Contacts of the helix formed by residues 145 - 158 (chain D) in PDB entry 1MQ8
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
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Residue Dist Surf HB Arom Phob DC
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143D GLN* 2.7 27.1 + - - +
144D PRO* 1.3 77.1 - - + +
146D GLU* 1.3 77.1 + - - +
147D PHE 2.7 4.4 + - - -
148D GLN* 2.6 35.1 + - - +
149D LYS* 3.2 30.9 + - - +
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Residues in contact with GLU 146 (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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141D SER 4.4 1.2 - - - +
142D LEU* 3.1 24.4 - - + +
143D GLN* 2.6 56.4 + - + +
145D ASP* 1.3 89.4 + - - +
147D PHE* 1.3 58.5 + - - +
149D LYS* 3.7 12.7 - - + +
150D ILE* 3.1 30.4 + - - +
261D ILE* 3.8 34.0 - - + +
262D GLY* 4.4 8.8 - - - +
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Residues in contact with PHE 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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136D PHE* 4.1 25.8 - + - -
137D ASP 4.5 12.1 - - - -
138D GLY* 4.5 7.9 - - - -
142D LEU* 5.1 6.0 - - + +
143D GLN 3.6 3.1 + - - +
144D PRO* 3.8 16.6 - - + +
145D ASP 2.7 4.8 + - - -
146D GLU* 1.3 74.2 - - - +
148D GLN* 1.3 69.3 + - + +
150D ILE* 3.3 15.7 - - + +
151D LEU* 3.0 34.9 - - + +
172D GLN* 4.4 11.7 - - + -
199D VAL* 3.6 30.7 - - + -
200D LYS 4.9 0.4 - - - -
201D HIS* 3.8 45.5 - + + -
203D LEU* 5.7 6.3 - - + -
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Residues in contact with GLN 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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144D PRO 5.1 2.5 - - - +
145D ASP* 2.6 16.4 + - - +
147D PHE* 1.3 82.0 - - + +
149D LYS* 1.3 62.6 + - + +
150D ILE 3.2 1.8 - - - -
151D LEU* 3.3 32.9 + - - +
152D ASP* 2.8 37.3 + - - +
155D LYS* 4.6 10.3 - - - +
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Residues in contact with LYS 149 (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 ASP* 3.2 33.0 + - - +
146D GLU* 3.9 16.2 - - + +
147D PHE 3.3 0.2 - - - -
148D GLN* 1.3 79.3 - - + +
150D ILE* 1.3 62.1 + - - +
152D ASP* 3.5 26.9 + - - +
153D PHE 3.5 1.2 + - - -
261D ILE* 5.2 6.7 - - + -
291D THR* 6.0 4.5 - - + -
292D PHE* 3.2 20.5 - - + -
293D GLU* 5.9 1.2 - - - +
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Residues in contact with ILE 150 (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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136D PHE* 4.0 20.9 - - + -
137D ASP* 4.4 12.3 - - + +
142D LEU* 3.8 28.3 - - + -
146D GLU 3.1 15.4 + - - +
147D PHE* 3.3 15.3 - - + +
149D LYS* 1.3 75.7 - - - +
151D LEU* 1.3 76.0 + - + +
153D PHE* 2.9 15.8 + - - +
154D MET* 3.0 12.4 + - + +
237D ILE* 3.5 28.3 - - + -
261D ILE* 4.3 10.1 - - + -
292D PHE* 3.1 25.7 - - + -
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Residues in contact with LEU 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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136D PHE* 4.4 13.7 - - + -
147D PHE* 3.0 37.7 - - + +
148D GLN* 3.3 38.1 - - - +
150D ILE* 1.3 84.8 - - + +
152D ASP* 1.3 66.0 + - - +
154D MET* 2.8 37.7 + - + +
155D LYS* 2.9 28.7 + - - +
196D LEU* 4.2 20.2 - - + -
199D VAL* 5.5 6.3 - - + -
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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
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148D GLN* 2.8 27.3 + - - +
149D LYS* 3.5 24.1 + - - +
151D LEU* 1.3 75.6 - - - +
