Contacts of the helix formed by residues 142 - 152 (chain E) in PDB entry 6N0M
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 ASP 142 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E SER* 5.3 0.8 - - - -
136E PHE* 3.4 15.1 - - - -
140E GLY 3.3 4.5 + - - +
141E GLY* 1.3 68.7 - - - -
143E PRO* 1.4 76.3 - - - +
144E GLU* 2.9 22.4 + - - +
145E TRP* 3.0 45.7 + - + +
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Residues in contact with PRO 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E PHE* 4.6 1.3 - - + -
137E LEU* 3.9 26.2 - - + -
141E GLY 3.2 8.4 - - - +
142E ASP* 1.4 90.3 - - - +
144E GLU* 1.3 62.3 + - - +
145E TRP 3.1 0.2 - - - -
146E LEU* 2.9 22.2 + - - +
147E LEU* 4.0 4.2 + - - +
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Residues in contact with GLU 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E ASP* 2.9 20.2 + - - +
143E PRO* 1.3 77.9 - - - +
145E TRP* 1.3 57.6 + - + +
147E LEU* 2.7 58.5 + - + +
151E ARG* 3.7 35.2 + - + +
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Residues in contact with TRP 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E SER* 4.9 3.6 - - - -
111E TRP* 3.6 29.4 - + - -
114E TYR* 2.9 51.6 + + + +
136E PHE* 3.5 30.5 - + + -
142E ASP* 3.0 39.5 + - + +
144E GLU* 1.3 78.2 - - + +
146E LEU* 1.3 60.7 + - - +
148E GLY* 3.0 17.3 + - - +
151E ARG* 3.5 21.8 + - - -
152E ALA* 3.9 4.0 - - - -
153E PRO* 3.4 40.3 - - + +
156E LEU* 4.3 5.8 - - + -
315E PHE* 3.8 0.2 - - - -
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Residues in contact with LEU 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E TYR* 4.3 4.0 - - + -
117E ILE* 3.8 16.8 - - + -
133E MET* 3.5 44.6 - - + +
136E PHE* 3.3 29.6 - - + -
137E LEU* 3.6 38.4 - - + -
143E PRO* 2.9 14.7 + - + +
145E TRP* 1.3 77.1 - - - +
147E LEU* 1.3 62.0 + - + +
148E GLY 3.2 0.4 - - - -
311E ASP* 5.3 2.3 - - - +
314E CYS* 5.5 0.2 - - - +
315E PHE* 3.3 19.7 - - + -
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Residues in contact with LEU 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E PRO 4.6 2.2 - - - +
144E GLU* 2.7 40.9 + - + +
146E LEU* 1.3 73.3 - - - +
148E GLY* 1.3 56.1 + - - +
150E HIS* 3.9 11.3 - - - +
151E ARG* 3.5 40.4 - - + +
314E CYS* 3.9 15.7 - - - +
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Residues in contact with GLY 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E TYR* 3.4 4.0 + - - -
145E TRP 3.0 16.9 + - - +
146E LEU 3.2 0.6 - - - -
147E LEU* 1.3 81.4 - - - +
149E LEU* 1.3 66.5 + - - -
150E HIS* 3.3 12.3 + - - -
151E ARG* 3.1 15.3 + - - +
152E ALA 3.8 1.2 + - - -
314E CYS* 3.2 17.7 - - - -
315E PHE* 4.3 3.8 - - - -
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Residues in contact with LEU 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E TYR* 3.6 18.1 + - + +
118E MET* 3.7 36.6 - - + -
148E GLY* 1.3 72.4 - - - -
150E HIS* 1.3 54.8 + - - +
152E ALA* 2.8 32.6 + - + +
157E ARG* 3.8 26.7 - - + +
160E SER* 3.2 25.4 - - - +
314E CYS 2.6 18.2 + - - +
315E PHE* 3.3 24.4 - - - +
316E VAL* 4.0 12.1 - - - +
317E GLU* 4.5 4.0 - - - +
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Residues in contact with HIS 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E LEU* 3.9 8.6 + - - +
148E GLY* 3.8 22.7 - - - -
149E LEU* 1.3 78.5 + - - +
151E ARG* 1.3 96.6 + - + +
152E ALA 3.4 1.7 + - - +
157E ARG* 4.1 26.9 + - - +
314E CYS* 4.6 6.9 + - + -
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Residues in contact with ARG 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E GLU* 3.7 49.5 + - + +
145E TRP* 3.5 14.4 + - - -
147E LEU* 3.5 29.4 - - + +
148E GLY 3.1 10.8 + - - +
149E LEU 2.9 1.6 + - - -
150E HIS* 1.3 103.4 + - + +
152E ALA* 1.3 64.3 + - - +
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Residues in contact with ALA 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E TYR* 3.8 34.1 - - + +
145E TRP* 3.9 6.7 - - + -
148E GLY 3.8 1.4 + - - -
149E LEU* 2.8 19.0 + - + +
150E HIS 4.2 0.3 - - - +
151E ARG* 1.3 83.5 - - - +
153E PRO* 1.3 83.1 - - + +
156E LEU* 4.5 2.9 - - + -
157E ARG* 3.5 17.5 + - - +
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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