Contacts of the helix formed by residues 141 - 158 (chain A) in PDB entry 1QK0
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 LYS 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A TYR* 4.3 25.3 + - + +
134A MET* 4.2 13.9 - - - +
135A TRP 2.7 26.3 + - - +
136A LEU* 3.9 16.6 - - - +
137A ASP* 3.4 20.6 + - - +
138A THR* 3.1 21.7 + - + +
139A LEU 3.1 1.2 - - - -
140A ASP* 1.3 77.8 - - + +
142A THR* 1.3 59.0 + - - +
143A PRO* 3.3 1.3 - - - -
144A LEU* 2.8 64.8 + - + +
145A MET 3.6 2.1 + - - -
2C BGC 4.9 4.8 + - - -
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Residues in contact with THR 142 (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 LEU* 4.5 11.0 - - + -
138A THR 4.0 2.2 - - - +
139A LEU* 2.5 29.3 + - + +
141A LYS* 1.3 77.0 - - - +
143A PRO* 1.3 70.6 - - - +
145A MET* 2.8 22.3 + - - +
146A GLU 3.5 3.3 + - - -
198A TYR* 4.0 28.3 - - + -
201A THR* 3.6 31.3 - - + +
202A ILE* 4.2 12.8 - - + -
205A ILE* 3.7 9.4 - - - +
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Residues in contact with PRO 143 (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 3.6 1.6 - - - +
140A ASP* 3.0 23.3 - - - +
141A LYS 3.3 0.2 - - - -
142A THR* 1.3 99.4 - - - +
144A LEU* 1.3 58.9 + - - +
146A GLU* 3.3 10.1 + - + +
147A GLN* 3.2 20.6 + - - +
205A ILE* 5.3 1.6 - - + -
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Residues in contact with LEU 144 (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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103A TYR* 3.4 33.2 - - + +
134A MET* 4.0 16.2 - - + -
140A ASP 5.0 0.4 + - - +
141A LYS* 2.8 45.8 + - + +
143A PRO* 1.3 77.8 - - - +
145A MET* 1.3 60.6 + - - +
147A GLN* 3.4 33.4 - - - +
148A THR* 2.8 31.5 + - - +
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Residues in contact with MET 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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134A MET* 4.2 2.4 - - - -
136A LEU* 3.8 29.8 - - + -
141A LYS 3.6 2.4 + - - -
142A THR* 2.8 11.7 + - - +
144A LEU* 1.3 79.9 - - - +
146A GLU* 1.3 58.1 + - - +
148A THR* 3.3 3.3 + - - -
149A LEU* 3.0 31.9 + - + +
166A PHE* 3.7 45.5 - - + -
202A ILE* 3.9 21.8 - - + -
205A ILE* 3.9 22.4 - - + -
206A VAL* 3.9 25.8 - - + -
214A THR* 4.2 7.2 - - + -
216A LEU* 4.4 6.3 - - + -
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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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142A THR 3.5 2.2 + - - -
143A PRO* 3.3 11.6 + - + +
144A LEU 3.3 0.4 - - - -
145A MET* 1.3 77.5 - - - +
147A GLN* 1.3 54.5 + - - +
149A LEU* 3.1 3.6 + - - +
150A ALA* 2.7 33.9 + - + +
205A ILE* 4.1 30.9 - - + +
208A GLU* 5.3 1.9 - - - +
209A TYR* 3.4 33.8 + - + +
900A CO 2.3 32.2 + - - -
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Residues in contact with GLN 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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102A ALA* 5.2 9.5 - - - +
103A TYR 6.0 0.4 - - - +
143A PRO 3.2 13.0 + - - +
144A LEU* 3.4 30.4 - - - +
146A GLU* 1.3 78.2 - - - +
148A THR* 1.3 63.0 + - - +
150A ALA* 3.3 8.4 + - + +
151A ASP* 3.0 36.3 + - - +
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Residues in contact with THR 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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99A TRP* 3.8 25.6 - - + +
101A ASN* 4.3 11.8 - - + +
102A ALA 5.9 0.2 - - - +
134A MET* 3.2 20.8 - - + +
144A LEU* 2.8 24.5 + - - +
145A MET 3.5 5.4 - - - -
147A GLN* 1.3 78.6 + - - +
149A LEU* 1.3 63.0 + - - +
151A ASP* 3.0 13.0 + - - +
152A ILE* 3.0 24.7 + - + +
164A GLY* 5.5 0.9 - - - -
165A GLN 5.9 0.7 - - - +
166A PHE* 3.8 22.4 - - + -
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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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145A MET* 3.0 32.0 + - + +
