Contacts of the helix formed by residues 143 - 161 (chain A) in PDB entry 1MQA
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 GLN 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A MET 5.4 2.1 - - - +
141A SER 5.0 4.0 - - - +
142A LEU* 1.3 77.5 - - - +
144A PRO* 1.3 81.6 - - + +
145A ASP* 2.8 13.6 + - + +
146A GLU* 2.9 38.3 + - + +
147A PHE* 3.1 10.7 + - - +
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Residues in contact with PRO 144 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A LEU 3.9 2.2 - - - +
143A GLN* 1.3 96.8 - - + +
145A ASP* 1.3 60.7 + - + +
147A PHE* 3.7 8.4 + - + +
148A GLN* 3.3 21.5 + - - +
201A HIS* 4.8 7.4 - - - +
203A LEU* 6.5 0.9 - - + -
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Residues in contact with ASP 145 (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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143A GLN* 2.8 8.9 + - + -
144A PRO* 1.3 81.2 - - + +
146A GLU* 1.3 65.4 + - + +
148A GLN* 3.1 8.4 + - - +
149A LYS* 3.0 32.0 + - - +
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Residues in contact with GLU 146 (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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141A SER 4.1 4.9 - - - +
142A LEU* 3.5 27.9 - - + +
143A GLN* 2.9 42.9 + - + +
145A ASP* 1.3 78.0 - - + +
147A PHE* 1.3 62.6 + - - +
149A LYS* 3.2 24.3 + - - +
150A ILE* 3.1 26.0 + - - +
261A ILE* 4.7 7.4 - - + +
262A GLY* 3.9 23.0 + - - +
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Residues in contact with PHE 147 (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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136A PHE* 4.0 17.3 - + - -
137A ASP 3.7 13.2 - - - -
138A GLY* 3.5 25.8 - - - -
142A LEU* 4.4 3.7 - - + +
143A GLN 3.1 5.7 + - - +
144A PRO* 3.8 8.5 - - + +
146A GLU* 1.3 75.5 - - - +
148A GLN* 1.3 59.6 + - - +
150A ILE* 2.9 29.0 + - + +
151A LEU* 3.0 27.7 + - + +
172A GLN* 3.5 24.7 - - - -
199A VAL* 4.1 15.0 - - + -
201A HIS* 3.4 60.3 - + + +
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Residues in contact with GLN 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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144A PRO 3.3 11.7 + - - +
145A ASP* 3.1 12.3 + - - +
147A PHE* 1.3 79.3 - - - +
149A LYS* 1.3 56.6 + - - +
151A LEU* 3.3 25.1 + - - +
152A ASP* 2.9 67.7 + - - +
155A LYS* 4.7 7.9 - - - +
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Residues in contact with LYS 149 (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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145A ASP* 3.0 22.4 + - - +
146A GLU* 3.2 25.4 - - - +
147A PHE 3.1 0.2 - - - -
148A GLN* 1.3 76.7 - - - +
150A ILE* 1.3 56.7 + - - +
152A ASP* 3.8 8.6 - - + +
153A PHE* 2.9 28.6 + - - +
261A ILE* 4.8 10.2 - - + +
289A LEU* 3.8 26.1 - - + +
290A ASP* 4.7 9.9 + - - +
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Residues in contact with ILE 150 (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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136A PHE* 3.7 34.5 - - + -
137A ASP 3.7 21.8 - - - +
142A LEU* 4.3 8.3 - - + -
146A GLU 3.1 14.5 + - - +
147A PHE* 2.9 16.7 + - + +
149A LYS* 1.3 76.3 - - - +
151A LEU* 1.3 61.2 + - + +
153A PHE* 3.2 5.8 + - - +
154A MET* 2.9 31.9 + - - +
237A ILE* 4.0 18.2 - - + +
261A ILE* 3.7 39.7 - - + -
289A LEU* 4.3 1.8 - - + -
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Residues in contact with LEU 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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136A PHE* 4.4 19.5 - - + -
147A PHE* 3.0 35.0 + - + +
148A GLN* 3.6 31.9 - - - +
150A ILE* 1.3 74.5 - - + +
152A ASP* 1.3 58.4 + - - +
154A MET* 3.3 8.0 + - - +
155A LYS* 2.9 44.6 + - - +
196A LEU* 4.1 24.4 - - + +
199A VAL* 4.0 31.9 - - + +
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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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148A GLN* 2.9 50.3 + - - +
149A LYS* 3.8 8.0 - - + +
151A LEU* 1.3 75.1 - - - +
153A PHE* 1.3 57.5 + - - +
155A LYS* 3.3 15.4 + - - +
156A ASP* 2.8 43.6 + - - +
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Residues in contact with PHE 153 (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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134A PHE* 5.3 0.7 - + - -
