Contacts of the helix formed by residues 147 - 159 (chain N) in PDB entry 2X17
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 147 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1498 GLN* 2.9 29.6 + - - -
144N ALA* 3.9 18.4 - - - +
145N LYS 3.3 5.6 + - - -
146N ASP* 1.3 78.0 - - - +
148N PRO* 1.3 62.4 - - - +
149N GLN* 3.1 9.9 + - - -
150N ILE* 3.4 26.8 + - - +
151N LEU* 3.6 15.8 + - - +
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Residues in contact with PRO 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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1436 PHE* 3.6 39.0 - - + +
1506 ILE* 4.0 10.8 - - + +
146N ASP 3.7 7.6 - - - +
147N SER* 1.3 85.2 - - - +
149N GLN* 1.3 78.1 + - - +
150N ILE 3.4 0.2 - - - -
151N LEU* 3.7 10.3 + - + +
152N PHE* 3.2 18.2 + - - +
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Residues in contact with GLN 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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1476 SER* 3.4 32.4 + - - +
1496 GLN* 4.3 19.4 + - + +
1506 ILE* 3.9 16.2 - - + +
1536 MET* 4.3 7.7 - - + +
1498 GLN* 3.6 23.7 + - + -
146N ASP 5.1 0.3 - - - +
147N SER* 3.1 19.6 + - - +
148N PRO* 1.3 97.0 - - - +
150N ILE* 1.3 62.0 - - - +
152N PHE* 3.4 5.8 + - - +
153N MET* 3.3 28.4 + - + +
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Residues in contact with ILE 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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1488 PRO* 4.2 15.5 - - + +
1498 GLN* 3.9 37.9 - - + +
1528 PHE* 4.3 29.8 - - + -
140N LYS* 5.0 2.9 - - + +
143N PHE* 4.4 11.0 - - + +
144N ALA* 3.6 29.4 - - + -
147N SER* 3.4 22.0 + - - +
148N PRO 3.4 0.2 - - - -
149N GLN* 1.3 72.1 - - - +
151N LEU* 1.3 55.8 + - - +
152N PHE 3.2 0.4 - - - -
153N MET* 3.2 10.8 + - + +
154N LEU* 2.8 41.5 + - + +
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Residues in contact with LEU 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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1436 PHE* 3.8 26.9 - - + -
36N LEU* 4.3 16.5 - - + +
39N PHE* 4.1 15.4 - - + -
83N PRO* 4.3 23.6 - - + -
141N LEU* 3.8 28.7 - - + -
144N ALA* 4.8 4.8 - - + +
147N SER 3.6 11.9 + - - +
148N PRO* 3.8 10.3 - - + +
149N GLN 3.4 0.2 - - - -
150N ILE* 1.3 77.8 - - - +
152N PHE* 1.3 56.8 + - - +
154N LEU* 3.8 6.4 - - - +
155N ASP* 3.0 28.4 + - - +
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Residues in contact with PHE 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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1406 LYS* 4.5 24.0 - - + -
1436 PHE* 4.6 15.9 - + + -
1506 ILE* 4.0 22.0 - - + -
1536 MET* 3.7 43.7 - - + -
1546 LEU* 4.4 20.9 - - + -
1576 GLU* 3.7 30.7 - - + -
36N LEU* 5.6 1.8 - - - -
148N PRO 3.2 13.9 + - - +
149N GLN* 3.4 10.5 - - - +
150N ILE 3.2 0.2 - - - -
151N LEU* 1.3 78.0 - - - +
153N MET* 1.3 63.1 + - - +
155N ASP* 3.4 10.2 + - + +
156N LYS* 3.4 21.7 + - + +
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Residues in contact with MET 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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1536 MET* 3.7 22.0 - - + +
11736 AG 3.0 27.6 - - - -
1498 GLN* 4.2 15.0 - - + +
