Contacts of the helix formed by residues 142 - 154 (chain B) in PDB entry 3NJ8
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 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B GLU* 3.0 28.5 + - - -
140B GLU 3.3 4.1 + - - -
141B THR* 1.3 75.9 - - - +
143B ARG* 1.3 66.0 + - - +
144B LYS* 3.6 10.1 + - - +
145B GLY 3.0 8.7 + - - -
146B TYR* 2.8 22.1 + - - +
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B THR 4.1 0.4 + - - -
142B SER* 1.3 71.7 - - - +
144B LYS* 1.3 64.8 + - - +
146B TYR* 3.2 9.6 + - + +
147B LEU* 2.8 48.8 + - + +
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Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B GLU* 4.9 1.8 - - - +
142B SER* 3.2 10.0 + - - +
143B ARG* 1.3 77.4 - - - +
145B GLY* 1.3 52.7 + - - +
147B LEU* 3.9 4.3 - - - +
148B ALA* 2.8 36.7 + - + +
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Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PRO* 3.9 6.1 - - - +
133B GLU* 3.6 27.7 + - - -
141B THR* 4.3 0.7 - - - -
142B SER* 3.0 10.2 + - - -
144B LYS* 1.3 75.4 - - - +
146B TYR* 1.3 55.9 + - - +
148B ALA* 3.1 7.0 + - - +
149B ALA* 2.5 40.0 + - - +
191B GLY 4.3 4.3 - - - -
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Residues in contact with TYR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LEU* 4.8 11.4 - - + -
141B THR* 3.7 15.3 - - + +
142B SER 2.8 16.6 + - - +
143B ARG* 3.4 12.8 - - + +
145B GLY* 1.3 70.3 - - - +
147B LEU* 1.3 74.1 + - + +
149B ALA* 3.0 5.5 + - - +
150B SER* 2.9 32.1 + - - -
191B GLY 4.1 4.0 - - - -
192B GLY* 3.8 16.1 - - - +
195B SER* 3.2 39.8 + - - -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ARG* 2.8 43.8 + - + +
144B LYS* 4.0 3.4 - - - +
146B TYR* 1.3 84.9 - - + +
148B ALA* 1.3 60.3 + - - +
150B SER* 3.7 8.6 - - - +
151B SER* 2.8 34.1 + - - -
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ASN 4.2 0.7 - - - -
132B PRO* 3.4 26.5 - - + -
144B LYS* 2.8 24.8 + - + +
145B GLY* 3.1 2.4 + - - +
147B LEU* 1.3 73.1 - - - +
149B ALA* 1.3 61.0 + - - +
151B SER* 4.6 4.0 - - - -
152B ASN* 3.1 38.0 + - - +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ASN 3.4 14.4 - - - +
131B GLY* 4.1 11.9 - - - -
132B PRO* 3.9 0.6 - - + +
145B GLY 2.5 20.4 + - - +
146B TYR 3.3 5.6 - - - +
148B ALA* 1.3 74.2 - - - +
150B SER* 1.3 58.2 + - - +
153B SER* 3.0 30.3 + - - -
191B GLY 3.3 20.0 - - - +
192B GLY 4.0 12.1 - - - +
193B MET* 4.3 4.5 - - - +
196B ALA* 3.7 5.0 - - - +
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Residues in contact with SER 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B TYR* 2.9 19.5 + - - -
147B LEU* 3.7 13.6 - - - +
148B ALA 3.2 0.2 - - - -
149B ALA* 1.3 77.4 - - - +
151B SER* 1.3 60.1 + - - +
152B ASN 3.3 0.2 - - - -
154B ALA* 2.8 39.7 + - - +
155B TYR* 3.3 4.3 + - - +
192B GLY 5.7 0.7 - - - -
196B ALA* 3.8 17.8 - - - +
199B ALA* 5.4 3.1 - - - +
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Residues in contact with SER 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ALA 4.5 3.6 - - - +
82B ALA* 4.8 12.5 + - - +
147B LEU 2.8 18.4 + - - -
148B ALA* 4.1 4.9 - - - -
150B SER* 1.3 78.7 - - - +
152B ASN* 1.3 67.5 + - - +
155B TYR* 3.7 14.7 + - - +
156B SER* 3.3 22.2 + - - -
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Residues in contact with ASN 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ALA* 4.9 3.5 - - - +
82B ALA* 3.4 28.4 - - - +
128B LEU* 3.5 13.0 - - - +
129B ALA* 4.6 0.4 - - - -
130B ASN* 3.5 46.8 + - + +
132B PRO* 4.8 1.2 - - - +
148B ALA* 3.1 26.4 + - - +
151B SER* 1.3 78.9 + - - +
153B SER* 1.3 55.7 + - - +
156B SER* 2.6 25.8 + - - -
316B NAD 4.2 12.1 + - - +
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B HIS* 3.8 8.5 - - - -
128B LEU 4.0 9.4 - - - +
129B ALA* 3.3 15.0 - - - +
130B ASN 2.8 24.8 + - - -
149B ALA 3.0 18.9 + - - -
150B SER 3.4 1.6 + - - -
151B SER 3.4 0.2 - - - -
152B ASN* 1.3 76.9 - - - +
154B ALA* 1.3 59.4 + - - +
156B SER* 3.6 2.5 - - - -
193B MET* 3.6 14.1 - - - -
196B ALA* 4.5 7.0 - - - -
197B LYS* 4.5 7.9 + - - -
200B LEU* 3.6 20.5 - - - +
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B SER* 2.8 20.7 + - - +
152B ASN 3.6 0.2 - - - -
153B SER* 1.3 80.1 - - - +
155B TYR* 1.3 66.4 + - - +
156B SER 3.2 1.6 - - - -
157B PHE* 2.9 23.4 + - - +
158B VAL* 3.7 4.5 + - - +
196B ALA* 3.9 26.7 - - + +
199B ALA* 4.4 8.5 - - + -
200B LEU* 4.0 15.5 - - + +
203B ASP* 4.9 6.4 - - - +
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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