Contacts of the helix formed by residues 142 - 158 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ARG 5.2 3.8 - - - +
6A ARG* 6.2 0.2 - - - -
7A ARG* 3.6 37.4 - - + +
140C ALA 4.7 0.7 - - - +
141C CYS* 1.3 77.2 - - - +
143C ARG* 1.3 64.2 + - - +
144C ALA* 4.0 0.2 - - - +
145C GLU* 2.9 30.2 + - - +
146C ARG* 2.9 22.9 + - - +
204C ARG* 4.3 3.8 - - - +
14G GLU* 2.7 28.7 + - - +
49G ASP* 6.0 2.5 - - - +
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Residues in contact with ARG 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C THR* 1.3 75.5 - - - +
144C ALA* 1.3 58.1 + - - +
146C ARG* 3.3 13.5 + - - +
147C ARG* 2.8 53.0 + - - +
205C ASP* 3.0 41.3 + - + +
208C ASP* 4.9 3.8 - - - +
14G GLU* 2.6 44.6 + - - +
16G PRO* 3.8 33.2 - - - +
34G TYR* 3.5 4.4 + - - -
49G ASP* 3.3 32.0 + - - +
52G ILE* 4.5 6.3 - - - +
53G GLN* 4.1 12.9 + - - -
56G VAL* 4.1 15.9 - - - +
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Residues in contact with ALA 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C THR* 4.0 0.4 - - - +
143C ARG* 1.3 73.7 - - - +
145C GLU* 1.3 58.4 + - - +
147C ARG* 3.2 6.3 + - - +
148C GLU* 2.9 27.9 + - - +
9G TYR* 3.7 36.7 + - + -
13G ALA* 3.6 18.8 + - + +
14G GLU* 2.8 34.4 + - + +
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Residues in contact with GLU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 2.7 41.9 + - + -
10A PRO* 6.1 0.4 - - + -
44C THR* 5.2 1.9 - - - +
134C GLY 4.7 1.9 - - - +
135C LEU* 3.9 23.7 - - + +
136C SER* 2.9 35.2 + - - +
141C CYS* 3.3 13.6 - - + -
142C THR* 2.9 35.1 + - - +
144C ALA* 1.3 79.5 - - - +
146C ARG* 1.3 62.2 + - - +
148C GLU* 3.1 5.6 + - - +
149C VAL* 3.1 26.1 + - - +
9G TYR* 4.7 6.7 - - + -
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Residues in contact with ARG 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C PRO* 4.9 1.8 + - - +
141C CYS* 3.9 24.8 - - - +
142C THR 2.9 15.0 + - - +
143C ARG* 3.7 15.9 - - - +
145C GLU* 1.3 75.4 - - - +
147C ARG* 1.3 62.1 + - - +
149C VAL* 3.2 7.4 + - - +
150C GLU* 3.2 17.5 + - - +
201C GLY 5.4 0.2 + - - -
202C MET 6.2 0.4 - - - -
204C ARG* 3.4 37.2 + - - +
205C ASP* 2.9 39.0 + - - +
208C ASP* 3.5 25.1 + - - -
209C ALA* 4.0 5.4 - - + -
210C ARG* 3.3 29.9 - - - +
225C ASN* 3.3 35.3 + - + +
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Residues in contact with ARG 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ARG* 2.8 31.6 + - - +
144C ALA* 3.5 5.6 - - - +
146C ARG* 1.3 78.9 - - - +
148C GLU* 1.3 55.6 + - - +
150C GLU* 3.3 7.4 + - - +
151C ARG* 2.9 38.1 + - - +
208C ASP* 2.7 42.3 + - - +
209C ALA* 4.2 9.6 - - + -
151E ARG* 5.1 2.7 - - - +
262E ARG* 5.2 17.5 - - - +
12G SER 4.4 2.6 + - - -
13G ALA* 2.9 30.5 + - - +
14G GLU* 4.0 3.6 - - - +
15G TYR 3.0 29.5 + - - +
17G ASP* 4.0 10.3 - - - +
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Residues in contact with GLU 148 (chain C).
