Contacts of the helix formed by residues 148 - 166 (chain A) in PDB entry 3MQT
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 THR 148 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ASP 4.8 5.2 - - - +
147A ALA* 1.3 76.7 - - - +
149A LEU* 1.3 60.1 + - - +
150A SER* 3.7 7.5 + - - -
151A GLU* 3.1 40.3 + - - +
152A ILE* 2.9 27.6 + - - +
178A ASN* 5.8 0.7 - - - -
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Residues in contact with LEU 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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148A THR* 1.3 71.1 - - - +
150A SER* 1.3 67.3 + - - +
152A ILE* 3.3 20.1 + - + +
153A VAL* 2.9 29.7 + - - +
175A ILE* 5.9 2.2 - - + -
176A ILE 5.8 3.6 - - - +
178A ASN* 5.2 9.2 + - + +
181A VAL* 3.6 36.1 - - + -
185A GLU* 3.7 30.7 - - + +
186A ILE* 4.3 9.0 - - + -
189A TYR* 4.0 33.7 - - + -
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Residues in contact with SER 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A THR* 3.3 7.5 + - - -
149A LEU* 1.3 77.5 - - - +
151A GLU* 1.3 57.8 + - - +
153A VAL* 3.3 12.0 + - - +
154A GLU* 3.1 33.1 + - - +
192A GLU* 5.0 8.2 + - - -
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Residues in contact with GLU 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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143A VAL* 4.3 4.5 - - + +
146A ASP 4.8 0.7 - - - +
147A ALA* 3.8 14.5 - - + +
148A THR* 3.1 43.3 + - - +
150A SER* 1.3 75.5 - - - +
152A ILE* 1.3 61.9 + - - +
154A GLU* 3.4 10.4 + - + +
155A ALA* 3.0 27.0 + - - +
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Residues in contact with ILE 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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141A PRO* 4.0 10.9 - - + +
143A VAL* 4.2 16.4 - - + -
147A ALA* 3.8 26.9 - - + +
148A THR 2.9 22.4 + - - +
149A LEU* 3.7 22.2 - - + +
151A GLU* 1.3 72.9 - - - +
153A VAL* 1.3 66.5 + - - +
155A ALA* 3.2 3.1 + - - +
156A TYR* 2.9 35.2 + - + -
176A ILE* 4.3 24.0 - - + +
178A ASN* 6.0 1.1 - - - +
189A TYR* 3.5 25.1 - - + +
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Residues in contact with VAL 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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149A LEU 2.9 24.2 + - - +
150A SER* 3.4 8.5 - - - +
152A ILE* 1.3 75.7 - - - +
154A GLU* 1.3 64.9 + - - +
156A TYR* 2.9 20.7 + - - +
157A LYS* 3.2 27.4 + - - +
189A TYR* 3.8 22.9 - - + -
192A GLU* 3.8 40.4 - - + +
193A LEU* 4.4 14.8 - - + +
196A VAL* 4.6 8.9 - - + +
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Residues in contact with GLU 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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150A SER* 3.1 25.2 + - - +
151A GLU* 3.6 11.4 - - + +
153A VAL* 1.3 78.0 - - - +
155A ALA* 1.3 61.8 + - - +
157A LYS* 3.2 48.5 + - - +
158A PRO* 3.3 10.4 - - - +
192A GLU* 5.6 0.5 - - - +
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Residues in contact with ALA 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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141A PRO* 3.9 13.0 - - + +
142A SER 4.2 7.2 - - - +
143A VAL* 3.6 31.2 - - + -
151A GLU 3.0 11.0 + - - +
152A ILE 3.2 3.8 + - - +
154A GLU* 1.3 75.9 - - - +
156A TYR* 1.3 61.5 + - - +
158A PRO* 3.3 18.7 - - - +
159A LEU* 4.0 11.4 - - - +
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Residues in contact with TYR 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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139A LEU* 2.8 41.2 + - + -
140A TYR 4.4 0.2 - - - -
141A PRO* 3.6 23.8 - - + +
152A ILE* 2.9 26.6 + - + -
153A VAL 2.9 10.2 + - - +
155A ALA* 1.3 77.0 - - - +
157A LYS* 1.3 63.3 + - - +
159A LEU* 3.2 14.8 + - + +
160A ILE* 2.8 32.2 + - + +
173A VAL* 3.6 25.6 - - + -
174A CYS* 2.8 27.0 + - - +
176A ILE* 6.0 0.7 - - + -
189A TYR* 3.4 23.1 - - - -
193A LEU* 4.0 24.5 - - + -
196A VAL* 6.2 0.2 - - + -
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Residues in contact with LYS 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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153A VAL* 3.2 28.2 + - - +
154A GLU* 3.2 41.5 + - - +
156A TYR* 1.3 76.3 - - - +
