Contacts of the helix formed by residues 146 - 158 (chain N) in PDB entry 5GJQ
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 146 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141N CYS 3.9 6.1 - - - +
144N ASP* 2.9 11.9 + - + +
145N HIS* 1.3 77.5 - - - +
147N TYR* 1.3 60.2 + - - +
148N LYS* 3.6 2.0 - - + -
149N GLN* 2.7 34.8 - - + +
150N ALA 3.8 1.2 + - - -
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Residues in contact with TYR 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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141N CYS 4.9 1.3 - - - -
142N LEU* 4.6 12.1 - - + -
145N HIS* 4.2 16.1 + - - -
146N LYS* 1.3 75.7 - - - +
148N LYS* 1.3 54.0 - - - +
149N GLN 3.0 1.6 - - - -
150N ALA* 2.8 10.0 + - + +
151N ILE* 2.1 50.8 + - + +
167N ILE* 2.8 39.5 - - + -
176N MET* 5.3 9.2 - - + -
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Residues in contact with LYS 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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41K TYR* 5.1 2.9 - - - +
146N LYS* 3.6 0.6 - - - +
147N TYR* 1.3 72.8 - - - +
149N GLN* 1.3 63.2 + - - +
151N ILE* 3.4 15.4 - - + +
152N GLY* 2.5 31.2 + - - +
179N TYR* 2.4 70.0 + - + +
180N SER* 5.6 5.6 - - - +
183N LEU* 6.5 0.7 - - + -
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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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39K ASP 6.1 2.5 - - - +
41K TYR* 5.9 0.7 - - - +
141N CYS* 4.7 9.6 - - - -
144N ASP* 4.6 17.0 - - + -
146N LYS* 2.7 31.1 - - + +
148N LYS* 1.3 79.1 - - - +
150N ALA* 1.3 57.1 + - - +
153N ILE* 2.9 27.9 + - + +
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Residues in contact with ALA 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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138N PHE* 4.7 10.2 - - + +
141N CYS* 3.6 29.1 - - + +
142N LEU* 4.9 7.2 - - + +
146N LYS 3.8 0.2 + - - -
147N TYR* 2.8 23.0 + - + +
149N GLN* 1.3 77.3 - - - +
151N ILE* 1.3 53.2 + - + +
153N ILE* 3.1 10.8 - - - +
154N ALA* 2.7 37.4 + - + +
162N VAL* 6.5 1.3 - - + -
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Residues in contact with ILE 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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147N TYR* 2.1 47.8 + - + +
148N LYS* 3.0 12.1 + - + +
150N ALA* 1.3 67.4 - - + +
152N GLY* 1.3 52.0 + - - +
154N ALA* 2.6 12.5 + - - +
155N LEU* 2.1 40.9 + - + +
163N PHE* 5.0 12.1 - - + -
176N MET* 5.2 8.1 - - + +
180N SER* 4.5 23.8 - - - +
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Residues in contact with GLY 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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41K TYR* 2.7 61.9 - - - -
148N LYS* 2.5 20.6 + - - +
151N ILE* 1.3 72.6 - - - +
153N ILE* 1.3 62.3 + - - +
155N LEU* 3.4 5.4 - - - -
156N GLU* 3.1 4.0 + - - +
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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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25J LEU* 5.8 10.5 - - + -
41K TYR* 4.6 3.7 - - + +
105N ILE* 5.8 8.3 - - + -
108N TYR* 6.0 3.1 - - + -
134N VAL* 5.5 7.0 - - + -
138N PHE* 4.8 15.9 - - + -
141N CYS* 3.8 26.0 - - - -
149N GLN* 2.9 23.5 + - + +
150N ALA* 3.1 6.1 - - - +
152N GLY* 1.3 74.5 - - - +
154N ALA* 1.3 51.6 - - - +
156N GLU* 2.6 15.4 + - - +
157N THR* 2.2 40.3 + - - -
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Residues in contact with ALA 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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138N PHE* 6.1 2.5 - - + -
150N ALA* 2.7 16.6 + - + +
151N ILE* 2.6 7.1 + - - +
153N ILE* 1.3 69.3 - - + +
155N LEU* 1.3 55.8 + - - +
157N THR* 2.7 18.3 - - - -
158N ARG* 2.2 33.1 + - - -
159N ARG 3.3 9.0 + - - +
162N VAL* 4.2 13.7 - - + -
163N PHE* 3.4 28.6 - - + -
193N PHE* 3.6 2.6 - - - -
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Residues in contact with LEU 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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41K TYR* 1.9 63.7 - - + +
151N ILE* 2.1 32.3 + - + +
152N GLY* 3.1 6.3 - - - +
154N ALA* 1.3 69.9 - - - +
156N GLU* 1.3 59.9 + - - +
158N ARG* 3.2 5.4 + - - +
163N PHE* 4.7 1.6 - - - -
180N SER* 5.1 9.0 - - - +
183N LEU* 4.7 9.9 - - + -
184N CYS* 5.0 17.5 - - + -
187N LEU* 4.8 7.0 - - + -
188N MET* 4.9 11.7 - - + -
193N PHE* 3.0 42.3 - - + -
197N VAL* 6.1 1.1 - - + -
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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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41K TYR* 2.7 45.9 - - + +
44K TYR* 5.3 10.1 - - - -
45K LYS* 3.3 29.0 - - - +
48K GLN* 5.5 0.9 + - - -
109N THR* 3.3 37.2 + - - +
112N CYS* 4.6 2.9 - - - +
113N VAL* 4.9 6.2 + - + +
152N GLY 4.4 0.3 - - - +
153N ILE* 2.6 12.2 + - - +
155N LEU* 1.3 72.6 - - - +
157N THR* 1.3 64.2 + - - +
158N ARG* 3.0 13.1 + - - +
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Residues in contact with THR 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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108N TYR* 4.0 27.5 + - - -
109N THR* 5.9 0.9 - - - +
112N CYS* 4.4 5.9 - - - +
134N VAL* 5.9 1.3 - - - -
138N PHE* 6.3 1.3 - - - -
153N ILE* 2.2 31.0 + - - -
154N ALA* 2.7 30.5 + - - -
156N GLU* 1.3 68.7 - - - +
158N ARG* 1.3 59.9 + - - +
159N ARG* 2.9 28.2 + - - +
162N VAL* 6.2 0.2 - - - -
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Residues in contact with ARG 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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112N CYS* 5.6 1.1 - - + +
113N VAL* 5.6 1.6 - - + -
116N ALA* 4.0 26.9 - - + -
120N GLU* 5.4 8.3 - - + +
121N GLY* 4.9 12.2 + - - +
154N ALA 2.2 21.0 + - - -
155N LEU 3.5 8.7 - - - +
156N GLU* 3.0 15.2 - - - +
157N THR* 1.3 71.2 - - - +
159N ARG* 1.3 59.4 + - - +
160N LEU* 3.5 5.4 + - - +
193N PHE* 3.2 36.4 - - + -
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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