Contacts of the helix formed by residues 144 - 156 (chain A) in PDB entry 5DST
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 SER 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ALA* 3.2 21.9 - - - +
142A CYS 4.0 0.4 + - - -
143A SER* 1.3 71.2 + - - +
145A ILE* 1.3 63.7 + - - +
146A SER* 3.0 3.6 - - - -
147A ASP* 3.2 26.9 + - - +
148A TYR* 4.0 9.3 - - - -
166A LYS* 3.8 22.6 - - - +
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Residues in contact with ILE 145 (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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80A TYR 3.7 9.4 - - - +
81A ALA* 3.9 20.4 - - - +
83A PHE* 4.7 7.9 - - + -
86A HIS* 3.6 32.5 - - + +
121A GLY* 4.0 10.8 - - - -
122A THR* 4.2 13.0 - - - +
141A GLU* 3.6 28.9 - - + -
143A SER* 3.0 10.5 + - - -
144A SER* 1.3 80.2 + - - +
146A SER* 1.3 64.4 + - - +
148A TYR* 3.1 17.5 + - + +
149A SER* 3.0 17.8 + - - -
250B ILE* 4.4 22.4 - - + -
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Residues in contact with SER 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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121A GLY 4.6 0.2 - - - -
141A GLU* 4.0 20.8 + - - -
143A SER 2.6 22.3 + - - -
144A SER 3.8 0.2 - - - -
145A ILE* 1.3 78.5 - - - +
147A ASP* 1.3 61.0 + - - -
149A SER* 2.7 27.9 + - - -
150A GLU* 3.0 13.0 + - - +
164A ILE* 4.2 11.2 - - - -
166A LYS* 2.9 36.1 - - - +
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Residues in contact with ASP 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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144A SER* 3.2 19.1 + - - +
146A SER* 1.3 77.1 + - - +
148A TYR* 1.3 68.5 + - + +
150A GLU* 3.5 11.9 + - - +
151A LYS* 3.4 31.0 + - - +
166A LYS* 3.2 31.9 + - - +
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Residues in contact with TYR 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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81A ALA 5.4 4.9 - - - -
122A THR* 6.5 0.2 - - - -
144A SER* 4.0 15.7 - - - -
145A ILE* 3.1 20.9 + - + +
147A ASP* 1.3 80.1 - - + +
149A SER* 1.3 59.8 + - - +
151A LYS* 3.2 21.6 + - - +
152A ILE* 2.8 35.8 + - + +
249B CYS* 3.8 28.9 - - + -
250B ILE* 4.1 24.9 - - + -
253B VAL* 3.1 39.8 - - + +
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Residues in contact with SER 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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120A SER* 4.0 1.1 + - - -
121A GLY 3.3 18.4 + - - -
122A THR* 3.2 27.7 + - - +
123A GLY* 4.0 6.3 - - - -
145A ILE 3.0 6.4 + - - -
146A SER* 2.7 24.3 + - - -
148A TYR* 1.3 74.1 - - - +
150A GLU* 1.3 51.6 + - - +
152A ILE* 3.5 1.8 - - - +
153A ILE* 2.8 44.2 + - - +
164A ILE* 3.5 19.8 - - - +
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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 SER 3.0 14.5 + - - +
147A ASP* 3.7 13.2 - - - +
148A TYR 3.2 0.2 - - - -
149A SER* 1.3 71.7 - - - +
151A LYS* 1.3 66.6 + - + +
153A ILE* 3.3 8.2 + - - +
154A LYS* 2.9 25.5 + - - +
159A ASP* 5.7 0.5 - - - +
164A ILE* 3.9 34.5 + - + +
166A LYS* 6.2 0.8 - - - +
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Residues in contact with LYS 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 ASP* 3.4 16.7 + - - +
148A TYR* 3.2 27.8 + - + +
150A GLU* 1.3 78.9 - - + +
152A ILE* 1.3 57.8 + - - +
154A LYS* 3.5 6.6 + - - +
155A ALA* 3.0 29.5 + - - +
249B CYS* 4.0 26.0 - - + +
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Residues in contact with ILE 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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122A THR* 3.7 20.2 - - + +
127A MET* 3.9 21.1 - - + -
148A TYR* 2.8 30.6 + - + +
149A SER* 3.5 5.6 - - - +
151A LYS* 1.3 70.5 - - - +
153A ILE* 1.3 62.3 + - + +
155A ALA* 3.2 9.8 + - - +
156A ASN* 2.5 40.7 + - - +
246B ASP 3.6 15.9 - - - +
247B MET* 3.9 20.0 - - + -
249B CYS* 3.6 14.8 - - - -
250B ILE* 3.9 29.2 - - + -
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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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123A GLY* 4.8 9.0 - - - +
126A SER* 5.3 0.2 - - - -
127A MET* 4.1 25.1 - - + -
149A SER* 2.8 29.1 + - - +
150A GLU* 3.8 4.7 - - - +
152A ILE* 1.3 75.2 - - + +
154A LYS* 1.3 64.8 + - - +
156A ASN* 3.1 12.6 + - - +
157A HIS 3.3 0.2 + - - -
158A LEU* 3.3 45.8 + - + +
159A ASP* 3.6 9.4 - - + +
162A ILE* 3.7 32.1 - - + +
164A ILE* 3.8 23.3 - - + -
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Residues in contact with LYS 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 2.9 16.6 + - - +
151A LYS* 3.7 7.4 - - - +
153A ILE* 1.3 78.8 - - - +
155A ALA* 1.3 62.6 + - - +
157A HIS* 3.0 20.8 + - - -
159A ASP* 3.5 34.7 - - + +
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Residues in contact with ALA 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 LYS 3.0 17.6 + - - +
152A ILE* 3.2 8.7 + - - +
154A LYS* 1.3 76.2 - - - +
156A ASN* 1.3 61.1 + - - +
157A HIS* 3.4 17.6 + - - -
246B ASP* 4.1 24.5 - - - +
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Residues in contact with ASN 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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127A MET* 3.7 13.1 - - - -
131A LYS* 5.4 4.2 + - - -
152A ILE* 2.5 34.2 + - - +
153A ILE 3.1 7.1 + - - +
155A ALA* 1.3 75.8 - - - +
157A HIS* 1.3 74.7 + - - +
158A LEU* 3.4 13.4 + - + +
244B GLY 4.6 1.0 - - - +
245B PHE* 3.4 21.2 - - + +
246B ASP* 2.8 44.9 + - - +
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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