Contacts of the helix formed by residues 145 - 161 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ARG* 3.9 13.0 - - + +
134C PRO 3.6 22.7 - - - +
135C LEU* 3.5 14.8 - - + +
136C ARG* 3.0 30.0 + - - +
140C ASN* 3.7 3.1 - - - +
144C VAL* 1.3 77.1 - - - +
146C HIS* 1.3 60.0 + - - +
147C ALA* 2.9 20.2 + - - +
148C THR* 2.9 19.9 + - - +
149C ASP* 3.1 33.7 + - - +
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Residues in contact with HIS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ARG* 3.2 25.2 + - - +
119C VAL* 3.9 32.5 - - + -
120C ARG* 5.1 6.7 - - + -
129C TYR* 5.9 0.8 - + - -
130C VAL 4.9 0.6 + - - -
133C ARG* 3.5 51.2 + - + +
145C ASP* 1.3 75.1 - - - +
147C ALA* 1.3 61.0 + - - +
149C ASP* 3.9 5.6 + - - +
150C ALA* 3.1 28.2 + - - +
175C TYR* 4.4 7.5 + + - -
178C PHE* 3.7 19.9 - + - -
179C THR* 4.1 9.4 - - + +
182C MSE 3.5 27.1 - - + +
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Residues in contact with ALA 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU* 4.2 4.7 - - + +
145C ASP* 2.9 15.7 + - - +
146C HIS* 1.3 78.2 - - - +
148C THR* 1.3 59.3 + - + +
150C ALA* 3.4 4.0 + - - +
151C TRP* 3.1 27.1 + - - +
182C MSE 3.2 28.0 - - - +
183C ALA* 4.4 3.7 - - - +
185C THR* 3.4 13.0 - - - +
186C ASN* 4.6 16.9 - - + +
3001C GOL 5.6 0.4 - - - -
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Residues in contact with THR 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ARG* 3.5 39.0 - - - +
136C ARG* 4.6 9.2 - - - +
143C GLU 4.2 10.5 - - - +
144C VAL* 3.4 12.2 - - - +
145C ASP* 2.9 39.5 + - - +
147C ALA* 1.3 75.3 - - + +
149C ASP* 1.3 59.8 + - - +
151C TRP* 3.3 3.7 + - - +
152C ASP* 3.0 35.3 + - - +
3001C GOL 4.6 4.7 - - - +
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Residues in contact with ASP 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C MSE 3.4 23.8 - - - +
60C LEU* 4.0 4.2 - - - +
79C ARG* 3.5 21.7 + - - +
120C ARG* 3.0 55.4 + - - +
133C ARG* 5.6 0.7 - - - -
144C VAL* 4.3 1.0 - - - +
145C ASP 3.1 23.5 + - - +
146C HIS* 4.0 5.4 + - - +
148C THR* 1.3 81.8 + - - +
150C ALA* 1.3 53.9 + - - +
152C ASP* 4.9 0.5 - - - +
153C THR* 2.7 37.2 + - - -
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Residues in contact with ALA 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 5.6 0.4 - - + -
79C ARG* 3.8 25.7 - - - +
146C HIS 3.1 20.1 + - - +
147C ALA 3.7 4.3 - - - +
148C THR 3.3 0.2 - - - -
149C ASP* 1.3 74.0 - - - +
151C TRP* 1.3 60.4 + - - +
153C THR* 3.6 2.9 - - - -
154C ILE* 3.0 36.5 + - + +
170C MSE 4.5 5.6 - - + -
179C THR 5.1 0.4 - - - +
183C ALA* 3.8 26.0 - - + +
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Residues in contact with TRP 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ARG* 4.2 0.4 - - - +
147C ALA 3.1 14.0 + - - +
148C THR 3.6 8.1 - - - +
150C ALA* 1.3 75.0 - - - +
152C ASP* 1.3 71.9 + - - +
154C ILE 3.4 0.9 + - - -
155C ASP* 2.9 33.0 + - + +
186C ASN* 3.5 31.0 - - - +
187C PRO 3.2 21.1 - - - -
188C HIS* 3.5 34.1 + + - +
189C PRO* 3.7 23.6 - - + -
3001C GOL 3.5 49.6 - - - +
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Residues in contact with ASP 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ILE* 4.3 1.7 - - - +
53C PRO 4.6 3.4 - - - +
54C MSE 3.8 26.6 - - + +
55C ARG* 3.0 61.1 + - - +
148C THR 3.0 18.8 + - - +
149C ASP* 4.8 0.5 - - - +
151C TRP* 1.3 80.3 - - - +
153C THR* 1.3 62.2 + - - +
155C ASP* 3.8 5.3 - - - +
156C TRP* 3.1 24.3 + - - +
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Residues in contact with THR 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ILE* 4.3 10.2 - - + +