1528 PHE* 3.8 26.9 - - + -
1538 MET* 3.7 26.9 - - + +
149N GLN* 3.3 17.6 + - + +
150N ILE* 3.2 17.3 + - + +
152N PHE* 1.3 77.2 - - + +
154N LEU* 1.3 63.1 + - - +
156N LYS* 3.6 9.3 + - + +
157N GLU* 3.3 26.5 + - - +
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Residues in contact with LEU 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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1528 PHE* 4.7 9.4 - - + -
39N PHE* 4.1 7.0 - - + -
137N ILE* 4.3 11.9 - - + +
140N LYS* 3.8 48.9 - - + +
141N LEU* 4.1 23.6 - - + -
144N ALA* 5.9 1.3 - - + -
150N ILE* 2.8 22.5 + - + +
151N LEU* 3.8 8.1 - - - +
153N MET* 1.3 74.6 - - - +
155N ASP* 1.3 64.6 + - - +
157N GLU* 3.3 11.2 + - + +
158N LEU* 3.2 51.3 + - + +
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Residues in contact with ASP 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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1406 LYS* 5.4 7.6 + - - -
35N GLY 4.6 1.9 - - - +
36N LEU* 3.3 26.0 - - + +
37N GLU* 3.8 6.6 + - - +
38N GLY* 3.0 44.9 + - - -
39N PHE* 3.1 24.9 + - + +
151N LEU 3.0 16.7 + - - +
152N PHE* 3.5 10.6 - - + +
153N MET 3.3 0.2 - - - -
154N LEU* 1.3 77.8 - - - +
156N LYS* 1.3 60.1 + - - +
158N LEU* 3.6 0.7 + - - -
159N SER* 3.3 7.8 + - - -
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Residues in contact with LYS 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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1566 LYS* 5.4 9.7 - - - +
1576 GLU* 4.3 26.6 - - - +
1568 LYS* 5.1 12.4 - - - +
152N PHE* 3.4 11.8 + - + +
153N MET* 3.8 11.7 - - + +
154N LEU 3.3 0.6 - - - -
155N ASP* 1.3 78.7 - - - +
157N GLU* 1.3 62.1 + - + +
159N SER* 2.6 26.6 + - - +
160N ALA* 4.0 2.9 + - - +
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Residues in contact with GLU 157 (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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1528 PHE* 3.3 33.8 - - + -
1568 LYS* 4.5 25.8 - - + +
140N LYS* 3.8 19.1 + - - -
153N MET 3.3 12.0 + - - +
154N LEU* 3.3 16.1 + - + +
156N LYS* 1.3 79.5 - - + +
158N LEU* 1.3 63.9 + - + +
159N SER 3.6 0.3 + - - -
160N ALA* 3.6 18.2 - - - +
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Residues in contact with LEU 158 (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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38N GLY 3.6 18.7 - - - +
39N PHE* 3.7 47.6 - - + -
42N TRP* 3.7 29.6 - - + +
87N PHE* 4.9 1.3 - - + -
137N ILE* 3.8 31.4 - - + -
154N LEU* 3.2 21.2 + - + +
155N ASP 4.2 0.2 - - - +
156N LYS 3.3 0.2 - - - -
157N GLU* 1.3 75.7 - - + +
159N SER* 1.3 61.0 + - - +
160N ALA 3.1 6.1 - - - -
161N ARG* 3.2 24.9 + - - +
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Residues in contact with SER 159 (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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37N GLU 5.4 0.2 - - - -
38N GLY* 3.8 16.1 - - - -
41N ASN* 5.3 8.6 + - - +
155N ASP 3.3 14.5 + - - -
156N LYS* 2.6 28.6 + - - +
157N GLU 3.3 0.2 - - - -
158N LEU* 1.3 74.6 - - - +
160N ALA* 1.3 62.8 + - - +
161N ARG 3.2 7.9 + - - +
162N ALA* 4.6 5.9 + - - +
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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