Contacts of the helix formed by residues 141 - 158 (chain B) in PDB entry 1QK0
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 LYS 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B TYR* 4.5 21.2 + - - -
134B MET* 5.6 1.1 - - + -
135B TRP 3.5 19.0 + - - +
136B LEU* 3.9 22.1 - - + +
137B ASP* 2.7 30.1 + - - +
138B THR* 3.0 23.1 + - - +
139B LEU 3.0 1.0 - - - -
140B ASP* 1.3 83.0 - - + +
142B THR* 1.3 64.3 + - - +
143B PRO* 3.3 1.8 - - - -
144B LEU* 3.0 38.2 + - + +
145B MET 3.2 8.5 + - - -
2D GLC 4.0 10.3 + - - -
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Residues in contact with THR 142 (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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136B LEU* 5.1 3.6 - - + -
138B THR 4.9 1.8 - - - +
139B LEU* 2.7 33.9 + - + +
141B LYS* 1.3 78.9 - - - +
143B PRO* 1.3 74.3 - - - +
145B MET* 3.0 20.5 + - - +
146B GLU* 3.1 16.6 + - - +
198B TYR* 5.0 4.3 - - + -
201B THR* 3.7 27.8 - - + +
202B ILE* 4.3 20.4 - - + -
205B ILE* 3.6 15.6 - - + +
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Residues in contact with PRO 143 (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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139B LEU 3.9 0.4 - - - +
140B ASP* 3.0 23.8 - - - +
141B LYS 3.4 0.4 - - - -
142B THR* 1.3 101.0 - - - +
144B LEU* 1.3 55.2 + - - +
146B GLU* 3.4 19.5 + - - +
147B GLN* 3.0 27.9 + - - +
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Residues in contact with LEU 144 (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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103B TYR* 3.4 40.6 - - + +
134B MET* 3.1 33.0 - - + -
140B ASP 4.8 0.8 + - - +
141B LYS* 3.0 31.3 + - + +
143B PRO* 1.3 78.1 - - - +
145B MET* 1.3 63.7 + - - +
147B GLN* 3.4 24.6 + - - +
148B THR* 2.8 33.7 + - - +
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Residues in contact with MET 145 (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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134B MET* 4.3 1.7 - - - -
136B LEU* 3.9 31.4 - - + -
141B LYS 3.2 5.0 + - - +
142B THR* 3.0 11.3 + - - +
144B LEU* 1.3 77.0 - - - +
146B GLU* 1.3 62.8 + - - +
148B THR* 3.2 3.1 + - - -
149B LEU* 2.9 35.0 + - + +
166B PHE* 3.7 49.6 - - + -
202B ILE* 4.0 19.3 - - + -
205B ILE* 4.0 18.6 - - + -
206B VAL* 4.0 26.7 - - + -
214B THR* 4.4 4.5 - - + -
216B LEU* 4.6 2.2 - - + -
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Residues in contact with GLU 146 (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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142B THR 3.1 11.6 + - - +
143B PRO* 3.4 22.4 - - - +
144B LEU 3.2 0.2 - - - -
145B MET* 1.3 74.9 - - - +
147B GLN* 1.3 53.6 + - - +
149B LEU* 2.9 8.9 + - - +
150B ALA* 2.7 35.4 + - - +
205B ILE* 3.6 33.8 - - + +
209B TYR* 4.0 10.4 + - + +
900B CO 2.6 29.8 + - - +
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Residues in contact with GLN 147 (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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102B ALA* 5.3 9.1 - - - +
143B PRO 3.0 12.6 + - - +
144B LEU* 3.6 25.7 - - - +
146B GLU* 1.3 78.8 - - - +
148B THR* 1.3 62.4 + - - +
150B ALA* 3.5 8.0 + - - +
151B ASP* 3.1 41.2 + - - +
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Residues in contact with THR 148 (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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99B TRP* 3.8 27.4 - - + +
101B ASN* 4.3 10.8 - - + +
102B ALA 5.8 0.2 + - - -
134B MET* 3.2 20.9 - - + +
144B LEU* 2.8 24.6 + - - +
145B MET 3.4 4.7 - - - -
147B GLN* 1.3 75.2 - - - +
149B LEU* 1.3 60.0 + - - +
151B ASP* 3.1 10.9 + - - +
152B ILE* 3.0 34.2 + - + +
164B GLY* 5.8 0.2 - - - -
165B GLN 6.1 0.2 - - - +
166B PHE* 4.0 23.6 - - + -
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Residues in contact with LEU 149 (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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145B MET* 2.9 29.5 + - + +