54C MSE 3.6 9.2 - - - +
62C THR* 5.0 1.1 - - + -
77C LEU* 4.1 17.3 - - + -
79C ARG* 4.9 0.2 - - - -
117C GLN* 2.9 42.5 + - - +
149C ASP 2.7 22.1 + - - -
150C ALA* 3.6 7.6 - - - -
152C ASP* 1.3 75.9 - - - +
154C ILE* 1.3 65.0 + - - +
156C TRP* 3.3 4.2 + - - +
157C LEU* 3.0 39.3 + - + +
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Residues in contact with ILE 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 3.8 16.8 - - + -
150C ALA* 3.0 25.0 + - + +
151C TRP 3.9 2.5 - - - +
153C THR* 1.3 73.7 - - - +
155C ASP* 1.3 65.5 + - - +
157C LEU* 3.2 7.4 + - + +
158C VAL* 3.1 23.2 + - - +
168C VAL* 4.0 26.0 - - + -
170C MSE 4.2 23.8 - - - -
183C ALA* 5.6 0.9 - - + -
188C HIS* 3.6 33.2 - - + +
190C ALA* 3.8 15.9 - - + -
191C LEU* 4.2 18.8 - - + +
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Residues in contact with ASP 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C TRP* 2.9 24.9 + - + +
152C ASP* 3.8 8.1 - - - +
154C ILE* 1.3 77.1 - - - +
156C TRP* 1.3 61.8 + - - +
158C VAL* 3.3 4.3 - - - +
159C LYS* 2.7 69.8 + - - +
188C HIS* 2.9 28.8 + - + +
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Residues in contact with TRP 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C VAL* 3.9 39.3 - - + -
51C MSE 6.1 0.2 - - - -
52C ILE* 3.6 40.6 - - + -
53C PRO* 4.5 14.6 - - + +
64C ILE* 4.1 7.4 - - + -
152C ASP 3.1 17.9 + - - +
153C THR 3.7 1.8 - - - +
154C ILE 3.3 0.2 - - - -
155C ASP* 1.3 76.2 + - - +
157C LEU* 1.3 75.4 + - + +
159C LYS* 3.4 2.6 + - - -
160C ASN* 2.9 75.6 + - + +
161C VAL* 4.4 5.2 - - + -
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ILE* 4.6 4.7 - - + -
64C ILE* 3.9 23.3 - - + -
75C ILE* 4.2 24.6 - - + +
77C LEU* 4.3 20.0 - - + -
115C VAL* 4.4 13.9 - - + -
153C THR* 3.0 38.7 + - + +
154C ILE* 3.2 9.6 + - + +
156C TRP* 1.3 87.8 - - + +
158C VAL* 1.3 60.5 + - + +
161C VAL* 3.0 53.1 + - + +
164C SER* 5.2 0.2 - - - -
168C VAL* 5.2 3.4 - - + -
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Residues in contact with VAL 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ILE* 5.6 2.9 - - + -
154C ILE 3.1 12.5 + - - +
155C ASP* 3.3 21.5 - - - +
157C LEU* 1.3 77.2 - - + +
159C LYS* 1.3 65.1 + - + +
161C VAL 4.7 6.8 - - - +
164C SER* 5.8 0.9 - - - -
166C GLY* 3.3 44.1 - - - +
168C VAL* 4.0 12.3 - - + -
188C HIS* 4.4 11.0 - - + -
190C ALA* 3.7 13.7 - - + -
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Residues in contact with LYS 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ASP* 2.7 51.8 + - - +
156C TRP* 5.3 0.7 - - - -
157C LEU 3.2 0.4 - - - -
158C VAL* 1.3 86.6 - - + +
160C ASN* 1.3 69.4 + - - +
161C VAL 3.9 0.7 - - - -
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Residues in contact with ASN 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ARG* 5.8 1.2 + - - -
156C TRP* 2.9 73.3 + - + +
159C LYS* 1.3 89.9 + - - +
161C VAL* 1.3 61.3 + - - +
162C SER* 3.5 5.9 + - - -
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Residues in contact with VAL 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ARG* 5.7 2.0 - - - +
64C ILE* 4.2 19.5 - - + -
66C LEU* 4.2 14.4 - - + -
75C ILE* 4.3 9.2 - - + -
113C ILE* 4.2 5.8 - - + -
156C TRP* 4.4 4.0 - - + -
157C LEU* 3.0 45.5 + - + +
158C VAL 4.7 5.7 - - - +
159C LYS 5.5 0.2 - - - -
160C ASN* 1.3 77.3 - - - +
162C SER* 1.3 63.0 + - - +
163C GLU* 3.7 17.3 - - - +
164C SER* 3.2 32.1 + - - +
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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
------------------------------------------------------------
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