Contacts of the helix formed by residues 142 - 158 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 2.7 29.2 + - - +
49A ASP* 6.0 2.5 - - - +
140E ALA 4.6 0.9 - - - +
141E CYS* 1.3 77.0 - - - +
143E ARG* 1.3 64.8 + - - +
145E GLU* 2.9 26.9 + - - +
146E ARG* 2.9 23.7 + - - +
204E ARG* 4.3 3.6 - - - +
5G ARG 5.1 5.4 - - - +
6G ARG* 6.2 0.2 - - - -
7G ARG* 3.4 38.5 - - + +
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Residues in contact with ARG 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 2.6 43.1 + - - +
16A PRO* 3.7 35.1 - - - +
34A TYR* 3.5 4.4 + - - -
49A ASP* 3.3 31.8 + - - +
52A ILE* 4.4 7.1 - - - +
53A GLN* 4.1 11.3 + - - -
56A VAL* 4.0 17.1 - - - +
142E THR* 1.3 75.9 - - - +
144E ALA* 1.3 58.3 + - - +
146E ARG* 3.3 12.9 + - - +
147E ARG* 2.9 53.5 + - - +
204E ARG* 5.2 0.2 - - - +
205E ASP* 3.0 41.6 + - + +
208E ASP* 4.9 4.2 - - - +
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Residues in contact with ALA 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.8 33.5 + - + -
13A ALA* 3.5 21.0 + - + +
14A GLU* 2.9 31.1 + - - +
142E THR* 3.9 0.2 - - - +
143E ARG* 1.3 75.6 - - - +
145E GLU* 1.3 62.3 + - - +
147E ARG* 3.3 6.4 + - - +
148E GLU* 3.0 23.9 + - - +
151E ARG* 5.8 0.2 + - - -
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Residues in contact with GLU 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 4.6 6.9 - - + -
44E THR* 5.2 1.9 - - - +
134E GLY 4.8 1.9 - - - +
135E LEU* 3.9 24.5 - - + +
136E SER* 2.9 34.7 + - - +
141E CYS* 3.2 9.6 - - + -
142E THR* 2.9 28.8 + - - +
144E ALA* 1.3 79.7 - - - +
146E ARG* 1.3 63.4 + - - +
148E GLU* 3.1 5.6 + - - +
149E VAL* 3.1 25.5 + - - +
7G ARG* 2.7 50.6 + - + -
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Residues in contact with ARG 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E PRO* 4.9 1.8 + - - +
141E CYS* 3.9 23.9 - - - +
142E THR 2.9 16.1 + - - +
143E ARG* 3.7 18.1 - - - +
145E GLU* 1.3 76.2 - - - +
147E ARG* 1.3 61.8 + - - +
149E VAL* 3.2 14.3 + - - +
150E GLU* 3.3 2.8 + - - +
201E GLY 5.4 0.2 + - - -
202E MET 6.2 0.4 - - - -
204E ARG* 3.5 36.7 + - - +
205E ASP* 2.9 40.0 + - - +
208E ASP* 3.4 25.9 + - - +
209E ALA* 4.0 3.8 - - + -
210E ARG* 3.3 29.4 - - - +
225E ASN* 3.2 42.6 + - + +
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Residues in contact with ARG 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER 4.6 2.4 + - - -
13A ALA* 3.0 27.1 + - - +
14A GLU 4.0 3.4 - - - -
15A TYR 2.9 29.3 + - - +
16A PRO* 4.1 1.8 - - - +
17A ASP* 3.8 12.7 - - - +
262C ARG* 5.0 18.5 + - - +
143E ARG* 2.9 29.4 + - - +
144E ALA* 3.6 5.4 - - - +
145E GLU 3.2 0.2 - - - -
146E ARG* 1.3 76.5 - - - +
148E GLU* 1.3 57.5 + - - +
150E GLU* 3.3 7.6 + - - +
151E ARG* 3.0 36.5 + - + +
208E ASP* 2.8 41.9 + - - +
209E ALA* 4.1 9.9 - - + -
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Residues in contact with GLU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 2.7 30.5 + - - +
151C ARG* 4.2 8.7 + - - -
135E LEU* 4.0 10.3 - - + -
144E ALA 3.0 12.4 + - - +
145E GLU 3.1 10.1 + - - +
147E ARG* 1.3 75.0 - - - +
149E VAL* 1.3 66.6 + - - +
151E ARG* 2.6 45.0 + - - +
152E VAL* 2.9 35.9 + - - +
264E TRP* 4.0 28.2 - - + -
9G TYR* 4.5 3.5 - - - -
10G PRO* 4.9 0.2 - - + -
13G ALA* 5.2 6.4 - - - +
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Residues in contact with VAL 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ILE* 4.6 5.4 - - + -
135E LEU* 3.7 24.7 - - + -
136E SER 5.2 0.9 - - - +
145E GLU 3.1 14.9 + - - +
146E ARG* 3.2 10.3 + - - +
148E GLU* 1.3 77.2 - - - +
150E GLU* 1.3 57.9 + - - +
152E VAL* 3.3 3.8 + - - +
153E VAL* 2.9 40.6 + - + +
224E VAL* 4.5 1.8 - - + -
225E ASN* 3.4 22.9 - - - +
229E HIS* 3.7 51.1 - - + +
