Contacts of the helix formed by residues 148 - 167 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146O ASP 4.5 5.4 - - - +
147O ALA* 1.3 73.5 - - - +
149O LEU* 1.3 65.8 + - - +
150O SER* 3.3 10.4 + - - -
151O GLU* 2.8 44.8 + - - +
152O ILE* 3.0 25.9 + - - +
178O ASN* 5.8 0.4 - - - -
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Residues in contact with LEU 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148O THR* 1.3 72.5 - - - +
150O SER* 1.3 63.3 + - - +
152O ILE* 3.2 17.4 + - + +
153O VAL* 3.1 28.5 + - - +
175O ILE* 6.1 1.6 - - + -
176O ILE 6.0 1.1 - - - +
178O ASN* 4.6 14.1 + - + +
181O VAL* 3.7 33.1 - - + +
185O GLU* 3.6 35.4 - - + +
186O ILE* 4.4 9.9 - - + -
189O TYR* 4.1 32.0 - - + -
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Residues in contact with SER 150 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148O THR* 3.1 9.9 + - - -
149O LEU* 1.3 82.1 - - - +
151O GLU* 1.3 58.1 + - - +
153O VAL* 3.5 7.4 + - - +
154O GLU* 3.2 32.4 + - - +
192O GLU* 5.2 7.1 + - - -
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Residues in contact with GLU 151 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143O VAL* 4.4 4.2 - - + +
146O ASP 4.4 0.9 - - - +
147O ALA* 3.3 15.9 - - + -
148O THR* 2.8 51.2 + - - +
150O SER* 1.3 76.1 - - - +
152O ILE* 1.3 61.1 + - - +
153O VAL 3.4 0.2 - - - -
154O GLU* 3.6 9.1 + - - +
155O ALA* 3.1 25.3 + - - +
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Residues in contact with ILE 152 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141O PRO* 4.0 11.9 - - + -
143O VAL* 4.3 10.3 - - + -
147O ALA* 4.0 25.1 - - + +
148O THR 3.0 22.1 + - - +
149O LEU* 3.7 17.9 - - + +
151O GLU* 1.3 76.0 - - - +
153O VAL* 1.3 60.1 + - - +
155O ALA* 3.2 7.1 + - - +
156O TYR* 2.9 39.9 + - + -
176O ILE* 3.6 30.3 - - + -
178O ASN* 5.6 2.5 - - - +
189O TYR* 3.4 26.0 - - + +
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Residues in contact with VAL 153 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149O LEU 3.1 17.1 + - - +
150O SER* 3.7 8.1 - - - +
152O ILE* 1.3 77.5 - - - +
154O GLU* 1.3 66.3 + - - +
156O TYR* 3.1 16.7 + - - +
157O LYS* 3.2 29.6 + - - +
189O TYR* 3.8 24.2 - - + -
192O GLU* 3.8 37.2 - - + +
193O LEU* 3.9 20.6 - - + -
196O VAL* 4.6 7.9 - - + -
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Residues in contact with GLU 154 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150O SER* 3.2 22.3 + - - +
151O GLU* 3.8 11.0 - - - +
152O ILE 3.3 0.2 - - - -
153O VAL* 1.3 77.8 - - - +
155O ALA* 1.3 63.2 + - - +
157O LYS* 3.1 50.1 + - - +
158O PRO* 3.4 10.4 - - - +
192O GLU* 5.6 0.5 - - - +
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Residues in contact with ALA 155 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141O PRO* 3.8 12.9 - - + +
142O SER 4.5 4.5 - - - +
143O VAL* 3.4 33.0 - - + -
151O GLU 3.1 11.9 + - - +
152O ILE 3.2 4.2 + - - +
154O GLU* 1.3 75.7 - - - +
156O TYR* 1.3 61.5 + - - +
157O LYS 3.4 0.3 + - - -
158O PRO* 3.5 15.8 - - - +
159O LEU* 4.1 10.4 - - - +
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Residues in contact with TYR 156 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139O LEU* 2.7 48.7 + - + -
141O PRO* 3.5 27.0 - - + +
152O ILE* 2.9 27.5 + - + -
153O VAL 3.1 10.0 + - - +
155O ALA* 1.3 75.6 - - - +
157O LYS* 1.3 65.1 + - - +
159O LEU* 3.2 10.8 + - + +
160O ILE* 2.9 38.4 + - + +
173O VAL* 3.7 21.3 - - + -
174O CYS* 2.8 24.6 + - - +
176O ILE* 5.5 0.4 - - + +
189O TYR* 3.5 22.0 - - - -
193O LEU* 4.0 17.7 - - + -
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Residues in contact with LYS 157 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153O VAL* 3.2 17.8 + - - +
154O GLU* 3.1 43.8 + - - +
155O ALA 3.3 0.2 - - - -
156O TYR* 1.3 76.5 - - - +
158O PRO* 1.3 66.9 - - + +
160O ILE* 3.3 6.6 + - - +
161O ALA* 2.9 29.6 + - - +
192O GLU* 5.6 2.6 + - - -
196O VAL* 4.2 36.4 - - + +
