Contacts of the helix formed by residues 145 - 161 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ARG* 3.8 12.8 - - - +
134A PRO 3.6 11.9 - - - +
135A LEU* 3.5 15.3 - - + +
136A ARG* 2.9 31.5 + - - +
140A ASN* 3.6 14.4 - - - +
144A VAL* 1.3 77.1 - - - +
146A HIS* 1.3 60.3 + - - +
147A ALA* 2.9 20.1 + - - +
148A THR* 3.0 18.5 + - - +
149A ASP* 3.0 32.3 + - - +
182A MSE 6.1 0.2 - - - -
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Residues in contact with HIS 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 3.2 26.0 + - - +
119A VAL* 3.9 32.5 - - + -
120A ARG* 5.1 8.1 - - + -
129A TYR* 5.8 1.5 - + - -
130A VAL 5.0 0.8 + - - -
133A ARG* 3.6 44.5 + - + +
145A ASP* 1.3 76.9 - - - +
147A ALA* 1.3 57.4 - - - +
149A ASP* 3.9 4.9 + - - -
150A ALA* 3.1 28.4 + - - +
175A TYR* 4.3 7.1 + + - -
178A PHE* 3.5 27.9 - + - -
179A THR* 4.4 6.6 - - + +
182A MSE 3.5 26.6 - - + +
183A ALA 4.7 0.2 + - - -
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 4.1 7.1 - - + +
145A ASP* 2.9 14.0 + - - +
146A HIS* 1.3 77.8 - - - +
148A THR* 1.3 63.3 + - + +
150A ALA* 3.4 3.1 + - - +
151A TRP* 3.0 26.5 + - - +
182A MSE 3.3 27.3 - - - +
183A ALA* 4.5 3.3 - - - +
185A THR* 3.5 12.3 - - - +
186A ASN* 4.6 16.7 - - + +
3011A GOL 5.4 0.9 - - - -
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Residues in contact with THR 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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55A ARG* 3.6 38.1 - - - +
136A ARG* 4.4 9.2 - - - +
143A GLU 4.0 12.6 - - - +
144A VAL* 3.3 13.2 - - - +
145A ASP* 3.0 33.1 + - - +
147A ALA* 1.3 74.9 - - + +
149A ASP* 1.3 63.4 + - - +
151A TRP* 3.2 2.7 + - - +
152A ASP* 2.9 36.2 + - - -
3011A GOL 4.4 5.2 - - - +
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Residues in contact with ASP 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A MSE 3.4 24.7 - - - +
60A LEU* 4.0 2.7 - - - +
79A ARG* 3.4 21.5 + - - +
120A ARG* 2.9 55.8 + - - +
133A ARG* 5.6 0.9 - - - -
144A VAL* 4.2 0.7 - - - +
145A ASP 3.0 22.4 + - - +
146A HIS* 4.1 5.7 + - - +
148A THR* 1.3 84.4 + - - +
150A ALA* 1.3 52.9 + - - +
152A ASP* 4.9 0.3 - - - +
153A THR* 2.7 37.1 + - - -
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 5.7 0.4 - - + -
79A ARG* 3.8 25.3 - - - +
146A HIS 3.1 20.3 + - - +
147A ALA 3.8 4.3 - - - +
149A ASP* 1.3 74.3 - - - +
151A TRP* 1.3 60.2 + - - +
153A THR* 3.6 2.6 - - - -
154A ILE* 3.0 36.1 + - + +
170A MSE 4.6 5.2 - - + -
179A THR 5.1 0.7 - - - +
183A ALA* 3.8 26.7 - - + -
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Residues in contact with TRP 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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55A ARG* 3.9 5.4 - - - +
147A ALA 3.0 17.5 + - - +
148A THR 3.2 5.3 + - - +
150A ALA* 1.3 77.6 - - - +
152A ASP* 1.3 69.7 + - - +
154A ILE 3.4 0.7 + - - -
155A ASP* 3.0 31.0 + - + +
186A ASN* 3.4 30.7 - - - +
187A PRO 3.2 20.4 - - - -
188A HIS* 3.4 37.8 + + - +
189A PRO* 3.7 23.8 - - + -
3011A GOL 3.6 46.4 - - - +
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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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52A ILE* 4.2 1.7 - - - +
53A PRO 4.6 3.9 - - - +
54A MSE 3.8 26.6 - - + +
55A ARG* 3.0 61.5 + - - +
148A THR 2.9 19.4 + - - +
149A ASP* 4.9 0.3 - - - +
151A TRP* 1.3 82.0 - - - +
153A THR* 1.3 61.3 + - - +
155A ASP* 3.9 5.0 - - - +
156A TRP* 3.1 24.3 + - - +
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Residues in contact with THR 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 4.1 9.3 - - + +
54A MSE 3.6 10.4 - - - +
62A THR* 5.2 0.7 - - + -
77A LEU* 4.0 17.7 - - + -
79A ARG* 5.1 0.2 - - - +
117A GLN* 2.9 41.4 + - + +
149A ASP 2.7 22.5 + - - -
