Contacts of the helix formed by residues 145 - 161 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ARG* 3.8 12.8 - - - +
134D PRO 3.5 24.0 - - - +
135D LEU* 3.5 14.9 - - + +
136D ARG* 3.0 32.1 + - - +
140D ASN* 3.6 2.9 - - - +
144D VAL* 1.3 76.1 - - - +
146D HIS* 1.3 60.5 + - - +
147D ALA* 2.9 19.9 + - - +
148D THR* 3.0 18.9 + - - +
149D ASP* 3.0 33.3 + - - +
182D MSE 6.1 0.2 - - - -
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Residues in contact with HIS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ARG* 3.2 25.2 + - - +
119D VAL* 3.9 32.8 - - + -
120D ARG* 5.1 5.6 - - + -
129D TYR* 6.0 1.1 - + - -
130D VAL 5.0 0.4 + - - -
133D ARG* 3.4 51.0 + - + +
145D ASP* 1.3 74.6 - - - +
147D ALA* 1.3 64.1 + - - +
149D ASP* 3.9 6.9 + - - +
150D ALA* 3.2 24.8 + - - +
175D TYR* 4.3 8.3 + + - -
178D PHE* 3.6 21.2 - + - -
179D THR* 4.1 9.3 - - + +
182D MSE 3.5 27.1 - - + +
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Residues in contact with ALA 147 (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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135D LEU* 4.2 5.1 - - + +
145D ASP* 2.9 16.1 + - - +
146D HIS* 1.3 78.5 - - - +
148D THR* 1.3 58.6 + - + +
150D ALA* 3.4 3.5 + - - +
151D TRP* 3.1 26.2 + - - +
182D MSE 3.3 28.2 + - - +
183D ALA* 4.5 3.7 - - - +
185D THR* 3.5 11.9 - - - +
186D ASN* 4.6 17.1 - - + +
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Residues in contact with THR 148 (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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55D ARG* 3.3 40.8 - - - +
136D ARG* 4.2 12.1 - - - -
143D GLU 4.1 12.1 - - - +
144D VAL* 3.4 12.6 - - - +
145D ASP* 3.0 32.3 + - - +
147D ALA* 1.3 74.7 - - + +
149D ASP* 1.3 61.4 + - - +
151D TRP* 3.3 2.4 + - - +
152D ASP* 3.0 37.1 + - - +
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Residues in contact with ASP 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D MSE 3.3 23.6 - - - +
60D LEU* 4.0 4.5 - - - +
79D ARG* 3.4 21.9 + - - +
120D ARG* 2.9 54.5 + - - +
133D ARG* 5.6 0.7 - - - -
144D VAL* 4.4 0.9 - - - +
145D ASP 3.0 22.7 + - - +
146D HIS* 4.1 5.5 + - - +
148D THR* 1.3 83.0 + - - +
150D ALA* 1.3 57.6 + - - +
152D ASP* 4.9 0.5 - - - +
153D THR* 2.8 33.4 + - - -
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Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU* 5.6 0.4 - - + -
79D ARG* 3.8 24.6 - - - +
146D HIS 3.2 21.4 + - - +
147D ALA 3.7 3.6 - - - +
148D THR 3.3 0.2 - - - -
149D ASP* 1.3 74.0 - - - +
151D TRP* 1.3 59.6 + - - +
153D THR* 3.6 2.9 - - - -
154D ILE* 3.0 37.2 + - + +
170D MSE 4.6 6.3 - - + -
179D THR 5.1 0.2 - - - +
183D ALA* 3.8 26.2 - - + -
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Residues in contact with TRP 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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55D ARG* 3.9 14.6 - - - +
147D ALA 3.1 17.2 + - - +
148D THR* 3.5 6.1 - - - +
150D ALA* 1.3 78.1 - - - +
152D ASP* 1.3 70.3 + - - +
154D ILE* 3.4 0.6 + - - -
155D ASP* 3.0 31.5 + - + +
186D ASN* 3.5 36.3 - - - +
187D PRO 3.3 20.0 - - - -
188D HIS* 3.4 36.8 + + - +
189D PRO* 3.8 20.4 - - + -
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Residues in contact with ASP 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D ILE* 4.3 2.1 - - - +
53D PRO 4.6 3.4 - - - +
54D MSE 3.9 25.8 - - + +
55D ARG* 3.0 57.3 + - - +
148D THR* 3.0 22.3 + - - +
149D ASP* 4.9 0.3 - - - +
151D TRP* 1.3 82.5 - - - +
153D THR* 1.3 60.9 + - - +
155D ASP* 3.9 4.8 - - - +
156D TRP* 3.2 23.2 + - - +
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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
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52D ILE* 4.2 10.9 - - + +
54D MSE 3.4 9.3 - - - +
62D THR* 5.0 1.6 - - + -
77D LEU* 4.2 16.6 - - + -
79D ARG* 4.9 0.2 - - - -
117D GLN* 2.8 41.7 + - - +
149D ASP 2.8 22.3 + - - -