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Residues in contact with PRO 158 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154O GLU 3.4 11.7 - - - +
155O ALA* 3.5 12.3 - - - +
157O LYS* 1.3 91.6 - - + +
159O LEU* 1.3 63.3 + - + +
161O ALA* 3.4 7.1 + - + +
162O LYS* 2.9 30.0 + - - +
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Residues in contact with LEU 159 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139O LEU* 4.2 22.3 - - + +
140O TYR 3.9 32.8 - - - +
141O PRO* 3.9 19.5 - - + -
155O ALA 4.1 9.4 - - - +
156O TYR* 3.2 9.6 + - + +
158O PRO* 1.3 79.3 - - + +
160O ILE* 1.3 63.3 + - - +
162O LYS* 3.2 7.4 + - + +
163O ALA* 3.0 23.2 + - - +
339O ASP 4.9 2.5 - - - +
340O PHE* 3.8 36.5 - - + +
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Residues in contact with ILE 160 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139O LEU* 4.0 22.2 - - + -
156O TYR* 2.9 40.6 + - + +
157O LYS 3.7 3.4 - - - +
159O LEU* 1.3 76.4 - - - +
161O ALA* 1.3 62.8 + - - +
163O ALA* 3.2 5.6 + - - +
164O LYS* 3.0 43.9 + - - +
171O VAL* 5.3 0.4 - - + -
173O VAL* 4.9 1.3 - - + -
193O LEU* 4.2 10.5 - - + -
196O VAL* 3.8 26.5 - - + +
197O ILE* 3.9 34.5 - - + -
201O MET* 4.5 5.2 - - + -
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Residues in contact with ALA 161 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157O LYS 2.9 17.6 + - - +
158O PRO* 3.7 8.1 - - + +
160O ILE* 1.3 78.7 - - - +
162O LYS* 1.3 56.1 + - - +
164O LYS* 3.3 10.7 + - - +
165O GLU* 2.9 27.5 + - - +
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Residues in contact with LYS 162 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158O PRO 2.9 20.4 + - - +
159O LEU* 3.2 6.9 + - + +
161O ALA* 1.3 69.8 - - - +
163O ALA* 1.3 60.3 + - - +
165O GLU* 3.1 6.5 + - + +
166O ARG* 2.9 66.9 + - + +
339O ASP* 3.1 52.3 + - + +
340O PHE* 4.0 6.7 - - + -
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Residues in contact with ALA 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139O LEU* 4.7 2.0 - - + -
159O LEU 3.0 12.6 + - - +
160O ILE* 3.4 11.2 - - - +
162O LYS* 1.3 76.0 - - - +
164O LYS* 1.3 60.2 + - - +
166O ARG* 3.2 3.5 + - - -
167O GLY 3.1 4.7 + - - -
168O ALA* 2.9 33.8 + - + +
171O VAL* 3.7 30.1 - - + -
201O MET* 4.4 2.9 - - + -
340O PHE* 3.5 20.5 - - + -
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Residues in contact with LYS 164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160O ILE* 3.0 26.4 + - - +
161O ALA* 3.7 11.0 - - - +
162O LYS 3.3 0.2 - - - -
163O ALA* 1.3 73.9 - - - +
165O GLU* 1.3 66.4 + - - +
167O GLY* 3.0 13.7 + - - +
168O ALA 4.8 0.9 - - - +
196O VAL 2.7 26.6 + - - -
197O ILE 2.9 25.4 + - - -
198O GLY* 4.2 3.4 - - - +
201O MET* 3.9 20.8 - - + -
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Residues in contact with GLU 165 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161O ALA 2.9 14.6 + - - +
162O LYS* 3.1 11.2 + - - +
164O LYS* 1.3 77.9 - - - +
166O ARG* 1.3 91.4 + - - +
167O GLY* 3.4 0.7 + - - -
355O LYS* 4.8 4.1 + - - -
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Residues in contact with ARG 166 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162O LYS* 2.9 56.3 + - + +
163O ALA* 3.2 6.0 + - - +
165O GLU* 1.3 105.5 + - - +
167O GLY* 1.3 58.7 + - - +
168O ALA* 3.4 1.6 - - + +
339O ASP* 3.0 36.7 + - - +
340O PHE* 4.7 3.6 - - + -
355O LYS* 3.0 32.2 - - - +
356O ILE* 3.6 36.8 - - + +
358O ASP* 3.3 10.9 + - - -
359O GLY 3.0 18.4 + - - -
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Residues in contact with GLY 167 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O ALA 3.1 0.2 + - - -
164O LYS* 3.0 16.7 + - - -
165O GLU 3.2 1.2 - - - -
166O ARG* 1.3 80.0 - - - +
168O ALA* 1.3 68.9 + - - +
169O LYS* 3.3 10.0 + - - +
358O ASP* 3.6 13.2 - - - +
359O GLY* 3.1 18.1 + - - -
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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
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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