Contacts of the helix formed by residues 147 - 156 (chain N) in PDB entry 1KD1
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 LEU 147 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53N GLY* 4.1 19.5 - - - +
55N LYS* 4.2 17.7 - - + -
57N LYS* 5.5 1.3 - - + -
60N ILE* 4.1 29.6 - - + -
115N LEU* 4.4 24.2 - - + -
134N ILE* 4.7 10.8 - - + -
141N ILE* 4.4 17.6 - - + +
144N ASP* 3.2 18.4 + - + +
146N GLN* 1.3 85.4 - - + +
148N SER* 1.3 66.6 + - - +
149N TRP* 2.8 14.0 + - + +
150N ILE* 3.0 26.5 + - + +
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Residues in contact with SER 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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141N ILE 3.5 8.6 + - - -
142N LYS* 3.4 24.5 - - - -
144N ASP 2.8 20.7 + - - -
145N ASP* 4.1 9.9 + - - -
146N GLN 3.7 0.2 - - - -
147N LEU* 1.3 78.1 - - - +
149N TRP* 1.3 58.0 + - - +
150N ILE 3.1 0.4 - - - -
151N SER* 2.9 29.5 + - - -
152N ARG* 4.0 12.3 + - - -
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Residues in contact with TRP 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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432A G 3.4 30.3 + - - -
433A C 3.4 42.1 - - - +
115N LEU* 3.6 24.7 - - + -
145N ASP 5.7 0.7 - - - -
146N GLN 3.3 28.5 + - - -
147N LEU* 2.8 11.9 + - + +
148N SER* 1.3 78.1 + - - +
150N ILE* 1.3 103.8 + - + +
151N SER 3.1 0.9 - - - -
152N ARG* 2.8 40.1 + - + +
155N HIS* 3.5 33.1 - + - -
158N ARG* 3.7 16.2 - - - -
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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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113N ARG* 2.8 34.5 + - + +
114N VAL 4.0 8.3 - - - +
115N LEU* 3.8 18.4 - - + -
134N ILE* 3.8 36.6 - - + -
136N PRO* 3.8 6.9 - - + +
141N ILE* 4.8 0.7 - - + -
147N LEU* 3.0 15.9 + - + +
149N TRP* 1.3 113.0 - - + +
151N SER* 1.3 65.3 + - - +
152N ARG 3.2 2.0 - - - -
155N HIS* 4.0 2.9 - - + +
158N ARG* 3.8 22.9 - - - -
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Residues in contact with SER 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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113N ARG* 3.3 8.8 + - - -
136N PRO* 3.0 36.6 + - - +
141N ILE* 4.4 6.9 - - - +
142N LYS* 4.1 21.3 - - - +
148N SER* 2.9 16.4 + - - -
150N ILE* 1.3 80.1 - - - +
152N ARG* 1.3 68.2 + - - +
153N THR* 3.4 1.6 + - - -
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Residues in contact with ARG 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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434A U 5.4 4.9 - - - +
113N ARG* 2.7 24.3 + - - -
148N SER* 4.3 9.9 + - - -
149N TRP* 2.8 39.8 - - + +
150N ILE 3.2 0.6 - - - -
151N SER* 1.3 79.1 - - - +
153N THR* 1.3 57.7 + - - +
154N ARG* 4.1 13.2 - - + +
155N HIS* 2.9 21.7 + - + +
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Residues in contact with THR 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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183A A 4.0 4.0 - - - +
184A G 3.1 41.1 - - - +
185A G 5.1 4.9 - - - +
113N ARG* 4.5 1.3 - - - +
151N SER 3.4 3.3 + - - -
152N ARG* 1.3 68.2 - - - +
154N ARG* 1.3 58.3 + - + +
155N HIS 2.8 11.4 + - - -
156N ARG* 3.0 43.5 + - - +
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Residues in contact with ARG 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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183A A 4.1 8.9 + - - -
184A G 4.4 13.9 - - - +
186A A 5.7 2.6 + - - -
187A A 2.6 42.5 + - - +
188A C 4.0 15.4 + - - +
434A U 4.2 20.3 + - - +
435A A 2.7 40.1 + - - -
436A A 4.6 8.3 + - - -
152N ARG* 3.1 11.5 - - + +
153N THR* 1.3 77.1 - - + +
155N HIS* 1.3 65.4 + - + +
156N ARG 3.5 0.4 - - - -
161N ARG* 2.8 20.4 + - - -
163N LEU* 4.6 0.5 - - - +
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Residues in contact with HIS 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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433A C 4.1 4.9 + - - -
434A U 3.8 28.2 + - - -
113N ARG* 3.4 12.9 - - - +
149N TRP* 3.5 35.8 - + - -
150N ILE 4.0 6.1 - - - +
152N ARG* 2.9 16.0 + - + +
153N THR 2.8 1.8 + - - -
154N ARG* 1.3 83.8 - - + +
156N ARG* 1.3 66.8 + - - +
157N LEU 3.1 0.5 + - - -
158N ARG* 2.7 75.1 + - + +
161N ARG* 3.7 2.5 - - - +
163N LEU* 4.4 14.1 - - + +
168N ARG* 5.1 2.5 - - - -
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Residues in contact with ARG 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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43A U 5.4 1.2 + - - -
44A G 3.6 21.4 + - - -
146A U 4.3 22.4 + - - -
147A G 5.7 1.8 + - - -
183A A 3.7 24.4 + - - +
184A G 3.4 26.5 + - - -
113N ARG* 2.9 32.0 - - - +
153N THR* 3.0 33.2 + - - +
154N ARG 3.5 0.8 - - - -
155N HIS* 1.3 75.3 - - - +
157N LEU* 1.3 68.7 + - + +
161N ARG* 2.9 23.0 + - - -
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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