Contacts of the helix formed by residues 143 - 161 (chain N) in PDB entry 3D1N
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 ASN 143 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144N MSE 1.3 70.3 + - - +
145N GLU 3.5 2.0 - - - -
146N GLU* 3.1 33.2 - - - +
147N ILE* 3.1 14.2 + - - +
199N GLN* 4.7 18.0 + - - +
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Residues in contact with MSE 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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143N ASN* 1.3 74.7 - - - +
145N GLU* 1.3 63.6 + - + +
146N GLU 3.0 1.6 - - - -
147N ILE* 3.0 31.1 + - + -
148N ARG* 2.8 35.2 + - + +
191N LEU* 4.8 14.1 - - + -
195N PRO* 4.3 32.8 - - + -
198N ALA* 5.2 1.6 - - + -
199N GLN* 6.0 2.5 - - - -
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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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143N ASN 3.5 0.2 - - - -
144N MSE 1.3 78.8 - - + +
146N GLU* 1.3 57.6 + - - +
148N ARG* 3.5 7.1 + - - +
149N GLU* 3.1 34.1 + - + +
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Residues in contact with GLU 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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143N ASN* 3.1 22.7 + - - +
145N GLU* 1.3 80.6 - - - +
147N ILE* 1.3 59.8 + - + +
149N GLU* 3.6 6.2 - - - +
150N PHE* 3.2 20.3 + - - +
202N LYS* 4.2 23.7 + - - -
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Residues in contact with ILE 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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143N ASN 3.1 15.2 + - - +
144N MSE 3.0 29.2 + - + +
146N GLU* 1.3 76.4 - - + +
148N ARG* 1.3 67.7 + - - +
149N GLU 3.0 1.3 - - - -
150N PHE* 2.8 17.2 + - - +
151N ALA* 2.9 11.4 + - - +
188N PHE* 5.0 7.4 - - + -
191N LEU* 3.9 19.3 - - + -
195N PRO 4.8 0.7 - - - +
198N ALA* 3.5 31.2 - - + +
199N GLN* 3.6 29.2 - - + +
202N LYS* 4.0 18.8 - - + -
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Residues in contact with ARG 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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144N MSE 2.8 21.6 + - + +
145N GLU* 3.9 7.9 - - - +
147N ILE* 1.3 72.3 - - - +
149N GLU* 1.3 66.3 + - - +
151N ALA* 3.4 2.6 + - - +
152N LYS* 3.1 23.1 + - - +
191N LEU* 3.7 24.0 - - + +
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Residues in contact with GLU 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 3.1 20.4 + - - +
146N GLU* 3.6 7.4 - - - +
147N ILE 3.0 0.4 - - - -
148N ARG* 1.3 80.5 - - - +
150N PHE* 1.3 64.7 + - - +
152N LYS* 3.1 37.9 + - - +
153N ASN* 2.9 40.6 + - - +
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Residues in contact with PHE 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 GLU 3.2 3.9 + - - +
147N ILE 2.8 13.0 + - - +
149N GLU* 1.3 74.4 - - - +
151N ALA* 1.3 52.7 + - - +
153N ASN* 3.0 9.0 + - + +
154N PHE* 2.6 51.2 + + + +
157N ARG* 4.5 14.1 - - - -
188N PHE* 3.7 29.2 - + - -
202N LYS* 3.6 49.6 - - + -
205N LEU* 3.9 11.0 - - + -
206N GLU* 3.5 51.8 - - + -
209N LEU* 5.0 0.9 - - + -
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Residues in contact with ALA 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 ILE 2.9 10.4 + - - +
148N ARG 3.8 7.0 - - - +
150N PHE* 1.3 73.1 - - - +
152N LYS* 1.3 67.9 + - - +
154N PHE* 3.1 11.9 + - - +
155N LYS* 3.2 14.2 + - - +
188N PHE* 3.9 41.1 - - + +
189N GLU* 4.4 15.7 - - - +
191N LEU* 4.1 17.7 - - + -
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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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148N ARG 3.1 12.8 + - - +
149N GLU* 3.1 37.9 + - - +
151N ALA* 1.3 78.9 - - - +
153N ASN* 1.3 64.8 + - - +
155N LYS* 3.5 5.4 + - - +
156N ILE* 3.4 32.8 + - + +
189N GLU 5.5 0.2 + - - -
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Residues in contact with ASN 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 GLU* 2.9 40.0 + - - +