158A PRO* 1.4 66.1 - - + +
160A ILE* 3.2 2.4 + - - +
161A ALA* 2.8 30.5 + - - +
192A GLU* 5.0 3.8 + - - -
196A VAL* 4.2 32.2 - - + +
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Residues in contact with PRO 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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154A GLU 3.3 8.3 - - - +
155A ALA* 3.3 19.1 - - - +
157A LYS* 1.4 91.9 - - + +
159A LEU* 1.3 65.5 + - + +
161A ALA* 3.8 7.3 - - + +
162A LYS* 3.1 26.7 + - - +
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Residues in contact with LEU 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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139A LEU* 4.4 16.7 - - + +
140A TYR 3.8 17.0 - - - +
141A PRO* 3.6 38.1 - - + -
155A ALA 4.0 9.4 - - - +
156A TYR* 3.2 15.0 + - + +
158A PRO* 1.3 78.9 - - + +
160A ILE* 1.3 65.4 + - - +
162A LYS* 3.2 8.0 + - + +
163A ALA* 3.1 20.1 + - - +
339A ASP 5.0 2.9 - - - +
340A PHE* 3.8 35.9 - - + +
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Residues in contact with ILE 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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139A LEU* 3.9 22.0 - - + -
156A TYR* 2.8 39.6 + - + +
157A LYS 3.7 2.7 - - - +
159A LEU* 1.3 73.6 - - - +
161A ALA* 1.3 63.6 + - - +
163A ALA* 3.2 5.8 + - - +
164A LYS* 3.2 31.1 + - - +
171A VAL* 5.1 0.7 - - + -
173A VAL* 4.9 2.0 - - + -
193A LEU* 4.2 12.1 - - + -
196A VAL* 3.9 38.8 - - + +
197A ILE* 3.7 34.8 - - + -
201A MET* 4.4 5.2 - - + -
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Residues in contact with ALA 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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157A LYS 2.8 17.4 + - - +
158A PRO* 3.8 8.7 - - + +
159A LEU 3.2 0.2 - - - -
160A ILE* 1.3 78.3 - - - +
162A LYS* 1.3 62.9 + - - +
164A LYS* 3.3 10.9 + - - +
165A GLU* 3.0 22.6 + - - +
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Residues in contact with LYS 162 (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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158A PRO 3.1 18.9 + - - +
159A LEU* 3.2 6.6 + - + +
161A ALA* 1.3 75.0 - - - +
163A ALA* 1.3 64.3 + - - +
165A GLU* 3.2 7.4 + - - +
166A ARG* 3.1 67.4 + - + +
339A ASP* 3.4 33.5 + - + +
340A PHE* 4.0 9.4 - - + -
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Residues in contact with ALA 163 (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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139A LEU* 4.8 1.6 - - + -
159A LEU 3.1 12.8 + - - +
160A ILE* 3.5 11.7 - - - +
162A LYS* 1.3 76.1 - - - +
164A LYS* 1.3 61.2 + - - +
166A ARG* 3.2 7.8 + - - +
168A ALA* 3.0 31.7 + - + +
171A VAL* 3.6 30.7 - - + -
201A MET* 4.2 4.5 - - + -
340A PHE* 3.6 21.0 - - + -
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Residues in contact with LYS 164 (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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160A ILE* 3.2 20.7 + - + +
161A ALA* 3.3 9.6 + - - +
163A ALA* 1.3 75.9 - - - +
165A GLU* 1.3 62.9 + - - +
167A GLY* 3.0 15.3 + - - +
168A ALA 4.9 0.7 - - - +
195A GLU 5.3 0.2 + - - -
196A VAL 2.7 26.7 + - - -
197A ILE 3.1 24.1 + - - -
198A GLY* 4.3 2.2 - - - +
201A MET* 3.8 19.3 - - + -
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Residues in contact with GLU 165 (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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161A ALA 3.0 13.9 + - - +
162A LYS* 3.2 12.3 + - - +
164A LYS* 1.3 79.0 - - - +
166A ARG* 1.3 92.2 + - - +
167A GLY 3.3 0.6 + - - -
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Residues in contact with ARG 166 (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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162A LYS* 3.1 59.9 + - + +
163A ALA* 3.2 5.1 + - - +
164A LYS 3.1 0.4 - - - -
165A GLU* 1.3 114.6 + - - +
167A GLY* 1.3 58.2 + - - +
168A ALA* 3.6 1.1 + - + +
339A ASP* 3.1 29.0 + - - +
340A PHE* 4.9 2.0 - - + -
355A LYS* 3.3 34.3 - - - +
356A ILE* 3.7 33.3 - - + +
357A ILE 4.0 0.2 - - - -
358A ASP* 3.2 11.4 + - - -
359A GLY 2.9 19.4 + - - -
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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