149A LYS 2.9 20.0 + - - +
150A ILE 3.4 4.0 - - - +
152A ASP* 1.3 75.8 - - - +
154A MET* 1.3 57.3 + - - +
156A ASP* 3.2 8.4 + - + +
157A VAL* 2.9 47.4 + - + +
235A ILE* 4.8 3.1 - - + -
237A ILE* 3.5 31.6 - - + -
259A ILE* 4.0 20.2 - - + -
289A LEU* 3.7 32.1 - - + -
292A PHE* 3.4 44.0 - + + -
295A LEU* 3.5 27.6 - - + -
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Residues in contact with MET 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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134A PHE* 3.5 33.7 - - + -
136A PHE* 3.3 34.8 - - + -
150A ILE* 2.9 22.1 + - - +
151A LEU* 3.5 7.0 - - - +
153A PHE* 1.3 77.2 - - - +
155A LYS* 1.3 62.7 + - - +
157A VAL* 3.2 3.5 + - - +
158A MET* 3.0 32.9 + - + +
170A ALA* 3.4 32.1 - - + -
196A LEU* 4.0 22.9 - - + -
237A ILE* 3.5 18.8 - - + -
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Residues in contact with LYS 155 (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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148A GLN* 4.7 6.7 - - - +
151A LEU* 2.9 39.1 + - - +
152A ASP* 3.5 15.9 + - - +
154A MET* 1.3 75.6 - - - +
156A ASP* 1.3 60.1 + - - +
158A MET* 3.2 5.6 + - - +
159A LYS* 2.8 38.0 + - - +
192A PRO* 4.0 19.8 - - + +
193A ASP* 4.0 41.4 + - - +
196A LEU* 3.6 35.4 + - + +
197A LYS* 5.8 0.8 - - - +
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Residues in contact with ASP 156 (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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152A ASP* 2.8 30.6 + - - +
153A PHE* 3.6 7.0 - - + +
155A LYS* 1.3 74.6 - - - +
157A VAL* 1.3 65.6 + - - +
159A LYS* 3.3 21.9 + - - +
160A LYS* 3.0 42.5 + - - +
292A PHE* 6.1 2.7 - - + -
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Residues in contact with VAL 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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132A LEU* 5.2 0.2 - - + -
134A PHE* 3.8 22.7 - - + -
153A PHE* 2.9 55.9 + - + +
154A MET 3.6 5.6 - - - +
156A ASP* 1.3 76.1 - - + +
158A MET* 1.3 63.6 + - - +
160A LYS* 3.3 4.4 + - - +
161A LEU* 3.2 39.0 + - + +
168A PHE* 5.1 0.7 - - + -
235A ILE* 4.6 11.4 - - + -
292A PHE* 5.3 3.1 - - + -
295A LEU* 4.5 5.2 - - + -
298A LEU* 5.7 1.3 - - + -
299A PHE* 4.0 20.6 - - + -
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Residues in contact with MET 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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134A PHE* 3.5 27.8 - - + -
154A MET* 3.0 26.4 + - + +
155A LYS* 3.5 10.1 - - - +
157A VAL* 1.3 77.4 - - - +
159A LYS* 1.3 60.8 + - - +
161A LEU 3.1 4.7 + - - -
162A SER* 3.1 20.6 + - - -
168A PHE* 3.6 34.4 - - + -
181A PHE* 3.8 29.4 - - + -
186A TYR* 4.3 14.2 + - + -
192A PRO* 3.7 21.8 - - + -
196A LEU* 3.9 27.6 - - + -
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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 LYS* 2.8 24.8 + - - +
156A ASP* 3.7 21.2 + - - +
157A VAL 3.3 0.2 - - - -
158A MET* 1.3 70.8 - - - +
160A LYS* 1.3 62.0 + - + +
161A LEU 3.0 4.7 - - - -
162A SER* 3.0 26.6 + - - +
192A PRO* 4.3 13.9 - - + -
193A ASP* 3.2 35.6 + - - -
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Residues in contact with LYS 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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156A ASP* 3.0 31.8 + - + +
157A VAL 3.3 5.1 + - - +
159A LYS* 1.3 76.3 - - + +
161A LEU* 1.3 61.1 + - - +
162A SER* 3.4 2.2 + - - +
164A THR* 5.9 0.7 - - - +
292A PHE* 3.0 43.4 - - - -
299A PHE* 3.9 41.1 - - + +
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Residues in contact with LEU 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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132A LEU* 4.9 2.0 - - + -
157A VAL* 3.2 26.1 + - + +
158A MET 3.1 5.8 + - - +
159A LYS 3.0 1.2 - - - -
160A LYS* 1.3 78.7 - - - +
162A SER* 1.3 58.9 + - - +
163A ASN 3.7 0.2 + - - -
164A THR* 2.5 32.6 + - + +
166A TYR* 3.7 46.5 - - + +
168A PHE* 3.7 34.9 - - + -
186A TYR* 4.5 1.4 + - - -
298A LEU* 3.7 20.6 - - + +
299A PHE* 3.8 26.7 - - + +
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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