Contacts of the helix formed by residues 142 - 158 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ARG 5.1 3.8 - - - +
7B ARG* 3.6 37.9 - - + +
140D ALA 4.7 0.7 - - - +
141D CYS* 1.3 76.8 - - - +
143D ARG* 1.3 65.3 + - - +
144D ALA* 4.0 0.3 - - - +
145D GLU* 2.9 26.2 + - - +
146D ARG* 3.0 22.1 + - - +
204D ARG* 4.2 4.9 - - - +
14H GLU* 2.7 29.4 + - - +
49H ASP* 6.0 2.0 - - - +
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Residues in contact with ARG 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D THR* 1.3 74.2 - - - +
144D ALA* 1.3 58.4 + - - +
146D ARG* 3.3 11.3 + - - +
147D ARG* 2.9 55.8 + - - +
205D ASP* 3.0 42.5 + - + +
208D ASP* 5.1 3.1 - - - +
14H GLU* 2.5 44.5 + - - +
16H PRO* 3.7 34.1 - - - +
34H TYR* 3.5 4.6 + - - -
49H ASP* 3.3 32.6 + - - +
52H ILE* 4.5 6.5 - - - +
53H GLN* 4.2 10.9 + - - -
56H VAL* 4.2 15.9 - - - +
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Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D THR* 4.0 0.2 - - - +
143D ARG* 1.3 76.7 - - - +
145D GLU* 1.3 58.2 + - - +
147D ARG* 3.3 6.8 + - - +
148D GLU* 2.9 27.9 + - - +
9H TYR* 3.7 36.7 + - + -
13H ALA* 3.6 21.0 + - + +
14H GLU* 2.9 28.8 + - - +
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Residues in contact with GLU 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ARG* 2.9 39.4 + - + -
8B LEU 6.1 0.2 - - - +
10B PRO* 6.1 0.7 - - + -
44D THR* 5.2 1.9 - - - +
134D GLY 4.8 1.9 - - - +
135D LEU* 3.9 19.4 - - + +
136D SER* 2.8 34.7 + - - +
141D CYS* 3.2 14.1 - - + -
142D THR* 2.9 35.2 + - - +
143D ARG 3.2 0.6 - - - -
144D ALA* 1.3 78.6 - - - +
146D ARG* 1.3 61.1 + - - +
148D GLU* 3.1 9.7 + - - +
149D VAL* 3.1 25.7 + - - +
9H TYR* 4.6 7.2 - - + -
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Residues in contact with ARG 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D PRO* 4.9 1.6 + - - +
141D CYS* 3.9 23.3 - - - +
142D THR 3.0 16.3 + - - +
143D ARG* 3.7 17.5 - - - +
145D GLU* 1.3 75.8 - - - +
147D ARG* 1.3 63.3 + - - +
149D VAL* 3.2 13.5 + - - +
150D GLU* 3.2 2.3 + - - +
201D GLY 5.4 0.4 + - - -
202D MET 6.2 0.6 - - - -
204D ARG* 3.4 36.8 + - - +
205D ASP* 2.9 39.4 + - - +
208D ASP* 3.4 25.7 + - - +
209D ALA* 4.0 4.0 - - + -
210D ARG* 3.3 29.6 - - - +
225D ASN* 3.2 41.1 + - - +
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Residues in contact with ARG 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ARG* 2.9 31.9 + - - +
144D ALA* 3.6 5.2 - - - +
146D ARG* 1.3 76.9 - - - +
148D GLU* 1.3 60.7 + - - +
150D GLU* 3.5 8.2 + - - +
151D ARG* 3.2 33.5 + - - +
208D ASP* 2.7 43.0 + - - +
209D ALA* 4.0 11.2 - - + -
262F ARG* 4.8 19.9 + - - +
12H SER 4.6 2.8 + - - -
13H ALA 2.9 29.5 + - - -
14H GLU 3.9 3.4 - - - -
15H TYR 2.9 29.5 + - - +
17H ASP* 3.9 11.3 - - - +
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Residues in contact with GLU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 4.6 6.8 - - - -
10B PRO* 4.9 0.2 - - + -
13B ALA* 5.0 5.2 - - - +
135D LEU* 3.8 21.3 - - + -
144D ALA 2.9 13.1 + - - +
145D GLU 3.2 10.8 - - - +
146D ARG 3.0 0.4 - - - -
147D ARG* 1.3 76.4 - - - +
149D VAL* 1.3 66.2 + - - +
151D ARG* 3.3 21.2 + - - +
152D VAL* 3.0 33.3 + - - +
264D TRP* 4.1 17.3 - - + -
148F GLU* 5.2 1.2 - - - +
151F ARG* 4.7 6.1 + - - -
9H TYR* 2.6 36.8 + - - +
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Residues in contact with VAL 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ILE* 4.6 5.4 - - + -
135D LEU* 3.7 24.9 - - + +
136D SER 5.2 0.9 - - - +
145D GLU 3.1 14.2 + - - +
146D ARG* 3.5 9.4 - - - +
148D GLU* 1.3 76.4 - - - +
150D GLU* 1.3 63.5 + - - +
152D VAL* 3.8 3.1 - - - +
153D VAL* 2.9 34.4 + - + +
224D VAL* 4.5 1.6 - - + -
225D ASN* 3.4 22.7 - - - +