146B GLU 3.5 6.3 - - - +
148B THR* 1.3 72.4 - - - +
150B ALA* 1.3 61.0 + - - +
152B ILE* 3.2 9.5 + - + -
153B ARG* 2.8 25.5 + - - +
164B GLY* 4.7 1.3 - - - -
166B PHE* 4.0 21.5 - - + -
205B ILE* 3.5 33.7 - - + +
206B VAL* 5.2 1.8 - - - +
209B TYR* 3.7 28.3 - - + -
212B ILE* 3.2 39.3 - - + +
214B THR* 4.3 11.0 - - - +
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Residues in contact with ALA 150 (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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146B GLU 2.7 16.9 + - - +
147B GLN* 3.6 10.5 - - - +
149B LEU* 1.3 72.4 - - - +
151B ASP* 1.3 66.0 + - - +
153B ARG* 3.1 4.8 + - - +
154B THR* 3.0 27.8 + - - -
209B TYR* 3.5 23.9 - - - +
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Residues in contact with ASP 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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99B TRP* 3.9 23.4 + - + +
102B ALA* 4.4 18.2 + - - +
147B GLN* 3.1 25.6 + - - +
148B THR* 3.3 12.4 - - - +
150B ALA* 1.3 81.6 - - - +
152B ILE* 1.3 56.3 + - - +
154B THR* 3.6 5.8 + - - +
155B ALA* 3.0 28.4 + - - +
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Residues in contact with ILE 152 (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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99B TRP* 3.5 43.3 - - + -
148B THR* 3.0 22.8 + - + +
149B LEU* 3.6 13.7 - - + +
150B ALA 3.1 0.4 - - - -
151B ASP* 1.3 74.4 - - - +
153B ARG* 1.3 66.3 + - - +
155B ALA* 3.2 5.8 + - - +
156B ASN* 2.8 30.9 + - - +
162B TYR* 3.4 35.0 - - + +
164B GLY* 3.7 25.8 - - - +
212B ILE* 3.9 10.5 - - + -
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Residues in contact with ARG 153 (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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149B LEU 2.8 14.0 + - - +
150B ALA* 3.5 8.5 - - - +
152B ILE* 1.3 74.8 - - - +
154B THR* 1.3 64.1 + - - +
156B ASN* 3.2 9.5 + - - +
157B LYS* 3.1 30.4 + - + +
208B GLU* 2.8 39.6 + - - +
209B TYR* 3.3 31.5 + - + -
211B ASP* 2.8 55.3 + - - +
212B ILE* 3.6 9.8 - - + +
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Residues in contact with THR 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 ALA 3.0 16.6 + - - -
151B ASP* 3.7 6.5 - - - +
153B ARG* 1.3 77.4 - - - +
155B ALA* 1.3 64.2 + - - +
157B LYS* 2.9 37.1 + - - +
158B ASN* 3.5 6.1 + - - +
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Residues in contact with ALA 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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99B TRP* 3.6 28.9 - - + -
151B ASP 3.0 18.3 + - - +
152B ILE 3.2 4.2 + - - +
154B THR* 1.3 79.1 - - - +
156B ASN* 1.3 59.6 + - - +
157B LYS 3.4 0.9 + - - -
158B ASN* 3.6 8.5 + - - +
160B GLY* 2.8 24.0 + - - -
162B TYR* 3.9 12.1 - - + -
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Residues in contact with ASN 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 ILE* 2.8 27.8 + - - +
153B ARG* 3.6 6.4 - - - +
154B THR 3.1 0.2 - - - -
155B ALA* 1.3 74.3 - - - +
157B LYS* 1.3 65.4 + - - +
159B GLY* 3.8 4.3 + - - -
160B GLY 2.9 18.3 - - - +
161B ASN* 2.9 11.1 + - - +
162B TYR* 2.6 47.7 + - - -
211B ASP 5.2 4.2 + - - -
212B ILE* 4.4 11.3 - - - +
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Residues in contact with LYS 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 ARG* 3.1 24.5 + - + +
154B THR* 2.9 23.8 + - - +
156B ASN* 1.3 79.9 - - - +
158B ASN* 1.3 59.8 + - + +
159B GLY 3.2 5.1 + - - -
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Residues in contact with ASN 158 (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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154B THR 3.5 6.8 + - - +
155B ALA* 3.6 5.2 + - - +
156B ASN 3.4 0.2 - - - -
157B LYS* 1.3 78.6 + - + +
159B GLY* 1.3 53.7 + - - +
160B GLY 3.3 7.2 + - - -
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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