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Residues in contact with GLU 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E ARG 3.3 7.6 + - - +
147E ARG* 3.3 13.4 + - - +
148E GLU 3.2 0.4 - - - -
149E VAL* 1.3 76.5 - - - +
151E ARG* 1.3 67.6 + - - +
153E VAL* 4.9 0.2 - - - -
154E VAL* 2.9 38.7 + - + +
168E TYR* 2.5 31.1 + - - +
170E ARG* 3.5 37.7 + - - +
209E ALA* 3.5 39.4 - - - +
210E ARG 4.1 0.2 - - - +
224E VAL* 4.3 10.8 - - + -
225E ASN* 4.2 1.1 - - - +
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Residues in contact with ARG 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 4.5 2.8 - - - -
147C ARG* 4.8 1.6 + - - +
148C GLU* 3.2 36.4 + - - +
151C ARG* 2.8 79.3 - - - +
144E ALA 5.8 0.4 + - - -
147E ARG* 3.0 21.4 + - + +
148E GLU* 2.6 45.2 + - - +
150E GLU* 1.3 75.8 - - + +
152E VAL* 1.3 63.5 + - - +
154E VAL* 4.2 2.6 - - - +
155E ASP* 3.1 31.9 + - - +
170E ARG* 6.1 4.3 - - - +
9G TYR* 4.5 3.6 - - - -
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Residues in contact with VAL 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ARG* 5.5 3.4 - - - +
132E ILE* 4.5 15.0 - - + -
135E LEU* 5.2 0.7 - - + -
148E GLU* 2.9 28.2 + - - +
149E VAL* 3.7 4.9 - - - +
151E ARG* 1.3 79.3 - - + +
153E VAL* 1.3 65.8 + - - +
155E ASP* 3.7 5.8 - - - +
156E ALA* 3.3 18.2 + - - +
259E ILE* 4.5 12.6 - - + +
264E TRP* 3.5 65.5 - - + +
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Residues in contact with VAL 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ILE* 4.3 19.5 - - + -
149E VAL* 2.9 29.7 + - + +
150E GLU* 4.1 2.0 - - - +
152E VAL* 1.3 72.5 - - - +
154E VAL* 1.3 57.1 + - - +
156E ALA* 2.8 27.9 + - - +
157E LEU* 2.9 36.5 + - + +
222E ILE* 5.0 2.2 - - + -
224E VAL* 4.2 20.4 - - + -
230E THR* 3.7 28.0 - - + -
255E VAL* 6.2 3.4 - - + -
259E ILE* 5.2 3.6 - - + -
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Residues in contact with VAL 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E GLU* 2.9 31.3 + - + +
151E ARG* 4.2 3.1 - - - +
153E VAL* 1.3 77.8 - - + +
155E ASP* 1.3 66.9 + - - +
157E LEU* 4.0 7.5 - - + +
158E SER* 3.2 24.8 + - - -
168E TYR* 3.7 56.1 - - + -
170E ARG* 5.4 6.3 - - - +
224E VAL* 5.5 0.9 - - + -
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Residues in contact with ASP 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ARG* 3.1 30.6 + - - -
151E ARG 3.1 23.4 + - - +
152E VAL* 3.7 5.7 - - - +
153E VAL 3.1 0.2 - - - -
154E VAL* 1.3 81.2 - - - +
156E ALA* 1.3 60.6 + - - +
158E SER* 3.1 18.8 + - - -
159E GLY* 3.9 4.2 + - - -
262E ARG* 5.8 11.2 + - + +
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Residues in contact with ALA 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E VAL 3.3 3.8 + - - +
153E VAL* 2.8 10.5 + - - +
155E ASP* 1.3 79.3 - - - +
157E LEU* 1.3 64.4 + - + +
159E GLY 3.1 9.9 + - - -
160E LEU* 3.8 1.0 + - - +
255E VAL* 4.5 10.5 - - + +
258E LEU* 3.1 40.8 - - + +
259E ILE* 3.5 33.0 - - + +
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Residues in contact with LEU 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E VAL* 2.9 38.0 + - + +
154E VAL* 4.0 8.1 - - - +
156E ALA* 1.3 71.3 - - - +
158E SER* 1.3 58.7 - - - +
159E GLY 3.0 9.8 + - - -
160E LEU* 3.1 31.6 + - + +
166E GLY 5.4 1.9 + - - -
168E TYR* 5.1 4.5 - - + -
213E TRP* 3.4 54.8 + - + +
222E ILE* 3.7 30.3 - - + -
224E VAL* 5.2 1.1 - - + -
255E VAL* 4.0 23.8 - - + -
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Residues in contact with SER 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E VAL* 3.2 15.5 + - - -
155E ASP* 3.1 16.6 + - - -
157E LEU* 1.3 76.4 - - - +
159E GLY* 1.3 58.9 + - - +
160E LEU 3.4 4.4 - - - +
213E 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