146A GLU 3.6 4.5 - - - +
148A THR* 1.3 75.8 - - - +
150A ALA* 1.3 57.4 + - - +
152A ILE* 3.2 8.0 + - + -
153A ARG* 2.9 24.9 + - - +
164A GLY* 4.7 0.4 - - - -
166A PHE* 3.9 18.8 - - + -
205A ILE* 3.5 32.8 - - + +
206A VAL* 5.1 2.2 - - - +
209A TYR* 3.8 26.7 - - + -
212A ILE* 2.9 45.4 - - + +
214A THR* 4.1 11.2 - - - +
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Residues in contact with ALA 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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146A GLU* 2.7 21.4 + - + +
147A GLN* 3.4 10.8 - - - +
148A THR 3.1 0.2 - - - -
149A LEU* 1.3 70.8 - - - +
151A ASP* 1.3 67.7 + - - +
153A ARG* 3.3 4.2 + - - +
154A THR* 3.1 25.8 + - - -
209A TYR* 3.6 22.6 - - - +
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Residues in contact with ASP 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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99A TRP* 3.8 24.9 + - + +
102A ALA* 4.2 19.9 + - - +
147A GLN* 3.0 31.9 + - - +
148A THR* 3.0 11.6 + - - +
150A ALA* 1.3 77.8 - - - +
152A ILE* 1.3 58.6 + - - +
154A THR* 3.4 7.5 + - - -
155A ALA* 3.0 27.9 + - - +
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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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99A TRP* 3.6 35.0 - - + -
148A THR* 3.0 22.6 + - + +
149A LEU* 3.5 18.6 - - + +
151A ASP* 1.3 73.9 - - - +
153A ARG* 1.3 55.9 + - - +
155A ALA* 3.0 6.3 + - - -
156A ASN* 2.7 57.6 + - - +
162A TYR* 3.6 16.4 - - + +
164A GLY* 3.5 35.2 - - - +
212A ILE* 3.6 12.3 - - + -
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Residues in contact with ARG 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 16.4 + - - +
150A ALA* 3.6 5.6 - - - +
151A ASP 3.3 0.2 - - - -
152A ILE* 1.3 76.0 - - - +
154A THR* 1.3 64.3 + - - +
156A ASN* 3.3 6.5 + - - +
157A LYS* 3.2 22.2 + - - +
208A GLU* 3.1 38.2 + - - -
209A TYR* 3.3 32.6 + - + -
211A ASP* 2.7 42.6 + - - +
212A ILE* 3.5 6.5 - - + +
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Residues in contact with THR 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 ALA 3.1 12.1 + - - -
151A ASP* 3.6 10.5 - - - -
153A ARG* 1.3 79.6 - - - +
155A ALA* 1.3 62.2 + - - +
157A LYS* 3.4 13.5 + - - +
158A ASN* 3.2 22.9 + - - +
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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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99A TRP* 3.6 28.5 - - + -
151A ASP 3.0 17.4 + - - +
152A ILE 3.6 3.6 - - - +
154A THR* 1.3 76.9 - - - +
156A ASN* 1.3 58.4 + - - +
158A ASN* 2.9 25.9 + - - +
160A GLY* 2.9 14.3 + - - -
162A TYR* 3.9 13.7 - - + -
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Residues in contact with ASN 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 ILE* 2.7 30.6 + - - +
153A ARG* 3.7 6.5 - - - +
155A ALA* 1.3 71.8 - - - +
157A LYS* 1.3 60.9 + - - +
158A ASN 3.1 0.7 + - - -
159A GLY* 3.7 2.6 + - - -
160A GLY* 3.1 30.4 + - - +
161A ASN* 4.6 2.0 - - - +
162A TYR* 2.9 47.6 + - - +
211A ASP 4.8 6.5 + - - -
212A ILE* 4.5 10.1 - - - +
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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 ARG 3.2 10.6 + - - +
154A THR* 3.6 13.2 - - - +
155A ALA 3.1 1.2 - - - -
156A ASN* 1.3 77.6 - - - +
158A ASN* 1.3 65.6 + - - +
159A GLY 3.5 3.3 + - - -
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Residues in contact with ASN 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 THR* 3.2 27.5 + - - +
155A ALA* 2.9 9.2 + - - +
157A LYS* 1.3 86.8 - - - +
159A GLY* 1.3 56.2 + - - +
160A GLY* 3.0 8.5 + - - -
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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