Contacts of the helix formed by residues 145 - 158 (chain B) in PDB entry 1MHQ
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
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Residue Dist Surf HB Arom Phob DC
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102B ALA* 3.7 21.1 - - - +
142B PHE* 2.9 21.8 + - + +
143B PRO 4.6 0.3 - - - +
144B GLU* 1.3 75.1 - - - +
146B ILE* 1.3 57.7 + - - +
147B LYS* 2.7 23.5 + - - +
148B ILE* 2.7 49.4 + - + +
149B ARG* 3.0 26.6 + - - +
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Residues in contact with ILE 146 (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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144B GLU 3.0 11.0 + - - +
145B ASP* 1.3 71.2 + - - +
147B LYS* 1.3 59.9 + - + +
149B ARG* 3.8 20.4 - - - +
150B ASP* 2.7 56.1 + - - +
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Residues in contact with LYS 147 (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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102B ALA 3.6 22.0 - - - +
103B LYS* 4.6 17.2 - - + +
104B PHE* 3.7 45.0 - - + +
107B LEU* 3.5 4.5 - - + +
145B ASP* 2.7 20.2 + - - +
146B ILE* 1.3 75.5 - - + +
148B ILE* 1.3 54.4 + - - +
150B ASP* 3.8 2.1 - - - +
151B ALA* 2.9 31.2 + - - +
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Residues in contact with ILE 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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101B VAL* 6.2 0.2 - - + -
102B ALA* 4.2 16.8 - - + +
107B LEU* 3.9 21.5 - - + -
135B LEU* 4.4 10.8 - - + +
138B TRP* 4.1 14.8 - - + -
139B THR* 3.7 34.8 - - + +
142B PHE* 3.8 30.3 - - + +
145B ASP* 2.7 41.3 + - + +
147B LYS* 1.3 70.5 - - - +
149B ARG* 1.3 68.3 + - - +
151B ALA* 3.3 2.5 + - - +
152B TYR* 3.0 23.0 + - - +
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Residues in contact with ARG 149 (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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139B THR* 4.9 6.5 - - - +
143B PRO 2.9 27.1 + - - +
144B GLU* 3.4 25.4 + - - +
145B ASP 3.0 15.3 + - - +
146B ILE* 3.4 19.5 - - - +
148B ILE* 1.3 79.3 - - - +
150B ASP* 1.3 68.6 + - - +
152B TYR* 3.2 5.1 + - - +
153B GLN* 2.9 39.5 + - + +
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Residues in contact with ASP 150 (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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104B PHE* 5.0 13.8 - - + -
146B ILE* 2.7 43.8 + - - +
147B LYS* 3.9 4.6 - - - +
149B ARG* 1.3 80.7 - - - +
151B ALA* 1.3 57.0 + - - +
153B GLN* 3.1 7.9 + - - +
154B MET* 2.7 37.9 + - - +
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Residues in contact with ALA 151 (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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104B PHE* 5.7 3.3 - - + -
107B LEU* 4.1 22.7 - - + -
111B ILE* 4.1 23.9 - - + +
135B LEU* 5.0 6.3 - - + -
147B LYS 2.9 22.1 + - - +
148B ILE* 3.8 3.8 - - - +
150B ASP* 1.3 73.1 - - - +
152B TYR* 1.3 62.8 + - - +
154B MET* 3.4 5.8 + - - +
155B LEU* 3.0 30.7 + - - +
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Residues in contact with TYR 152 (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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132B ILE* 4.0 6.6 - - + +
135B LEU* 3.7 27.5 - - + +
136B PHE* 3.3 47.3 - + + +
139B THR* 3.8 17.5 - - + -
148B ILE 3.0 16.8 + - - +
149B ARG 3.6 3.8 - - - +
151B ALA* 1.3 76.9 - - - +
153B GLN* 1.3 75.4 + - - +
155B LEU* 3.2 5.9 + - - +
156B LYS* 3.1 42.6 + - + +
161B ILE* 3.7 27.9 - - + +
164B ASP 3.1 24.7 + - - -
165B PRO* 4.0 1.9 - - - +
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Residues in contact with GLN 153 (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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149B ARG* 2.9 28.1 + - + +
150B ASP* 3.5 11.0 - - - +
152B TYR* 1.3 88.9 - - - +
154B MET* 1.3 52.1 + - - +
156B LYS* 3.0 16.2 + - - +
157B LYS* 2.7 63.9 + - + +
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Residues in contact with MET 154 (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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104B PHE* 6.3 2.7 - - + -
108B ASN* 5.9 1.8 - - - +
111B ILE* 4.3 30.5 - - + -
150B ASP 2.7 21.0 + - - +
151B ALA* 3.6 4.9 - - - +
153B GLN* 1.3 75.2 - - - +
155B LEU* 1.3 66.1 + - - +
157B LYS* 3.0 21.6 + - + +
158B GLN* 3.1 43.6 + - - +
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Residues in contact with LEU 155 (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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111B ILE* 3.6 37.7 - - + +
114B LEU* 3.6 21.3 - - + -
135B LEU* 3.3 34.1 - - + -
151B ALA 3.0 14.4 + - - +
152B TYR 3.5 2.7 - - - +
153B GLN 3.2 0.2 - - - -
154B MET* 1.3 81.4 - - - +
156B LYS* 1.3 60.0 + - - +
158B GLN* 4.3 0.9 - - - +
159B GLY 3.4 0.9 + - - -
160B ILE* 2.8 50.8 + - + +
161B ILE* 3.2 30.4 + - + -
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Residues in contact with LYS 156 (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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152B TYR* 3.1 41.7 + - + +
153B GLN* 3.0 20.6 + - - +
155B LEU* 1.3 74.5 - - - +
157B LYS* 1.3 69.2 + - + +
159B GLY* 2.9 13.2 + - - -
161B ILE* 3.8 22.7 - - + +
163B GLN* 4.0 36.5 - - - +
164B ASP 4.5 9.0 + - - +
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Residues in contact with LYS 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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153B GLN* 2.7 54.0 + - + +
154B MET* 3.0 12.5 + - + +
156B LYS* 1.3 74.8 - - + +
158B GLN* 1.3 61.7 + - + +
159B GLY 3.1 4.2 + - - -
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Residues in contact with GLN 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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111B ILE* 6.2 0.4 - - - +
154B MET* 3.1 49.6 + - - +
155B LEU* 4.3 1.8 - - - +
156B LYS 3.3 0.2 - - - -
157B LYS* 1.3 77.2 - - + +
159B GLY* 1.3 63.2 + - - +
160B ILE* 3.0 37.9 + - + +
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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
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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