Contacts of the helix formed by residues 149 - 164 (chain A) in PDB entry 1KRQ
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 ASN 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A HIS 3.4 0.2 + - - -
148A GLY* 1.3 78.1 + - - -
150A GLY* 1.3 63.4 + - - +
151A LEU* 3.5 2.0 - - - -
152A TYR* 3.2 19.3 + - + +
153A LEU* 3.0 37.0 + - + +
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Residues in contact with GLY 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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144A ILE* 3.6 14.6 - - - +
145A GLY 3.2 25.4 - - - -
146A GLU 4.3 1.5 + - - -
147A HIS 3.1 12.1 + - - -
148A GLY 3.2 1.8 + - - -
149A ASN* 1.3 74.9 - - - +
151A LEU* 1.3 52.7 + - - +
153A LEU* 3.1 4.0 + - - -
154A ALA* 2.7 36.8 + - - +
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Residues in contact with LEU 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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36A LEU* 4.7 19.1 - - + +
82A SER* 6.3 1.1 - - - -
83A LEU* 3.8 36.9 - - + +
141A ILE* 6.1 1.1 - - + -
145A GLY 4.1 2.2 + - - -
146A GLU* 4.4 21.2 + - + +
149A ASN 3.5 0.6 - - - -
150A GLY* 1.3 71.8 - - - +
152A TYR* 1.3 57.9 + - - +
154A ALA* 3.3 3.6 + - + +
155A ASP* 2.9 31.9 + - - +
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Residues in contact with TYR 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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149A ASN* 3.2 20.3 + - + +
150A GLY 3.1 0.6 - - - -
151A LEU* 1.3 78.0 - - - +
153A LEU* 1.3 80.9 + - + +
155A ASP* 3.1 7.4 + - + +
156A GLN* 2.9 61.8 + - + +
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Residues in contact with LEU 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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144A ILE* 4.3 20.0 - - + +
149A ASN* 3.0 28.3 + - + +
150A GLY* 3.7 5.2 - - - +
152A TYR* 1.3 93.5 - - + +
154A ALA* 1.3 63.3 + - - +
156A GLN* 3.3 7.8 + - + +
157A TYR* 3.0 23.0 + - - +
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Residues in contact with ALA 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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83A LEU* 3.8 19.3 - - + -
141A ILE* 4.6 17.9 - - + -
144A ILE* 3.9 21.5 - - + +
145A GLY 5.7 0.4 - - - +
150A GLY 2.7 22.8 + - - +
151A LEU* 3.6 4.9 - - + +
153A LEU* 1.3 74.0 - - - +
155A ASP* 1.3 62.2 + - - +
157A TYR* 3.1 13.9 + - - +
158A ILE* 3.1 20.0 + - - +
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Residues in contact with ASP 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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35A SER 4.2 2.5 - - - +
36A LEU* 3.3 30.9 - - + +
37A ASP* 3.6 10.2 + - - +
38A GLY* 2.9 22.0 + - - -
39A ALA* 2.8 28.8 + - - +
83A LEU* 4.5 3.6 - - + +
151A LEU 2.9 17.7 + - - +
152A TYR* 3.6 6.5 - - + +
154A ALA* 1.3 77.1 - - - +
156A GLN* 1.3 67.1 + - - +
158A ILE* 3.5 6.9 + - - +
159A LYS* 3.0 25.5 + - - +
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Residues in contact with GLN 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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37A ASP* 5.5 3.8 + - - -
38A GLY* 5.6 0.2 - - - -
152A TYR* 2.9 57.4 + - + +
153A LEU* 3.8 8.5 - - + +
154A ALA 3.2 0.2 - - - -
155A ASP* 1.3 85.8 + - - +
157A TYR* 1.3 66.6 + - - +
159A LYS* 3.3 31.9 + - - +
160A ASN* 3.1 31.1 + - - +
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Residues in contact with TYR 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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136A GLY 5.2 2.8 + - - -
137A ILE* 4.3 8.0 - - + +
140A LYS* 3.4 53.0 - - + +
141A ILE* 6.4 1.1 - - + -
144A ILE* 4.8 5.4 - - + -
153A LEU 3.0 13.1 + - - +
154A ALA* 3.1 11.4 + - - +
156A GLN* 1.3 78.0 - - - +
158A ILE* 1.3 69.5 + - + +
160A ASN* 3.2 20.6 + - + +
161A ILE* 3.2 45.5 + - + +
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Residues in contact with ILE 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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39A ALA* 3.8 15.5 - - + +
42A PHE* 3.6 33.6 - - + -
83A LEU* 4.3 9.4 - - + -
87A PHE* 3.7 29.4 - - + -
137A ILE* 3.8 25.8 - - + -
141A ILE* 4.2 12.6 - - + -
154A ALA 3.1 16.3 + - - +
155A ASP* 3.8 7.6 - - - +
157A TYR* 1.3 82.4 - - + +
159A LYS* 1.3 65.0 + - - +
161A ILE* 3.2 8.5 + - - +
162A ALA* 3.1 21.0 + - - +
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Residues in contact with LYS 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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37A ASP* 4.5 14.3 + - - +
38A GLY* 3.9 22.4 - - - +
41A ALA* 6.1 3.1 - - + -
155A ASP 3.0 18.7 + - - +
156A GLN* 3.5 33.4 + - - +
157A TYR 3.2 0.2 - - - -
158A ILE* 1.3 77.6 - - - +
160A ASN* 1.3 63.1 + - - +
162A ALA* 3.3 7.0 + - + +
163A LEU* 3.2 44.0 + - + +
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Residues in contact with ASN 160 (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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156A GLN* 3.1 26.9 + - - +
157A TYR* 3.5 12.3 - - + +
158A ILE 3.2 0.2 - - - -
159A LYS* 1.3 78.4 - - - +
161A ILE* 1.3 62.4 + - + +
163A LEU* 3.1 17.2 + - - +
164A SER* 3.0 25.0 + - - -
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Residues in contact with ILE 161 (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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42A PHE* 3.7 22.4 - - + -
133A LEU* 4.1 17.7 - - + -
137A ILE* 3.2 22.2 - - + -
157A TYR* 3.2 51.7 + - + +
158A ILE* 3.2 9.4 + - - +
160A ASN* 1.3 75.5 - - + +
162A ALA* 1.3 62.0 + - - +
164A SER* 3.0 20.4 + - - +
165A ARG* 3.3 17.0 - - - +
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Residues in contact with ALA 162 (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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38A GLY 5.0 0.7 - - - +
41A ALA* 4.7 7.0 - - + -
42A PHE* 4.0 36.3 - - + +
45A ALA* 5.8 4.0 - - + -
158A ILE 3.1 12.8 + - - +
159A LYS* 3.6 12.1 - - + +
160A ASN 3.2 0.2 - - - -
161A ILE* 1.3 76.0 - - - +
163A LEU* 1.3 66.6 + - + +
165A ARG* 3.4 22.6 + - - +
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Residues in contact with LEU 163 (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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159A LYS* 3.3 33.7 - - + +
160A ASN* 3.1 18.5 + - - +
162A ALA* 1.3 76.1 - - + +
164A SER* 1.3 52.4 + - - +
165A ARG* 2.7 20.5 + - - -
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Residues in contact with SER 164 (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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160A ASN 3.0 12.7 + - - -
161A ILE* 3.0 19.6 + - - +
162A ALA 3.4 0.2 - - - -
163A LEU* 1.3 73.0 - - - +
165A ARG* 1.3 59.7 + - - +
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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
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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