Contacts of the helix formed by residues 142 - 158 (chain A) in PDB entry 1QK1
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 142 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ALA 4.7 0.9 - - - +
141A CYS* 1.3 77.3 - - - +
143A ARG* 1.3 64.7 + - - +
144A ALA* 4.0 0.2 - - - +
145A GLU* 2.9 36.2 + - - +
146A ARG* 3.0 23.0 + - - +
204A ARG* 4.3 3.6 - - - +
5D ARG 5.2 3.6 - - - +
7D ARG* 4.0 24.9 - - + +
14E GLU* 2.8 32.6 + - - +
49E ASP* 5.9 4.0 - - - +
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Residues in contact with ARG 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A THR* 1.3 75.0 - - - +
144A ALA* 1.3 57.6 + - - +
146A ARG* 3.3 13.0 + - - +
147A ARG* 2.9 53.9 + - - +
205A ASP* 2.9 41.2 + - + +
208A ASP* 5.0 4.8 - - - +
14E GLU* 2.8 33.7 + - - +
16E PRO* 3.6 38.0 - - - +
17E ASP 5.0 0.4 - - - +
34E TYR* 3.9 1.0 + - - -
49E ASP* 3.5 29.7 + - - +
52E ILE* 4.4 6.7 - - - +
53E GLN* 4.0 12.3 + - - -
56E VAL* 3.7 18.9 - - - +
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Residues in contact with ALA 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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142A THR* 4.0 0.2 - - - +
143A ARG* 1.3 77.6 - - - +
145A GLU* 1.3 56.4 - - - +
147A ARG* 3.2 7.7 + - - +
148A GLU* 2.9 27.4 + - - +
151A ARG* 5.9 0.3 + - - -
9E TYR* 4.2 28.8 + - + -
13E ALA* 3.3 26.2 + - + +
14E GLU* 2.9 29.8 + - + +
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Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 5.2 1.6 - - - +
134A GLY 4.7 2.1 - - - +
135A LEU* 3.9 23.2 - - + +
136A SER* 2.9 34.0 + - - +
141A CYS* 3.2 14.1 - - + -
142A THR* 2.9 36.6 + - - +
144A ALA* 1.3 79.8 - - - +
146A ARG* 1.3 62.5 + - - +
148A GLU* 3.1 12.7 + - - +
149A VAL* 3.1 18.4 + - - +
7D ARG* 2.9 40.5 + - + +
9E TYR* 4.8 8.1 - - + -
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Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO* 4.9 2.2 + - - +
141A CYS* 3.9 23.1 + - - +
142A THR 3.0 15.9 + - - +
143A ARG* 3.7 16.6 - - - +
145A GLU* 1.3 75.8 - - - +
147A ARG* 1.3 62.8 + - - +
149A VAL* 3.3 8.0 + - - +
150A GLU* 3.2 8.8 + - - +
201A GLY 5.4 0.4 + - - -
202A MET 6.3 0.2 - - - -
204A ARG* 3.4 38.2 + - - +
205A ASP* 2.9 39.0 + - - +
208A ASP* 3.4 25.4 + - - -
209A ALA* 3.9 4.5 - - + -
210A ARG* 3.3 29.8 - - - +
225A ASN* 3.2 41.9 + - - +
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Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ARG* 2.9 29.8 + - - +
144A ALA* 3.6 5.6 - - - +
146A ARG* 1.3 76.0 - - - +
148A GLU* 1.3 64.4 + - - +
150A GLU* 3.4 8.6 + - - +
151A ARG* 3.0 33.7 + - + +
208A ASP* 3.1 39.5 + - - +
209A ALA* 4.1 9.9 - - + -
12E SER 4.7 1.8 + - - -
13E ALA 3.0 27.4 + - - -
14E GLU 4.1 2.6 - - - -
15E TYR 2.8 30.1 + - - -
16E PRO* 4.0 2.2 - - - +
17E ASP 3.7 10.5 - - - +
262H ARG* 4.1 21.6 + - - +
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Residues in contact with GLU 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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135A LEU* 3.9 15.5 - - + -
144A ALA 2.9 11.3 + - - +
145A GLU 3.1 9.6 + - - +
147A ARG* 1.3 76.7 - - - +
149A VAL* 1.3 62.9 + - - +
151A ARG* 2.7 45.2 + - - +
152A VAL* 2.9 30.5 + - - +
264A TRP* 3.8 34.3 - - + -
9D TYR* 4.6 3.3 - - - -
13D ALA* 5.0 7.1 - - - +
9E TYR* 2.8 30.2 + - - +
151H ARG* 5.4 1.7 + - - -
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Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 4.5 5.4 - - + -
135A LEU* 3.7 21.3 - - + +
136A SER 5.1 1.3 - - - +
145A GLU 3.4 14.6 - - - +
146A ARG* 3.4 9.4 - - - +
147A ARG 3.3 0.4 - - - -
148A GLU* 1.3 76.9 - - - +
150A GLU* 1.3 60.8 + - - +
152A VAL* 3.6 3.6 + - - +
153A VAL* 3.0 40.0 + - + +
224A VAL* 4.7 1.6 - - + -
225A ASN* 3.4 21.1 - - - +
229A HIS* 3.8 50.5 - - + +
