Contacts of the helix formed by residues 142 - 158 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ALA 4.7 0.7 - - - +
141B CYS* 1.3 75.7 - - - +
143B ARG* 1.3 64.8 + - - +
144B ALA* 4.0 0.2 - - - +
145B GLU* 2.9 35.1 + - - +
146B ARG* 3.0 23.7 + - - +
204B ARG* 4.3 4.5 - - - +
5C ARG 5.3 3.4 - - - +
7C ARG* 3.9 26.4 - - + +
14F GLU* 2.8 29.6 + - - +
49F ASP* 6.1 2.2 - - - +
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR* 1.3 74.7 - - - +
144B ALA* 1.3 59.1 + - - +
146B ARG* 3.3 14.0 + - - +
147B ARG* 2.9 55.1 + - - +
204B ARG* 5.2 0.2 - - - +
205B ASP* 3.0 41.8 + - + +
208B ASP* 5.1 4.3 - - - +
14F GLU* 2.7 42.7 + - - +
16F PRO* 3.8 33.7 - - - +
34F TYR* 3.6 2.4 + - - -
49F ASP* 3.3 32.2 + - - +
52F ILE* 4.5 6.5 - - - +
53F GLN* 4.0 12.5 + - - -
56F VAL* 4.0 17.1 - - - +
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR* 4.0 0.4 - - - +
143B ARG* 1.3 78.7 - - - +
145B GLU* 1.3 61.6 + - - +
147B ARG* 3.2 7.1 + - - +
148B GLU* 2.9 22.5 + - - +
9F TYR* 3.9 34.8 + - + -
13F ALA* 3.6 19.9 + - + +
14F GLU* 2.9 32.8 + - + +
151G ARG* 5.9 0.3 + - - -
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B THR* 5.2 1.4 - - - +
134B GLY 4.7 1.9 - - - +
135B LEU* 3.9 24.5 - - + +
136B SER* 2.9 34.2 + - - +
141B CYS* 3.3 12.1 - - + -
142B THR* 2.9 34.5 + - - +
144B ALA* 1.3 78.8 - - - +
146B ARG* 1.3 61.7 + - - +
148B GLU* 3.1 5.2 + - - +
149B VAL* 3.1 26.6 + - - +
7C ARG* 2.6 44.0 + - + +
9F TYR* 4.8 6.9 - - + -
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Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PRO* 4.9 2.4 + - - +
141B CYS* 3.9 23.3 - - - +
142B THR 3.0 16.1 + - - +
143B ARG* 3.7 15.9 + - - +
145B GLU* 1.3 76.0 - - - +
147B ARG* 1.3 62.5 + - - +
149B VAL* 3.3 6.9 + - - +
150B GLU* 3.1 17.8 + - - +
201B GLY 5.4 0.4 + - - -
202B MET 6.2 0.4 - - - -
204B ARG* 3.5 37.6 + - - +
205B ASP* 2.9 40.6 + - - +
208B ASP* 3.4 24.4 + - - +
209B ALA* 4.0 4.7 - - + -
210B ARG* 3.4 30.1 - - - +
225B ASN* 3.2 35.3 + - - +
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ARG* 2.9 38.2 + - - +
144B ALA* 3.6 5.4 - - - +
146B ARG* 1.3 73.2 - - - +
148B GLU* 1.3 59.3 + - - +
150B GLU* 3.4 6.7 + - - +
151B ARG* 3.0 42.8 + - - +
208B ASP* 2.8 42.5 + - - +
209B ALA* 4.2 10.8 - - + -
12F SER 4.6 1.8 + - - -
13F ALA 2.9 27.6 + - - -
14F GLU 4.0 3.4 - - - -
15F TYR 3.0 29.1 + - - -
17F ASP 3.9 7.3 - - - +
151G ARG* 5.9 1.1 - - - +
262G ARG* 3.8 23.3 + - - +
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 4.0 10.5 - - + -
144B ALA 2.9 8.9 + - - +
145B GLU 3.4 8.7 - - - +
147B ARG* 1.3 73.4 - - - +
149B VAL* 1.3 65.4 + - - +
151B ARG* 3.3 5.7 + - - +
152B VAL* 3.0 38.4 + - - +
264B TRP* 3.9 29.0 - - + -
9C TYR* 4.6 4.5 - - - -
10C PRO* 4.6 0.4 - - + -
13C ALA* 5.0 8.0 - - - +
9F TYR* 2.7 34.3 + - - +
151G ARG* 3.0 38.7 + - - +
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 4.5 5.4 - - + -
135B LEU* 3.6 25.4 - - + -
136B SER 5.1 0.4 - - - +
145B GLU 3.1 15.6 + - - +
146B ARG* 3.5 9.0 - - - +
147B ARG 3.3 0.2 - - - -
148B GLU* 1.3 77.0 - - - +
150B GLU* 1.3 62.3 + - - +
152B VAL* 3.8 4.1 - - - +
153B VAL* 3.1 35.5 + - + +
224B VAL* 4.7 0.9 - - + -
225B ASN* 3.5 22.0 - - - +
229B HIS* 3.7 49.6 - - + +