153D PHE* 1.3 56.9 + - - +
155D LYS* 3.2 19.6 + - - +
156D ASP* 2.8 26.0 + - - +
293D GLU* 5.0 12.5 - - - +
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Residues in contact with PHE 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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134D PHE* 5.2 2.0 - + - -
149D LYS 3.5 1.2 + - - -
150D ILE 2.9 10.6 + - - +
152D ASP* 1.3 75.9 - - - +
154D MET* 1.3 79.9 + - + +
155D LYS 3.0 1.3 - - - -
156D ASP* 2.8 30.9 + - + +
157D VAL* 3.3 30.6 + - + +
235D ILE* 4.6 16.8 - - + -
237D ILE* 4.7 0.9 - - + -
259D ILE* 3.3 35.7 - - + -
292D PHE* 3.4 58.6 - + + -
293D GLU* 5.4 1.8 - - - +
295D LEU* 4.9 3.6 - - + -
298D LEU* 4.0 21.8 - - + -
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Residues in contact with MET 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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134D PHE* 3.8 46.8 - - + -
136D PHE* 4.2 23.3 - - + -
150D ILE* 3.0 17.5 + - + +
151D LEU* 2.8 35.5 + - + +
153D PHE* 1.3 81.6 - - - +
155D LYS* 1.3 60.0 + - + +
157D VAL* 3.2 1.2 + - - -
158D MET* 2.9 34.1 + - - +
170D ALA* 5.0 4.5 - - + -
181D PHE* 5.7 2.7 - - + -
192D PRO* 6.3 0.4 - - + -
196D LEU* 4.6 22.4 - - + -
237D ILE* 3.8 22.7 - - + -
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Residues in contact with LYS 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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148D GLN* 4.6 10.9 - - - +
151D LEU* 2.9 28.5 + - - +
152D ASP* 3.4 15.8 + - - +
154D MET* 1.3 74.1 - - + +
156D ASP* 1.3 60.7 + - - +
157D VAL 3.0 6.4 + - - -
158D MET* 4.3 7.4 - - - -
159D LYS* 3.4 21.5 + - + +
160D LYS* 3.6 9.7 + - - +
192D PRO* 3.1 49.1 + - + +
193D ASP* 3.7 15.6 + - - +
196D LEU* 4.0 16.7 - - + +
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Residues in contact with ASP 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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152D ASP 2.8 13.6 + - - +
153D PHE* 2.8 25.8 + - + +
155D LYS* 1.3 75.4 - - - +
157D VAL* 1.3 61.2 + - + +
160D LYS* 2.9 54.1 + - - +
292D PHE 5.9 0.7 - - - -
293D GLU* 4.8 12.7 - - - +
295D LEU 4.0 10.1 - - - +
296D LYS 3.2 24.0 - - - +
297D ASP* 3.2 7.6 - - - +
298D LEU 4.4 1.9 + - - -
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Residues in contact with VAL 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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132D LEU* 5.8 3.4 - - + -
134D PHE* 4.4 12.6 - - + -
153D PHE* 3.5 44.2 - - + +
154D MET 3.2 3.1 + - - +
155D LYS 3.0 0.4 - - - -
156D ASP* 1.3 85.1 - - - +
158D MET* 1.3 59.6 + - - +
160D LYS* 4.6 0.4 - - - -
161D CYS* 3.0 41.0 + - + +
166D TYR* 6.2 0.4 - - - +
168D PHE* 5.0 3.9 - - + -
297D ASP* 4.6 1.3 - - - -
298D LEU* 4.0 37.7 - - + +
302D LEU* 4.1 15.9 - - + -
303D GLN* 5.9 0.7 - - - +
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Residues in contact with MET 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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134D PHE* 3.3 32.2 - - + -
154D MET* 2.9 21.4 + - - +
155D LYS* 4.3 1.1 - - - -
157D VAL* 1.3 75.5 - - - +
159D LYS* 1.3 61.4 + - - +
161D CYS 2.9 30.5 + - - +
162D SER* 3.2 2.6 + - - -
168D PHE* 3.3 41.3 - - + -
181D PHE* 3.3 36.3 - - + -
186D TYR* 4.7 7.6 - - + -
192D PRO* 3.9 30.3 - - + -
195D LEU* 5.4 2.0 - - - -
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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
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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