - - - +
148B THR* 1.3 60.9 + - + +
150B ALA* 3.4 3.3 + - - +
151B TRP* 3.0 26.9 + - - +
182B MSE 3.2 28.8 - - - +
183B ALA* 4.5 3.6 - - - +
185B THR* 3.4 12.3 - - - +
186B ASN* 4.6 17.1 - - + +
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Residues in contact with THR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ARG* 3.6 36.6 - - - +
136B ARG* 4.4 10.8 - - - +
143B GLU 4.0 13.7 - - - +
144B VAL* 3.4 11.6 - - - +
145B ASP* 2.9 33.9 + - - +
147B ALA* 1.3 74.9 - - + +
149B ASP* 1.3 65.1 + - - +
151B TRP* 3.3 2.6 + - - +
152B ASP* 3.0 35.8 + - - +
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Residues in contact with ASP 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B MSE 3.3 24.1 - - - +
60B LEU* 4.0 3.1 - - - +
79B ARG* 3.4 22.4 + - - +
120B ARG* 3.0 54.3 + - - +
133B ARG* 5.6 0.9 - - - -
144B VAL* 4.3 1.0 - - - +
145B ASP 3.0 22.3 + - - +
146B HIS* 4.1 6.1 + - - +
147B ALA 3.3 0.2 - - - -
148B THR* 1.3 81.9 + - - +
150B ALA* 1.3 54.5 + - - +
152B ASP* 4.9 0.3 - - - +
153B THR* 2.7 37.4 + - - -
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 5.7 0.4 - - + -
79B ARG* 3.8 24.4 - - - +
146B HIS 3.1 20.4 + - - +
147B ALA 3.7 4.5 - - - +
149B ASP* 1.3 77.2 - - - +
151B TRP* 1.3 58.6 + - - +
153B THR* 3.4 2.2 + - - -
154B ILE* 3.0 36.8 + - + +
170B MSE 4.5 4.7 - - + -
179B THR 5.1 0.9 - - - +
183B ALA* 3.8 27.4 - - + -
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Residues in contact with TRP 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ARG* 4.0 14.1 - - - +
147B ALA 3.0 17.6 + - - +
148B THR* 3.6 6.3 - - - +
150B ALA* 1.3 77.0 - - - +
152B ASP* 1.3 69.9 + - - +
154B ILE 3.4 0.9 + - - -
155B ASP* 3.0 32.8 + - + +
186B ASN* 3.5 29.6 - - - +
187B PRO 3.2 20.6 - - - -
188B HIS* 3.4 42.6 + + - +
189B PRO* 3.8 22.9 - - + -
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Residues in contact with ASP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 4.2 1.9 - - - +
53B PRO 4.6 3.4 - - - +
54B MSE 3.8 27.5 - - + +
55B ARG* 3.0 61.5 + - - +
148B THR 3.0 18.6 + - - +
149B ASP* 4.9 0.5 - - - +
151B TRP* 1.3 81.4 - - - +
153B THR* 1.3 61.6 + - - +
155B ASP* 3.8 4.8 - - - +
156B TRP* 3.2 23.9 + - - +
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Residues in contact with THR 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 4.2 14.3 - - + +
54B MSE 3.6 5.9 - - - +
62B THR* 5.2 0.9 - - + -
77B LEU* 4.0 17.7 - - + -
117B GLN* 2.9 41.1 + - + +
149B ASP 2.7 23.1 + - - -
150B ALA* 3.6 8.3 - - - -
151B TRP 3.2 0.2 - - - -
152B ASP* 1.3 75.3 - - - +
154B ILE* 1.3 61.4 + - - +
156B TRP* 3.4 3.5 + - - +
157B LEU* 3.0 43.6 + - + +
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Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.9 17.0 - - + -
150B ALA* 3.0 23.6 + - + +
151B TRP 4.0 2.9 - - - +
153B THR* 1.3 73.3 - - - +
155B ASP* 1.3 64.4 + - - +
157B LEU* 3.3 7.9 + - - +