150A ALA* 3.6 7.6 - - - -
151A TRP 3.2 0.2 - - - -
152A ASP* 1.3 75.3 - - - +
154A ILE* 1.3 59.4 + - - +
156A TRP* 3.4 3.1 + - - +
157A LEU* 3.0 49.0 + - + +
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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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77A LEU* 3.8 17.3 - - + -
150A ALA* 3.0 24.3 + - + +
151A TRP 4.0 2.9 - - - +
153A THR* 1.3 72.8 - - - +
155A ASP* 1.3 65.8 + - - +
157A LEU* 3.3 6.8 + - - +
158A VAL* 3.1 23.7 + - - +
168A VAL* 3.9 22.7 - - + -
170A MSE 4.2 21.8 - - - -
183A ALA* 5.6 0.9 - - + -
188A HIS* 3.7 17.9 - - + +
190A ALA* 3.7 29.2 - - + -
191A LEU* 4.2 24.5 - - + +
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Residues in contact with ASP 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A TRP* 3.0 22.1 + - + +
152A ASP* 3.9 7.0 - - - +
153A THR 3.3 0.2 - - - -
154A ILE* 1.3 76.3 - - - +
156A TRP* 1.3 62.3 + - - +
158A VAL* 3.3 18.5 - - - +
159A LYS* 2.8 51.7 + - - +
188A HIS* 2.8 32.9 + - + +
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Residues in contact with TRP 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 3.6 22.4 - - - -
50A VAL* 3.7 33.0 - - + -
51A MSE 5.2 3.1 + - - -
52A ILE* 3.5 39.0 - - + -
53A PRO* 4.3 17.7 - - + +
64A ILE* 4.4 3.8 - - + -
152A ASP 3.1 18.4 + - - +
153A THR 3.7 1.8 - - - +
155A ASP* 1.3 78.9 - - - +
157A LEU* 1.3 72.9 + - + +
159A LYS* 3.2 3.0 + - - -
160A ASN* 2.9 73.8 + - + +
161A VAL* 4.5 2.9 - - + -
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Residues in contact with LEU 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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52A ILE* 4.4 5.8 - - + -
62A THR* 4.7 0.2 - - + -
64A ILE* 4.1 15.7 - - + -
75A ILE* 4.3 24.0 - - + +
77A LEU* 4.3 15.5 - - + -
115A VAL* 4.3 24.9 - - + -
153A THR* 3.0 41.0 + - + +
154A ILE* 3.3 7.6 + - + +
156A TRP* 1.3 92.6 - - + +
158A VAL* 1.3 59.9 + - + +
161A VAL* 3.0 52.8 + - + +
168A VAL* 5.2 2.5 - - + -
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Residues in contact with VAL 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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75A ILE* 5.4 3.6 - - + -
154A ILE 3.1 15.6 + - - +
155A ASP* 3.3 22.9 - - - +
157A LEU* 1.3 76.2 - - - +
159A LYS* 1.3 66.4 + - + +
160A ASN 3.5 0.2 - - - -
161A VAL 4.7 6.8 - - - +
164A SER* 5.6 1.7 - - - -
166A GLY* 3.4 42.7 - - - +
168A VAL* 3.9 13.2 - - + -
188A HIS* 4.6 10.1 - - + -
190A ALA* 3.8 14.4 - - + -
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Residues in contact with LYS 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 ASP* 2.8 48.6 + - - +
156A TRP* 3.2 5.2 + - - +
158A VAL* 1.3 84.7 - - + +
160A ASN* 1.3 67.3 + - - +
161A VAL 3.9 0.7 - - - -
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Residues in contact with ASN 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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48A ARG* 3.3 20.9 + - - +
156A TRP* 2.9 72.7 + - + +
159A LYS* 1.3 89.7 + - - +
161A VAL* 1.3 61.6 + - - +
162A SER* 3.7 3.8 + - - -
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Residues in contact with VAL 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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48A ARG* 4.3 7.4 - - - +
64A ILE* 4.1 21.5 - - + -
66A LEU* 4.1 15.7 - - + -
75A ILE* 4.5 6.5 - - + -
113A ILE* 4.4 4.5 - - + -
156A TRP* 4.5 2.0 - - + -
157A LEU* 3.0 43.0 + - + +
158A VAL 4.7 5.8 - - - +
159A LYS 3.9 0.9 - - - -
160A ASN* 1.3 79.2 - - - +
162A SER* 1.3 63.1 + - - +
163A GLU* 3.6 16.6 - - - +
164A SER* 3.1 35.9 + - - +
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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