Contacts of the helix formed by residues 151 - 163 (chain A) in PDB entry 1G24
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 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A THR* 4.0 15.4 + - - +
143A LEU* 2.9 14.5 + - - +
144A LEU 5.3 0.2 - - - +
145A ASN* 3.1 31.0 + - - +
150A ILE* 1.3 71.7 - - - +
152A LYS* 1.3 63.2 + - - +
153A THR* 2.6 44.8 + - - -
154A ALA* 3.0 8.7 + - + +
155A PHE* 3.2 19.4 + - - +
235A LYS* 4.7 0.2 - - - +
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Residues in contact with LYS 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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150A ILE 3.2 1.4 + - - -
151A ASN* 1.3 72.1 + - - +
153A THR* 1.3 60.3 + - - +
155A PHE* 3.3 11.2 + - + +
156A GLU* 2.9 34.9 + - + +
230A LEU* 4.3 20.2 - - + -
235A LYS* 3.7 31.7 - - - +
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Residues in contact with THR 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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151A ASN* 2.6 21.9 + - - -
152A LYS* 1.3 70.1 - - - +
154A ALA* 1.3 62.1 + - - +
156A GLU* 3.2 9.6 + - + +
157A LYS* 3.1 49.0 + - + +
1153B THR* 3.8 23.7 + - + +
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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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139A PHE* 3.1 16.5 - - + -
142A THR* 3.4 36.8 - - + +
143A LEU* 3.7 19.3 - - + -
151A ASN* 3.0 13.9 + - + +
153A THR* 1.3 76.2 - - - +
155A PHE* 1.3 56.7 + - - +
157A LYS* 3.1 14.6 + - + +
158A ALA* 3.0 23.7 + - - +
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Residues in contact with PHE 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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143A LEU* 4.5 4.4 - - + +
150A ILE* 5.4 1.8 - - + -
151A ASN 3.2 11.8 + - - +
152A LYS* 3.4 13.9 - - + +
154A ALA* 1.3 80.4 - - - +
156A GLU* 1.3 66.0 + - - +
158A ALA* 3.1 18.3 + - + +
159A LYS* 3.2 50.8 + - + +
228A MET* 3.7 8.5 - - + -
229A ARG* 3.6 26.2 - - - -
230A LEU* 3.5 39.5 - - + -
237A ILE* 3.6 42.8 - - + -
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Residues in contact with GLU 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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152A LYS* 2.9 19.8 + - + +
153A THR* 3.2 12.5 + - + +
155A PHE* 1.3 80.9 - - - +
157A LYS* 1.3 61.9 + - + +
159A LYS* 3.1 37.8 + - - +
160A ALA* 3.4 20.6 + - - +
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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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138A GLU* 5.9 1.1 - - - +
139A PHE* 3.9 15.6 - - + -
142A THR* 5.1 13.0 - - + +
153A THR* 3.1 38.1 - - + +
154A ALA* 3.1 13.2 + - - +
156A GLU* 1.3 74.8 - - + +
158A ALA* 1.3 63.9 + - - +
160A ALA* 3.6 6.2 + - - +
161A LYS* 3.2 23.9 + - - +
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Residues in contact with ALA 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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135A LEU* 4.0 28.7 - - + -
139A PHE* 3.8 10.5 - - + -
143A LEU* 5.2 0.2 - - + -
154A ALA 3.0 12.0 + - - +
155A PHE* 3.1 16.8 + - + +
157A LYS* 1.3 78.4 - - - +
159A LYS* 1.3 56.7 + - - +
161A LYS* 3.4 2.8 + - - -
162A PHE* 3.0 37.0 + - - +
228A MET* 3.9 14.8 - - + +
237A ILE* 5.0 0.7 - - + -
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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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155A PHE* 3.2 46.9 + - + +
156A GLU* 3.1 38.7 + - - +
157A LYS 3.3 0.4 - - - -
158A ALA* 1.3 72.3 - - - +
160A ALA* 1.3 64.7 + - - +
161A LYS 3.0 1.9 + - - -
163A LEU* 2.6 50.0 + - + +
228A MET* 3.6 34.8 + - + -
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Residues in contact with ALA 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 GLU 3.4 11.8 + - - +
157A LYS* 4.0 6.1 - - - +
158A ALA 3.5 0.2 - - - -
159A LYS* 1.3 79.3 - - - +
161A LYS* 1.3 59.1 + - - +
163A LEU 5.2 0.7 - - - +
165A LYS* 3.4 20.1 + - - -
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Residues in contact with LYS 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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135A LEU 3.5 11.4 + - - +
136A GLY* 5.1 2.9 - - - -
138A GLU* 3.2 27.6 - - - +
139A PHE* 4.1 10.8 - - + -
157A LYS 3.2 17.4 + - - +
158A ALA 3.6 4.9 - - - +
159A LYS 3.0 0.6 - - - -
160A ALA* 1.3 79.8 - - - +
162A PHE* 1.3 102.1 + - + +
165A LYS* 3.6 19.9 + - - +
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Residues in contact with PHE 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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134A TYR* 6.2 0.2 - + - -
135A LEU* 3.2 47.6 - - + -
158A ALA* 3.0 26.1 + - - +
161A LYS* 1.3 119.4 - - + +
163A LEU* 1.3 67.4 + - - +
164A ASN 3.3 0.3 + - - -
165A LYS* 3.3 20.7 + - + +
167A ARG* 3.3 44.4 - - + -
225A ILE* 3.5 30.9 - - + +
228A MET* 4.1 6.1 - - + -
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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* 2.6 45.9 + - + +
160A ALA 5.2 0.5 - - - +
162A PHE* 1.3 73.8 - - - +
164A ASN* 1.3 94.2 + - - +
165A LYS* 3.4 11.8 + - - +
225A ILE* 4.0 5.4 - - + +
226A ASP 3.6 30.5 - - - +
227A ASP* 4.0 9.6 - - - +
228A MET* 4.0 13.9 - - + +
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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