158B VAL* 3.1 23.7 + - - +
168B VAL* 4.1 23.1 - - + -
170B MSE 4.2 21.8 - - - -
183B ALA* 5.7 0.4 - - + -
188B HIS* 3.6 31.0 - - + +
190B ALA* 3.6 17.5 - - + -
191B LEU* 4.1 24.9 - - + +
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Residues in contact with ASP 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B TRP* 3.0 22.6 + - + +
152B ASP* 3.8 7.9 - - - +
153B THR 3.3 0.2 - - - -
154B ILE* 1.3 77.1 - - - +
156B TRP* 1.3 62.0 + - - +
158B VAL* 3.2 19.8 - - - +
159B LYS* 2.9 50.9 + - - +
188B HIS* 2.8 32.0 + - + +
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Residues in contact with TRP 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ARG* 3.6 22.0 - - - -
50B VAL* 3.7 32.3 - - + -
51B MSE 5.2 3.3 + - - -
52B ILE* 3.5 39.3 - - + -
53B PRO* 4.3 16.9 - - + +
64B ILE* 4.4 4.9 - - + -
152B ASP 3.2 16.2 + - - +
153B THR 3.6 1.8 - - - +
155B ASP* 1.3 81.5 - - - +
157B LEU* 1.3 72.3 + - + +
159B LYS* 3.2 2.8 + - - -
160B ASN* 2.8 75.9 + - + +
161B VAL* 4.6 2.9 - - + -
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ILE* 4.5 5.2 - - + -
62B THR* 4.9 0.2 - - + -
64B ILE* 4.1 17.0 - - + -
75B ILE* 4.2 25.8 - - + +
77B LEU* 4.3 22.2 - - + -
115B VAL* 4.4 19.1 - - + -
153B THR* 3.0 39.4 + - + +
154B ILE* 3.3 8.0 + - + +
156B TRP* 1.3 88.6 - - + +
158B VAL* 1.3 59.7 + - + +
161B VAL* 3.0 54.2 + - + +
168B VAL* 5.1 3.4 - - + -
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ILE* 5.6 0.7 - - + -
154B ILE 3.1 13.6 + - - +
155B ASP* 3.2 22.2 - - - +
157B LEU* 1.3 76.4 - - - +
159B LYS* 1.3 65.0 + - + +
160B ASN 3.5 0.2 - - - -
161B VAL 4.7 6.2 - - - +
164B SER* 4.6 5.4 + - - +
166B GLY* 3.3 41.1 - - - +
168B VAL* 4.1 12.1 - - + -
188B HIS* 4.6 9.6 - - + -
190B ALA* 3.7 14.4 - - + -
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Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ASP* 2.9 48.0 + - - +
156B TRP* 3.2 1.9 + - - -
157B LEU 3.2 0.4 - - - -
158B VAL* 1.3 86.1 - - + +
160B ASN* 1.3 71.1 + - - +
161B VAL 3.9 0.4 - - - -
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Residues in contact with ASN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ARG* 3.2 21.4 + - - +
156B TRP* 2.8 73.5 + - + +
159B LYS* 1.3 90.5 + - - +
161B VAL* 1.3 60.7 + - - +
162B SER* 3.6 4.3 + - - -
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ARG* 4.3 7.6 - - - +
64B ILE* 4.1 18.6 - - + -
66B LEU* 4.1 7.6 - - + -
75B ILE* 4.4 6.7 - - + -
113B ILE* 4.1 16.8 - - + -
156B TRP* 4.6 2.0 - - + -
157B LEU* 3.0 43.8 + - + +
158B VAL 4.7 4.7 - - - +
159B LYS 5.5 0.4 - - - -
160B ASN* 1.3 78.3 - - - +
162B SER* 1.3 62.7 + - - +
163B GLU* 3.7 15.3 - - - +
164B SER* 3.1 38.6 + - - +
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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
------------------------------------------------------------
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