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Residues in contact with GLU 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 ARG 3.2 6.6 + - - +
147A ARG* 3.7 13.0 - - - +
148A GLU 3.2 0.6 - - - -
149A VAL* 1.3 76.6 - - - +
151A ARG* 1.3 61.5 + - - +
153A VAL* 4.1 0.4 - - - +
154A VAL* 2.8 44.4 + - + +
168A TYR* 2.8 28.0 + - - +
170A ARG* 3.3 42.6 + - - +
209A ALA* 3.9 37.2 - - - +
210A ARG 4.4 0.2 - - - +
224A VAL* 4.2 11.2 - - + -
225A ASN* 4.1 1.5 - - - +
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Residues in contact with ARG 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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144A ALA 5.9 0.2 + - - -
147A ARG* 3.0 24.7 + - + +
148A GLU* 2.7 45.4 + - - +
150A GLU* 1.3 78.3 - - + +
152A VAL* 1.3 64.6 + - + +
154A VAL* 4.0 3.3 - - - +
155A ASP* 3.0 32.0 + - - +
170A ARG* 6.0 3.6 - - - +
9D TYR* 4.8 3.8 - - - -
9E TYR* 4.8 2.0 - - - -
148H GLU* 2.8 39.2 + - - +
151H ARG* 2.7 68.9 - - - +
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 4.6 15.7 - - + -
148A GLU* 2.9 28.8 + - - +
149A VAL* 4.0 4.5 - - - +
151A ARG* 1.3 74.4 - - + +
153A VAL* 1.3 63.5 + - - +
155A ASP* 4.0 4.3 - - - +
156A ALA* 3.3 19.9 + - - +
259A ILE* 4.3 17.3 - - + -
264A TRP* 3.2 63.5 - - + +
151H ARG* 6.0 0.9 - - - +
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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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132A ILE* 4.4 17.3 - - + -
149A VAL* 3.0 28.7 + - + +
150A GLU* 4.1 1.8 - - - +
152A VAL* 1.3 75.8 - - + +
154A VAL* 1.3 59.3 + - - +
156A ALA* 3.1 6.7 + - - +
157A LEU* 2.9 50.8 + - + +
222A ILE* 4.9 2.2 - - + -
224A VAL* 4.2 21.5 - - + -
230A THR* 3.8 27.1 - - + -
255A VAL* 6.1 3.8 - - + -
259A ILE* 5.3 2.9 - - + -
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Residues in contact with VAL 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 GLU* 2.8 31.1 + - + +
151A ARG* 4.1 3.6 - - - +
153A VAL* 1.3 76.2 - - + +
155A ASP* 1.3 67.9 + - - +
157A LEU* 4.1 7.1 - - + +
158A SER* 3.2 24.2 + - - -
168A TYR* 3.6 56.3 - - + -
170A ARG* 5.3 7.9 - - - +
224A VAL* 5.6 0.4 - - + -
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Residues in contact with ASP 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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151A ARG* 3.0 21.4 + - - +
152A VAL* 4.0 4.4 - - - +
153A VAL 3.3 0.2 - - - -
154A VAL* 1.3 81.7 - - - +
156A ALA* 1.3 60.5 + - - +
158A SER* 2.7 22.6 + - - -
159A GLY* 3.7 4.3 + - - -
262A ARG* 5.7 11.0 + - + +
151H ARG* 3.2 30.5 + - - -
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Residues in contact with ALA 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 VAL 3.3 6.4 + - - +
153A VAL* 3.1 9.3 + - + +
155A ASP* 1.3 77.6 - - - +
157A LEU* 1.3 66.2 + - + +
159A GLY 2.9 11.3 + - - -
160A LEU* 5.1 0.2 - - - -
255A VAL* 4.6 8.7 - - + +
258A LEU* 3.2 40.0 - - + +
259A ILE* 3.6 31.9 - - + +
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Residues in contact with LEU 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* 2.9 40.0 + - + +
154A VAL* 4.1 7.0 - - - +
156A ALA* 1.3 76.5 - - + +
158A SER* 1.3 58.6 + - - +
159A GLY 3.0 4.6 + - - -
160A LEU* 3.1 39.1 + - + +
166A GLY 5.4 1.6 + - - -
168A TYR* 5.1 4.5 - - + -
213A TRP* 3.4 56.3 + - + +
222A ILE* 3.7 30.3 - - + -
224A VAL* 5.2 1.1 - - + -
255A VAL* 4.0 16.4 - - + -
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Residues in contact with SER 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 VAL* 3.2 15.1 + - - -
155A ASP* 2.7 23.2 + - - -
157A LEU* 1.3 76.2 - - - +
159A GLY* 1.3 58.9 + - - +
160A LEU 3.3 5.0 + - - +
213A TRP* 5.7 0.7 - - - +
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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