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ARG 3.1 10.8 + - - +
147B ARG* 3.8 10.8 - - - +
148B GLU 3.2 0.2 - - - -
149B VAL* 1.3 80.6 - - - +
151B ARG* 1.3 65.5 + - - +
153B VAL* 4.9 0.2 - - - -
154B VAL* 3.0 30.8 + - + +
168B TYR* 2.7 30.0 + - - +
170B ARG* 3.3 41.7 + - - +
209B ALA* 3.8 37.2 - - + +
210B ARG 4.3 0.7 - - - +
224B VAL* 4.2 11.0 - - + -
225B ASN* 4.0 1.1 - - - +
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Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ARG* 3.0 30.3 + - - +
148B GLU* 3.8 5.8 - - - +
150B GLU* 1.3 78.6 - - - +
152B VAL* 1.3 62.2 + - + +
154B VAL* 4.1 3.0 - - - +
155B ASP* 3.2 34.5 + - - +
170B ARG* 5.1 13.9 - - - +
148G GLU* 5.2 0.4 + - - -
151G ARG* 3.3 69.7 + - - +
155G ASP* 3.2 31.1 + - - -
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 4.6 15.5 - - + -
135B LEU* 5.4 0.4 - - + -
148B GLU* 3.0 27.9 + - - +
149B VAL* 3.8 5.4 - - - +
150B GLU 3.2 0.2 - - - -
151B ARG* 1.3 76.3 - - + +
153B VAL* 1.3 64.9 + - - +
155B ASP* 3.6 4.6 + - - +
156B ALA* 3.3 21.0 + - - +
259B ILE* 4.4 15.9 - - + +
264B TRP* 3.5 59.5 - - + +
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 4.6 15.7 - - + -
149B VAL* 3.1 27.5 + - + +
150B GLU* 4.1 2.2 - - - +
152B VAL* 1.3 73.5 - - - +
154B VAL* 1.3 62.4 + - - +
156B ALA* 3.0 8.0 + - + +
157B LEU* 2.9 56.3 + - + +
222B ILE* 4.8 2.9 - - + -
224B VAL* 4.1 21.1 - - + -
230B THR* 3.8 28.3 - - + -
255B VAL* 6.1 3.4 - - + -
259B ILE* 5.4 2.5 - - + -
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLU* 3.0 26.7 + - + +
151B ARG* 4.2 3.8 - - - +
153B VAL* 1.3 80.2 - - + +
155B ASP* 1.3 66.0 + - - +
157B LEU* 4.0 6.8 - - + +
158B SER* 3.2 24.6 + - - -
168B TYR* 3.6 58.1 - - + -
170B ARG* 5.4 6.7 - - - +
224B VAL* 5.5 0.7 - - + -
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Residues in contact with ASP 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ARG* 3.2 22.6 + - - +
152B VAL* 4.0 5.5 - - - +
153B VAL 3.2 0.4 - - - -
154B VAL* 1.3 82.6 - - - +
156B ALA* 1.3 61.1 + - - +
158B SER* 2.9 21.1 + - - -
159B GLY* 3.7 3.8 + - - -
262B ARG* 5.8 9.4 + - + +
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B VAL 3.3 5.9 + - - +
153B VAL* 3.0 9.7 + - - +
155B ASP* 1.3 77.4 - - - +
157B LEU* 1.3 60.3 + - + +
159B GLY* 2.9 17.7 + - - -
160B LEU* 3.8 0.6 + - - +
255B VAL* 4.5 11.0 - - + +
258B LEU* 3.2 37.5 - - + +
259B ILE* 3.5 32.8 - - + +
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B VAL* 2.9 40.2 + - + +
154B VAL* 4.0 7.4 - - - +
156B ALA* 1.3 76.6 - - - +
158B SER* 1.3 57.4 + - - +
159B GLY 3.0 4.7 + - - -
160B LEU* 3.0 32.3 + - + +
166B GLY 5.4 2.1 + - - -
168B TYR* 5.1 4.7 - - + -
213B TRP* 3.4 54.2 + - + +
222B ILE* 3.7 30.7 - - + -
224B VAL* 5.2 1.1 - - + -
255B VAL* 3.9 23.1 - - + -
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Residues in contact with SER 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 3.2 16.2 + - - -
155B ASP* 2.9 20.1 + - - -
157B LEU* 1.3 75.7 - - - +
159B GLY* 1.3 57.2 + - - +
160B LEU 3.3 4.5 + - - +
213B 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
------------------------------------------------------------
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