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* 4.6 3.1 - - - -
10A PRO* 4.9 0.2 - - + -
13A ALA* 5.2 6.3 - - - +
135C LEU* 3.8 12.3 - - + -
144C ALA 2.9 8.6 + - - +
145C GLU 3.1 9.4 + - - +
147C ARG* 1.3 74.3 - - - +
149C VAL* 1.3 65.0 + - - +
151C ARG* 3.4 5.4 - - - +
152C VAL* 3.0 32.4 + - - +
264C TRP* 3.9 32.6 - - + -
151E ARG* 3.2 39.2 + - - +
9G TYR* 2.6 35.9 + - - +
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Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ILE* 4.6 4.3 - - + -
135C LEU* 3.7 20.9 - - + -
136C SER 5.1 1.1 - - - +
145C GLU 3.1 18.2 + - - +
146C ARG* 3.2 10.1 + - - +
148C GLU* 1.3 76.7 - - - +
150C GLU* 1.3 64.2 + - - +
152C VAL* 3.8 2.7 - - - +
153C VAL* 2.9 34.1 + - + +
224C VAL* 4.6 1.1 - - + -
225C ASN* 3.3 22.7 - - - +
229C HIS* 3.7 53.8 - - + +
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Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C ARG 3.2 6.8 + - - +
147C ARG* 3.7 11.0 - - - +
149C VAL* 1.3 77.8 - - - +
151C ARG* 1.3 58.3 + - - +
153C VAL* 3.1 1.6 + - - -
154C VAL* 2.7 45.9 + - + +
168C TYR* 2.6 31.0 + - - +
170C ARG* 3.3 39.7 + - - +
209C ALA* 3.7 39.4 - - + +
210C ARG 4.4 0.2 - - - +
224C VAL* 4.1 11.9 - - + -
225C ASN* 4.1 0.4 - - - +
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Residues in contact with ARG 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ARG* 2.9 25.0 + - - +
148C GLU* 3.4 9.4 - - - +
150C GLU* 1.3 79.4 + - - +
152C VAL* 1.3 62.6 + - + +
154C VAL* 4.1 3.5 - - - +
155C ASP* 3.2 34.4 + - - +
170C ARG* 5.9 7.8 - - - +
148E GLU* 4.2 6.9 + - - -
151E ARG* 2.8 70.6 - - - +
152E VAL* 5.3 3.2 - - - +
155E ASP* 3.1 29.3 + - - -
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Residues in contact with VAL 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ILE* 4.5 17.0 - - + -
135C LEU* 5.2 0.2 - - + -
148C GLU* 3.0 27.0 + - - +
149C VAL* 3.8 4.5 - - - +
151C ARG* 1.3 76.5 - - + +
153C VAL* 1.3 63.7 + - - +
155C ASP* 3.4 8.0 + - - +
156C ALA* 3.3 19.6 + - - +
259C ILE* 4.3 16.9 - - + +
264C TRP* 3.4 61.5 - - + +
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Residues in contact with VAL 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ILE* 4.3 20.2 - - + -
149C VAL* 2.9 27.3 + - + +
150C GLU* 3.9 2.0 - - - +
152C VAL* 1.3 74.0 - - + +
154C VAL* 1.3 68.9 + - - +
156C ALA* 3.1 7.5 + - + +
157C LEU* 3.0 45.4 + - + +
222C ILE* 4.9 2.9 - - + -
224C VAL* 4.1 21.5 - - + -
230C THR* 3.8 27.1 - - + -
255C VAL* 6.2 2.7 - - + -
259C ILE* 5.3 2.7 - - + -
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Residues in contact with VAL 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C GLU* 2.7 31.5 + - + +
151C ARG* 4.3 2.7 - - - +
153C VAL* 1.3 74.9 - - + +
155C ASP* 1.3 64.4 + - - +
157C LEU* 4.2 7.4 - - + +
158C SER* 3.3 23.0 + - - -
168C TYR* 3.5 58.3 - - + -
170C ARG* 5.4 6.3 - - - +
224C VAL* 5.5 0.7 - - + -
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Residues in contact with ASP 155 (chain C).
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* 3.2 26.7 + - - +
152C VAL* 3.7 6.5 - - - +
153C VAL 3.1 1.2 - - - -
154C VAL* 1.3 78.9 - - - +
156C ALA* 1.3 68.2 + - - +
158C SER* 3.0 19.1 + - - -
159C GLY* 3.7 3.1 + - - -
262C ARG* 5.5 14.9 + - + +
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Residues in contact with ALA 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C VAL 3.3 4.0 + - - +
153C VAL* 3.1 8.6 + - + +
155C ASP* 1.3 81.4 - - - +
157C LEU* 1.3 59.0 + - + +
159C GLY* 2.8 17.7 + - - -
160C LEU* 5.0 0.4 - - - -
255C VAL* 4.4 11.2 - - + +
258C LEU* 3.2 39.9 - - + +
259C ILE* 3.5 32.8 - - + +
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C VAL* 3.0 39.3 + - + +
154C VAL* 4.2 7.2 - - + +
156C ALA* 1.3 76.1 - - + +
158C SER* 1.3 58.7 + - - +
159C GLY 3.0 4.2 + - - -
160C LEU* 3.1 32.4 + - + +
166C GLY 5.4 1.7 + - - -
168C TYR* 5.1 4.7 - - + -
213C TRP* 3.4 55.4 + - + +
222C ILE* 3.7 29.4 - - + -
224C VAL* 5.2 1.1 - - + -
255C VAL* 4.0 24.0 - - + -
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Residues in contact with SER 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C VAL* 3.3 15.6 + - - -
155C ASP* 3.0 15.9 + - - -
156C ALA 3.2 0.2 - - - -
157C LEU* 1.3 77.0 - - - +
159C GLY* 1.3 58.2 + - - +
160C LEU 3.4 4.7 - - - +
213C 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