Contacts of the helix formed by residues 141 - 158 (chain N) in PDB entry 6CIM
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 LYS 141 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101N ALA* 5.4 0.2 - - - +
105N PHE* 6.1 1.3 - - + -
133N TRP* 4.1 26.6 - - + +
136N THR* 3.8 24.6 - - + +
140N ASP* 1.3 76.9 - - - +
142N GLN* 1.3 63.7 + - - +
143N PRO* 3.5 3.1 - - - -
144N TYR* 3.3 21.2 + - + +
145N GLU* 3.5 5.7 + - - +
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Residues in contact with GLN 142 (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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140N ASP 3.3 6.3 - - - +
141N LYS* 1.3 77.4 - - - +
143N PRO* 1.3 74.1 - - + +
145N GLU* 3.0 10.4 + - + +
146N LYS* 3.0 58.6 + - - +
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Residues in contact with PRO 143 (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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140N ASP 3.6 15.7 - - - +
141N LYS 3.6 0.9 - - - -
142N GLN* 1.3 98.2 - - + +
144N TYR* 1.3 57.5 + - - +
146N LYS* 3.3 11.6 + - + +
147N LYS* 2.9 30.1 + - - +
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Residues in contact with TYR 144 (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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101N ALA* 3.4 35.5 - - + +
104N LEU* 6.0 2.3 - - + +
105N PHE* 4.7 13.0 - - + +
133N TRP* 5.1 3.4 - - + +
141N LYS* 3.3 17.9 + - + +
142N GLN 3.2 0.6 - - - -
143N PRO* 1.3 81.1 - - - +
145N GLU* 1.3 56.5 + - - +
147N LYS* 3.3 6.7 + - - +
148N ALA* 2.9 24.4 + - - +
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Residues in contact with GLU 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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101N ALA* 3.6 13.6 - - + +
141N LYS 3.5 6.5 + - - +
142N GLN* 3.0 13.9 + - + +
144N TYR* 1.3 78.7 - - - +
146N LYS* 1.3 65.4 + - - +
148N ALA* 3.3 3.0 + - - +
149N ALA* 2.9 29.6 + - - +
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Residues in contact with LYS 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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142N GLN* 3.0 53.7 + - - +
143N PRO* 3.5 9.9 - - + +
145N GLU* 1.3 85.6 + - - +
147N LYS* 1.3 64.1 - - - +
149N ALA* 3.1 13.8 + - - +
150N LYS* 3.0 23.8 + - - +
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Residues in contact with LYS 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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104N LEU* 5.9 7.2 - - + -
143N PRO 2.9 16.0 + - - +
144N TYR* 3.8 5.8 - - - +
146N LYS* 1.3 75.7 - - - +
148N ALA* 1.3 57.3 + - - +
150N LYS* 3.3 6.9 + - - +
151N LEU* 2.9 41.0 + - + +
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Residues in contact with ALA 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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98N PRO* 5.2 0.9 - - - +
99N PRO 4.2 12.5 - - - +
100N SER* 4.8 1.1 - - - -
101N ALA* 3.6 30.1 - - + +
144N TYR 2.9 17.6 + - - +
145N GLU* 3.5 5.6 - - - +
146N LYS 3.1 0.2 - - - -
147N LYS* 1.3 77.4 - - - +
149N ALA* 1.3 57.1 + - - +
151N LEU* 3.4 3.9 + - - +
152N LYS* 2.8 31.4 + - - +
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Residues in contact with ALA 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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145N GLU 2.9 16.4 + - - +
146N LYS* 3.1 16.4 + - - +
148N ALA* 1.3 76.0 - - - +
150N LYS* 1.3 63.3 + - - +
152N LYS* 3.2 18.6 + - + +
153N GLU* 3.0 34.8 + - - +
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Residues in contact with LYS 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 LYS 3.0 15.5 + - - +
147N LYS* 3.7 7.6 - - - +
149N ALA* 1.3 76.5 - - - +
151N LEU* 1.3 67.6 + - + +
153N GLU* 3.1 16.4 - - - +
154N LYS* 2.9 23.5 + - - +
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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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98N PRO* 3.9 15.7 - - + +
99N PRO* 4.1 25.4 - - + +
104N LEU* 6.2 2.7 - - + -
147N LYS* 2.9 27.4 + - + +
148N ALA* 3.9 4.5 - - - +
150N LYS* 1.3 81.4 - - + +
152N LYS* 1.3 57.0 + - - +
154N LYS* 3.4 9.5 + - + +
155N TYR* 2.9 30.5 + - - +
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Residues in contact with LYS 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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28G T 5.1 14.1 + - - +
98N PRO* 3.8 17.2 - - + +
148N ALA 2.8 19.8 + - - +
149N ALA* 3.3 16.4 - - - +
151N LEU* 1.3 75.3 - - - +
153N GLU* 1.3 68.4 + - - +
155N TYR* 3.0 5.4 + - - +
156N GLU* 2.9 48.3 + - + +
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Residues in contact with GLU 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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149N ALA* 3.0 21.2 + - - +
150N LYS* 3.1 23.0 - - - +
152N LYS* 1.3 85.6 + - + +
154N LYS* 1.3 62.4 + - - +
156N GLU* 3.2 13.2 + - + +
157N LYS* 3.0 23.2 + - - +
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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 LYS 2.9 17.9 + - - +
151N LEU* 3.5 11.7 - - + +
153N GLU* 1.3 79.6 - - - +
155N TYR* 1.3 61.2 + - - +
157N LYS* 3.3 14.0 + - - +
158N ASP* 3.4 10.6 + - - +
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Residues in contact with TYR 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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97N ARG* 5.4 1.8 - - - -
98N PRO* 3.9 25.1 - - + -
151N LEU 2.9 17.1 + - - +
152N LYS 3.6 4.0 - - - +
154N LYS* 1.3 73.0 - - - +
156N GLU* 1.3 68.0 + - - +
158N ASP* 3.1 26.9 + - - +
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Residues in contact with GLU 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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152N LYS* 2.9 39.2 + - + +
153N GLU* 3.2 15.7 + - + +
155N TYR* 1.3 78.5 - - - +
157N LYS* 1.3 63.6 + - - +
158N ASP 3.2 6.1 + - - +
159N ILE* 5.3 0.2 - - - -
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Residues in contact with LYS 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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153N GLU 3.0 11.7 + - - +
154N LYS* 3.6 11.4 - - - +
155N TYR 3.2 0.2 - - - -
156N GLU* 1.3 77.0 - - - +
158N ASP* 1.3 62.2 + - - +
159N ILE* 3.1 9.9 + - - +
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Residues in contact with ASP 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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154N LYS 3.4 8.2 + - - +
155N TYR* 3.1 22.8 + - - +
156N GLU 3.6 4.3 - - - +
157N LYS* 1.3 74.7 - - - +
159N ILE* 1.3 63.3 + - - +
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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