229D HIS* 3.7 52.7 - - + +
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Residues in contact with GLU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ARG 3.2 7.4 + - - +
147D ARG* 3.8 12.3 - - - +
148D GLU 3.2 0.4 - - - -
149D VAL* 1.3 80.1 - - - +
151D ARG* 1.3 57.9 + - - +
153D VAL* 4.0 0.2 - - - +
154D VAL* 2.7 43.0 + - + +
168D TYR* 2.7 29.5 + - - +
170D ARG* 3.2 41.9 + - - +
209D ALA* 3.7 39.6 - - + +
210D ARG 4.4 0.3 - - - +
224D VAL* 4.1 11.4 - - + -
225D ASN* 4.0 1.1 - - - +
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Residues in contact with ARG 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ARG* 3.2 23.6 + - - +
148D GLU* 3.6 24.2 - - - +
150D GLU* 1.3 78.3 + - - +
152D VAL* 1.3 61.4 + - - +
154D VAL* 4.5 4.5 - - - -
155D ASP* 3.0 31.7 + - - +
170D ARG* 5.6 10.0 - - - +
148F GLU* 4.2 7.7 + - - -
151F ARG* 3.0 66.4 + - - +
152F VAL* 6.1 1.4 - - - +
155F ASP* 3.2 33.9 + - - -
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Residues in contact with VAL 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ILE* 4.6 15.7 - - + -
135D LEU* 5.3 0.2 - - + -
148D GLU* 3.0 25.5 + - - +
149D VAL* 3.8 4.9 - - - +
151D ARG* 1.3 73.6 - - + +
153D VAL* 1.3 70.1 + - - +
155D ASP* 3.3 7.0 + - - +
156D ALA* 3.2 19.8 + - - +
259D ILE* 4.4 16.2 - - + +
264D TRP* 3.3 62.4 - - + +
151F ARG* 6.0 2.0 - - - +
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Residues in contact with VAL 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ILE* 4.4 18.2 - - + -
149D VAL* 2.9 27.9 + - + +
150D GLU* 4.0 1.8 - - - +
152D VAL* 1.3 78.7 - - + +
154D VAL* 1.3 63.4 + - + +
156D ALA* 3.0 9.8 + - + +
157D LEU* 3.0 44.9 + - + +
222D ILE* 4.9 3.1 - - + -
224D VAL* 4.0 22.0 - - + -
230D THR* 3.6 27.1 - - + -
255D VAL* 6.3 2.2 - - + -
259D ILE* 5.3 2.5 - - + -
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Residues in contact with VAL 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D GLU* 2.7 31.7 + - + +
151D ARG* 4.2 4.5 - - - +
153D VAL* 1.3 76.7 - - + +
155D ASP* 1.3 66.4 + - - +
157D LEU* 3.5 6.6 + - + +
158D SER* 3.3 24.3 + - - -
168D TYR* 3.7 56.1 - - + -
170D ARG* 5.3 7.6 - - - +
224D VAL* 5.6 0.7 - - + -
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Residues in contact with ASP 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ARG* 3.0 27.7 + - - +
152D VAL* 3.7 6.1 - - - +
153D VAL 3.2 0.2 - - - -
154D VAL* 1.3 80.4 - - - +
156D ALA* 1.3 62.2 + - - +
158D SER* 3.0 19.9 + - - -
159D GLY* 3.9 2.9 + - - -
262D ARG* 5.3 15.7 + - + +
151F ARG* 3.5 25.2 + - - -
170F ARG* 5.7 2.1 + - - -
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Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D VAL 3.2 4.1 + - - +
153D VAL* 3.0 10.0 + - + +
155D ASP* 1.3 77.6 - - - +
157D LEU* 1.3 60.9 + - + +
159D GLY* 2.8 19.2 + - - -
255D VAL* 4.5 11.0 - - + +
258D LEU* 3.3 37.3 - - + +
259D ILE* 3.5 33.2 - - + +
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D VAL* 3.0 39.2 + - + +
154D VAL* 3.5 6.9 + - + +
155D ASP 3.5 0.2 - - - -
156D ALA* 1.3 75.6 - - - +
158D SER* 1.3 58.9 + - - +
159D GLY 2.9 5.1 + - - -
160D LEU* 3.0 39.8 + - + +
166D GLY 5.4 1.6 + - - -
168D TYR* 5.1 4.9 - - + -
213D TRP* 3.4 56.3 + - + +
222D ILE* 3.7 28.7 - - + -
224D VAL* 5.3 0.7 - - + -
255D VAL* 4.0 16.8 - - + -
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Residues in contact with SER 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D VAL* 3.3 14.4 + - - -
155D ASP* 3.0 17.7 + - - -
156D ALA 3.1 0.6 + - - -
157D LEU* 1.3 77.4 - - - +
159D GLY* 1.3 57.6 + - - +
160D LEU 3.4 5.0 - - - +
213D TRP* 5.7 0.9 - - - +
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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