Contacts of the helix formed by residues 144 - 156 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81N ALA* 3.3 23.4 + - - +
142N CYS 4.0 0.2 + - - -
143N SER* 1.3 70.4 + - - +
145N ILE* 1.3 65.5 + - - +
146N SER* 2.9 6.8 + - - -
147N ASP* 3.2 24.7 + - - +
148N TYR* 4.1 9.1 - - - -
166N LYS* 3.9 18.6 - - - +
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Residues in contact with ILE 145 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250M ILE* 4.8 10.1 - - + -
80N TYR 3.7 12.3 - - - +
81N ALA* 3.9 18.6 - - - +
83N PHE* 4.7 12.3 - - + -
86N HIS* 3.6 29.6 - - + +
121N GLY* 3.9 11.0 - - - -
122N THR* 4.1 14.1 - - + +
141N GLU* 3.5 30.3 - - + -
143N SER* 3.0 9.4 + - - -
144N SER* 1.3 81.2 + - - +
146N SER* 1.3 63.6 + - - +
148N TYR* 2.9 34.3 + - + +
149N SER* 3.1 9.4 + - - -
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Residues in contact with SER 146 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141N GLU* 4.1 14.6 - - - -
143N SER 2.6 24.7 + - - -
144N SER* 3.7 0.2 - - - -
145N ILE* 1.3 81.3 - - - +
147N ASP* 1.3 61.7 + - - +
149N SER* 2.6 28.9 + - - -
150N GLU* 3.0 12.9 + - - +
164N ILE* 4.2 14.6 - - - -
166N LYS* 2.9 37.6 - - - +
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Residues in contact with ASP 147 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144N SER* 3.2 19.7 + - - +
146N SER* 1.3 75.1 + - - +
148N TYR* 1.3 67.6 + - + +
150N GLU* 3.6 13.9 + - - +
151N LYS* 3.4 33.0 + - - +
166N LYS* 3.3 32.0 + - - +
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Residues in contact with TYR 148 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249M CYS* 4.0 25.4 - - + -
250M ILE* 4.3 23.6 - - + -
253M VAL* 3.2 39.6 - - + +
81N ALA 5.4 5.2 - - - -
122N THR* 6.3 0.2 - - - -
144N SER 4.1 10.5 - - - -
145N ILE* 2.9 25.3 + - + +
147N ASP* 1.3 77.8 - - + +
149N SER* 1.3 66.4 + - - +
150N GLU 2.9 2.1 + - - -
151N LYS* 3.0 24.5 + - - +
152N ILE* 2.8 30.9 + - + +
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Residues in contact with SER 149 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120N SER* 4.2 1.0 + - - -
121N GLY 3.3 19.0 + - - -
122N THR* 3.2 27.7 + - - +
123N GLY* 4.0 5.8 - - - -
145N ILE 3.1 5.3 + - - -
146N SER* 2.6 26.3 + - - -
148N TYR* 1.3 74.5 - - - +
150N GLU* 1.3 55.8 + - - +
152N ILE* 3.4 2.0 - - - +
153N ILE* 2.8 41.3 + - - +
164N ILE* 3.6 19.6 - - - +
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Residues in contact with GLU 150 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146N SER* 3.0 15.4 + - - +
147N ASP* 3.7 14.9 - - - +
148N TYR 3.0 0.2 - - - -
149N SER* 1.3 75.2 + - - +
151N LYS* 1.3 65.9 + - + +
153N ILE* 3.8 6.4 - - - +
154N LYS* 3.0 24.4 + - - +
159N ASP* 5.7 0.3 - - - +
164N ILE* 3.8 36.1 + - + +
166N LYS* 6.1 2.3 - - - +
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Residues in contact with LYS 151 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249M CYS* 4.1 26.0 - - + -
147N ASP* 3.4 18.3 + - - +
148N TYR* 3.0 29.2 + - + +
150N GLU* 1.3 77.8 - - + +
152N ILE* 1.3 57.8 + - - +
154N LYS* 3.4 5.6 + - - +
155N ALA* 2.9 30.1 + - - +
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Residues in contact with ILE 152 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246M ASP 3.8 8.1 - - - +
247M MET* 4.1 23.8 - - + -
249M CYS* 3.6 17.5 - - - -
250M ILE* 3.8 28.9 - - + -
122N THR* 3.6 22.9 - - + +
127N MET* 3.9 21.5 - - + -
148N TYR* 2.8 22.5 + - + +
149N SER 3.4 4.7 - - - +
151N LYS* 1.3 75.3 - - - +
153N ILE* 1.3 63.6 + - + +
155N ALA* 3.1 13.3 + - - +
156N ASN* 2.5 38.0 + - - +
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Residues in contact with ILE 153 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123N GLY* 4.8 8.1 - - - -
126N SER* 5.5 0.2 - - - -
127N MET* 4.2 25.8 - - + -
149N SER* 2.8 28.7 + - - +
150N GLU* 3.8 5.4 - - - +
152N ILE* 1.3 74.3 - - + +
154N LYS* 1.3 63.9 + - - +
156N ASN* 3.1 11.8 + - - +
158N LEU* 3.2 33.2 + - + +
159N ASP* 3.5 28.0 - - + +
162N ILE* 3.7 31.2 - - + +
164N ILE* 3.7 24.9 - - + -
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Residues in contact with LYS 154 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150N GLU 3.0 17.4 + - - +
151N LYS* 3.7 6.5 - - - +
153N ILE* 1.3 77.3 - - - +
155N ALA* 1.3 63.1 + - - +
157N HIS* 3.0 19.9 + - - -
159N ASP* 3.5 35.0 - - + +
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Residues in contact with ALA 155 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246M ASP* 4.2 22.8 - - - +
249M CYS* 6.5 1.1 - - + -
151N LYS 2.9 14.9 + - - +
152N ILE* 3.3 13.0 - - - +
154N LYS* 1.3 76.9 - - - +
156N ASN* 1.3 62.5 + - - +
157N HIS* 3.6 14.9 + - - -
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Residues in contact with ASN 156 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244M GLY 4.6 1.0 - - - +
245M PHE* 3.5 24.9 - - + +
246M ASP* 2.7 46.8 + - - +
127N MET* 3.9 9.1 - - - -
131N LYS* 5.4 4.0 + - - -
152N ILE* 2.5 36.0 + - - +
153N ILE 3.1 6.4 + - - +
155N ALA* 1.3 77.1 - - - +
157N HIS* 1.3 75.0 + - - +
158N LEU* 3.4 12.9 + - + +
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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