150N PHE* 3.0 10.2 + - + +
152N LYS* 1.3 80.3 - - - +
154N PHE* 1.3 63.5 + - - +
155N LYS 3.2 0.2 - - - -
156N ILE* 3.7 19.7 - - - +
157N ARG* 3.0 44.6 + - - +
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Residues in contact with PHE 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 PHE* 2.6 43.9 + + + +
151N ALA* 3.1 8.4 + - - +
153N ASN* 1.3 74.7 - - - +
155N LYS* 1.3 58.1 + - - +
157N ARG* 3.9 0.9 - - - +
158N ARG* 3.0 34.9 + - + +
168N VAL* 4.2 23.6 - - + -
172N MSE 4.5 5.2 - - + -
185N ILE* 4.0 17.3 - - + -
188N PHE* 4.7 8.1 - + + -
189N GLU* 3.1 37.9 - - + -
205N LEU* 4.1 23.1 - - + -
209N LEU* 3.6 39.7 - - + -
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Residues in contact with LYS 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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10F A 4.3 16.0 + - - -
159M LEU 5.4 4.3 - - - -
162M GLY* 6.5 1.1 - - - -
151N ALA 3.2 10.8 + - - +
152N LYS* 3.7 9.0 - - - +
153N ASN 3.2 0.2 - - - -
154N PHE* 1.3 74.2 - - - +
156N ILE* 1.3 67.0 + - + +
158N ARG* 3.0 28.3 + - - +
159N LEU* 2.8 43.1 + - + +
165N GLN* 5.6 1.2 - - - +
189N GLU* 3.7 30.3 + - + +
190N LYS* 6.1 2.6 - - - +
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Residues in contact with ILE 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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160M SER* 4.9 14.9 + - - +
152N LYS* 3.4 25.9 + - + +
153N ASN* 3.7 26.7 - - - +
155N LYS* 1.3 79.6 - - + +
157N ARG* 1.3 58.4 + - + +
159N LEU* 3.1 12.2 + - + +
160N SER* 2.8 42.5 + - - +
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Residues in contact with ARG 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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150N PHE* 4.5 16.2 - - - -
153N ASN* 3.0 30.8 + - + +
154N PHE 3.9 0.2 - - - +
156N ILE* 1.3 82.9 - - + +
158N ARG* 1.3 64.1 + - - +
160N SER* 3.3 7.7 + - - +
161N LEU* 3.0 31.5 + - + +
206N GLU* 4.9 5.7 - - - +
209N LEU* 3.2 42.9 - - + +
210N ASN* 3.7 19.8 + - - +
213N GLU* 2.7 42.6 + - - +
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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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9F T 4.3 4.2 + - - -
154N PHE* 3.0 28.1 + - + +
155N LYS* 3.6 23.1 - - - +
157N ARG* 1.3 75.7 - - - +
159N LEU* 1.3 80.0 + - - +
161N LEU* 3.2 13.9 + - - +
163N LEU* 2.9 60.9 + - + +
164N THR* 3.9 6.3 - - - +
165N GLN* 3.7 28.9 - - - +
168N VAL* 3.6 25.1 - - + -
185N ILE* 4.7 0.6 - - - +
189N GLU* 2.9 40.5 + - - +
209N LEU* 4.7 5.9 - - + +
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Residues in contact with LEU 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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156M ILE* 3.8 17.3 - - + +
159M LEU* 3.8 56.5 - - + +
160M SER* 3.9 18.4 - - - +
155N LYS* 2.8 40.2 + - + +
156N ILE* 3.3 8.5 - - - +
158N ARG* 1.3 98.7 - - - +
160N SER* 1.3 57.9 + - - +
161N LEU 3.0 1.3 - - - -
162N GLY* 2.7 26.3 + - - +
163N LEU 4.8 2.2 - - - +
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Residues in contact with SER 160 (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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156M ILE* 3.9 31.1 - - - +
156N ILE* 2.8 28.7 + - - +
157N ARG* 3.3 10.9 + - - +
159N LEU* 1.3 75.6 - - - +
161N LEU* 1.3 64.9 + - - +
162N GLY 3.2 0.6 + - - -
216N ASN* 5.4 1.6 + - - +
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Residues in contact with LEU 161 (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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157N ARG* 3.0 18.9 + - + +
158N ARG* 3.6 8.7 - - - +
159N LEU 3.0 0.8 - - - -
160N SER* 1.3 84.8 - - - +
162N GLY* 1.3 64.3 + - - +
163N LEU* 3.7 21.2 - - + +
209N LEU* 4.2 15.0 - - + -
212N ALA* 3.7 31.0 - - + -
213N GLU* 4.0 26.5 - - + +
216N ASN* 4.8 15.6 - - + +
223N LEU* 3.5 27.1 - - + +
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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