Contacts of the helix formed by residues 145 - 159 (chain A) in PDB entry 1K27
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 CYS 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A PRO 4.3 0.4 + - - -
144A PHE* 1.3 70.1 - - - +
146A PRO* 1.3 73.0 - - - +
147A LYS* 3.9 4.7 - - - -
148A THR* 3.5 27.7 - - - +
149A ARG* 3.1 24.3 + - - +
211A CYS* 3.5 42.2 - - + -
212A TYR 2.8 22.5 + - - +
263A TRP* 3.9 7.6 - - - -
266A THR* 4.6 6.1 - - - -
270A LEU* 5.3 3.4 - - + -
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Residues in contact with PRO 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLU* 5.6 10.8 - - + +
144A PHE 3.1 12.5 - - - +
145A CYS* 1.3 83.6 - - + +
147A LYS* 1.3 87.5 + - + +
149A ARG* 3.3 17.3 + - + +
150A GLU* 2.9 29.5 + - - +
266A THR* 6.3 0.2 - - + -
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Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A CYS* 3.4 1.5 - - - -
146A PRO* 1.3 101.5 - - + +
148A THR* 1.3 63.2 + - - +
150A GLU* 3.3 16.3 + - - +
151A VAL* 3.2 25.6 + - - +
262A GLU 5.9 1.8 - - - +
263A TRP* 3.5 24.5 - - + -
266A THR* 3.7 37.9 + - - +
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Residues in contact with THR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A HIS* 3.6 12.7 - - + -
90A ILE* 4.1 26.2 - - + -
145A CYS* 3.4 20.9 + - - +
146A PRO 3.3 0.4 - - - -
147A LYS* 1.3 74.7 - - - +
149A ARG* 1.3 66.8 + - - +
151A VAL* 3.2 7.0 + - - +
152A LEU* 3.0 25.1 + - + +
211A CYS* 4.3 2.3 + - - +
213A ALA* 3.4 26.2 - - + -
258A ILE* 4.2 8.7 - - + +
263A TRP* 3.4 20.1 - - - -
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Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ILE* 3.0 28.6 + - + +
110A ILE 3.0 24.3 + - - +
111A ASP* 3.5 23.6 - - - +
142A GLU* 5.9 0.6 + - - -
144A PHE* 3.5 21.3 - - + -
145A CYS 3.1 21.5 + - - +
146A PRO* 3.6 13.5 + - - +
147A LYS 3.3 0.2 - - - -
148A THR* 1.3 75.5 - - - +
150A GLU* 1.3 58.1 + - - +
152A LEU* 3.2 6.0 + - - +
153A ILE* 2.9 42.6 + - - +
165A SER 2.8 29.9 + - - -
166A LYS* 4.0 0.8 - - - +
213A ALA* 4.2 14.8 - - + -
214A SER 5.5 0.2 - - - +
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PRO 2.9 17.0 + - - +
147A LYS* 3.4 16.0 - - - +
148A THR 3.2 0.2 - - - -
149A ARG* 1.3 76.7 - - - +
151A VAL* 1.3 59.6 + - + +
153A ILE* 3.4 9.7 + - - +
154A GLU* 3.0 30.2 + - + +
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LYS 3.3 15.5 - - - +
148A THR* 3.2 9.5 + - - +
150A GLU* 1.3 75.9 - - + +
152A LEU* 1.3 57.9 + - - +
154A GLU* 3.4 4.9 + - - +
155A THR* 2.7 45.1 + - - +
254A THR* 3.6 22.0 - - + +
257A GLN* 3.9 24.7 - - + +
258A ILE* 4.5 11.2 - - + -
261A THR* 5.7 7.2 - - + -
263A TRP* 5.2 6.1 - - + -
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ILE* 4.4 9.0 - - + -
109A ILE* 4.0 20.0 - - + -
148A THR* 3.0 22.4 + - + +
149A ARG* 3.5 11.2 - - - +
151A VAL* 1.3 77.6 - - - +
153A ILE* 1.3 57.8 + - - +
155A THR 3.4 0.2 + - - -
156A ALA* 3.0 30.8 + - - +
213A ALA* 3.9 24.9 - - + -
214A SER 5.0 2.2 - - - +
215A ILE* 3.9 29.4 - - + -
250A LEU* 3.6 22.1 - - + +
251A LEU* 5.5 0.4 - - + -
254A THR* 3.5 31.6 - - + +
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Residues in contact with ILE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ILE* 3.8 20.9 - - + -
149A ARG* 2.9 34.3 + - + +
150A GLU* 3.7 7.9 - - - +
152A LEU* 1.3 76.4 - - - +
154A GLU* 1.3 63.6 + - - +
156A ALA* 3.4 7.0 + - - +
157A LYS* 3.2 22.2 + - + +
163A CYS* 4.8 4.5 - - - +
164A HIS 5.0 0.2 - - - +
165A SER* 3.4 51.1 - - - +
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Residues in contact with GLU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLU* 3.0 19.2 + - + +
151A VAL* 3.9 5.6 - - - +
153A ILE* 1.3 78.8 - - - +
155A THR* 1.3 58.3 + - - +
157A LYS* 3.3 23.4 + - - +
158A LYS* 3.0 68.6 + - - +
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Residues in contact with THR 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A VAL* 2.7 33.9 + - - +
152A LEU 3.8 2.5 - - - -
154A GLU* 1.3 76.8 - - - +
156A ALA* 1.3 64.6 + - - +
158A LYS* 3.2 12.0 + - + +
159A LEU* 3.0 24.2 + - + +
250A LEU* 3.7 8.7 - - + -
253A THR* 3.5 38.3 + - + -
254A THR* 3.5 26.6 + - - +
257A GLN* 4.9 4.9 - - - +
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ILE* 5.5 0.7 - - + -
152A LEU 3.0 18.1 + - - +
153A ILE 3.7 3.4 - - - +
154A GLU 3.3 0.2 - - - -
155A THR* 1.3 76.0 - - - +
157A LYS* 1.3 61.1 + - - +
159A LEU* 3.2 6.1 + - - +
160A GLY 3.1 4.0 + - - -
161A LEU* 3.0 38.9 + - + -
163A CYS* 3.7 35.2 - - + -
250A LEU* 3.7 16.7 - - + +
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Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ILE* 3.2 13.5 + - + +
154A GLU* 3.4 29.3 + - - +
155A THR 3.1 0.4 - - - -
156A ALA* 1.3 75.3 - - - +
158A LYS* 1.3 60.4 + - - +
160A GLY* 2.9 20.7 + - - -
161A LEU 5.0 2.7 - - - +
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Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLU* 3.0 49.1 + - - +
155A THR* 3.2 16.1 + - + +
157A LYS* 1.3 76.5 - - + +
159A LEU* 1.3 62.6 + - + +
160A GLY 3.3 1.1 + - - -
253A THR* 6.1 4.0 - - + -
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A THR* 3.0 26.0 + - + +
156A ALA 3.6 4.7 - - - +
157A LYS 3.0 0.4 - - - -
158A LYS* 1.3 81.3 - - + +
160A GLY* 1.3 62.9 + - - +
161A LEU* 3.3 25.9 + - + +
249A SER* 3.9 17.9 - - - +
250A LEU* 3.9 31.9 - - + +
253A THR* 4.0 18.8 - - + +
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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