150D ALA* 3.6 6.7 - - - -
152D ASP* 1.3 75.2 - - - +
154D ILE* 1.3 65.5 + - - +
156D TRP* 3.2 3.8 + - - +
157D LEU* 3.0 40.2 + - + +
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Residues in contact with ILE 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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77D LEU* 3.9 17.3 - - + -
150D ALA* 3.0 23.0 + - + +
151D TRP 3.9 3.1 - - - +
153D THR* 1.3 76.4 - - - +
155D ASP* 1.3 61.6 + - - +
157D LEU* 3.3 7.4 + - + +
158D VAL* 3.1 24.1 + - - +
168D VAL* 4.1 24.2 - - + -
170D MSE 4.3 18.4 - - - -
183D ALA* 5.6 0.7 - - + -
188D HIS* 3.6 32.5 - - + +
190D ALA* 3.7 16.8 - - + -
191D LEU* 4.1 25.8 - - + +
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Residues in contact with ASP 155 (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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151D TRP* 3.0 23.1 + - + +
152D ASP* 3.9 8.1 - - - +
154D ILE* 1.3 78.2 - - - +
156D TRP* 1.3 61.7 + - - +
158D VAL* 3.4 4.7 - - - +
159D LYS* 2.8 66.9 + - - +
188D HIS* 2.8 30.4 + - + +
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Residues in contact with TRP 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ARG* 6.1 1.1 - - - -
50D VAL* 4.0 39.0 - - + -
51D MSE 6.0 0.7 - - - -
52D ILE* 3.6 39.5 - - + -
53D PRO* 4.5 15.2 - - + +
64D ILE* 4.3 7.6 - - + -
152D ASP 3.2 15.3 + - - +
153D THR 3.2 2.4 + - - +
155D ASP* 1.3 80.6 - - - +
157D LEU* 1.3 76.9 + - + +
159D LYS* 3.4 1.9 + - - -
160D ASN* 2.9 72.5 + - + +
161D VAL* 4.3 5.4 - - + -
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Residues in contact with LEU 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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52D ILE* 4.5 5.6 - - + -
62D THR* 4.9 0.2 - - + -
64D ILE* 4.1 18.4 - - + -
75D ILE* 4.2 27.4 - - + -
77D LEU* 4.4 19.3 - - + -
115D VAL* 4.4 16.2 - - + -
153D THR* 3.0 38.2 + - + +
154D ILE* 3.7 9.6 - - + +
156D TRP* 1.3 88.6 - - + +
158D VAL* 1.3 59.4 + - + +
161D VAL* 3.0 51.8 + - + +
164D SER* 4.3 0.7 + - - -
168D VAL* 5.2 4.0 - - + -
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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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75D ILE* 5.5 1.3 - - + -
154D ILE 3.1 13.9 + - - +
155D ASP* 3.4 18.6 - - - +
157D LEU* 1.3 75.9 - - - +
159D LYS* 1.3 67.2 + - + +
161D VAL 4.7 5.5 - - - +
164D SER* 4.6 4.1 + - - +
166D GLY* 3.4 43.9 - - - +
168D VAL* 4.0 12.8 - - + -
188D HIS* 4.5 11.2 - - + -
190D ALA* 3.8 13.5 - - + -
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Residues in contact with LYS 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 ASP* 2.8 49.9 + - - +
156D TRP* 4.7 0.7 - - - -
157D LEU 3.2 0.8 - - - -
158D VAL* 1.3 86.8 - - + +
160D ASN* 1.3 69.8 + - - +
161D VAL 3.9 0.4 - - - -
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Residues in contact with ASN 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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48D ARG* 5.7 1.9 + - - -
156D TRP* 2.9 74.8 + - + +
159D LYS* 1.3 87.4 + - - +
161D VAL* 1.3 61.4 + - - +
162D SER* 3.5 6.5 + - - -
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Residues in contact with VAL 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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48D ARG* 4.7 7.2 - - - +
64D ILE* 4.2 18.2 - - + -
66D LEU* 4.1 15.7 - - + -
75D ILE* 4.4 6.3 - - + -
113D ILE* 4.3 7.0 - - + -
156D TRP* 4.3 4.5 - - + -
157D LEU* 3.0 43.8 + - + +
158D VAL 4.8 4.1 - - - +
159D LYS 5.5 0.7 - - - -
160D ASN* 1.3 76.8 - - - +
162D SER* 1.3 60.6 + - - +
163D GLU* 3.7 16.4 - - - +
164D SER* 2.9 40.0 + - - +
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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
------------------------------------------------------------
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