Contacts of the helix formed by residues 141 - 149 (chain A) in PDB entry 3KHE
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 THR 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A ASP* 5.9 1.3 - - - +
137A SER* 5.3 0.9 - - - +
139A LYS 4.2 3.8 - - - +
140A ILE* 1.3 77.3 - - - +
142A ASN* 1.3 66.3 + - - +
143A GLU* 3.4 17.6 + - - +
144A GLU* 3.1 32.5 + - - +
145A LEU 3.0 17.8 + - - -
159A TRP* 3.4 12.5 - - - -
172A GLY 5.1 0.2 - - - -
173A GLU* 3.7 34.3 - - + +
193A CA 4.5 2.2 - - - -
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Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A THR* 1.3 74.4 - - - +
143A GLU* 1.3 64.5 + - - +
145A LEU* 3.0 5.4 + - - +
146A GLY* 2.9 25.3 + - - -
153A GLU* 3.3 11.1 + - - +
154A VAL* 2.7 57.5 + - - +
155A ASP 4.4 1.6 + - - -
156A ASP* 4.9 6.1 + - - -
159A TRP* 3.4 44.8 - - + +
172A GLY 5.2 0.2 + - - -
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A THR* 3.3 19.9 + - - +
142A ASN* 1.3 86.0 + - - +
144A GLU* 1.3 58.6 + - + +
146A GLY* 3.3 1.7 + - - -
147A ARG* 2.9 27.2 + - - +
151A VAL 4.4 0.2 - - - +
152A THR* 3.5 26.7 - - - +
153A GLU* 4.5 10.7 - - + +
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Residues in contact with GLU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PHE* 3.4 25.3 - - - +
133A ASP* 3.7 0.5 - - - +
134A SER* 3.3 13.8 + - - +
135A ASP* 2.9 30.0 + - - +
139A LYS 3.1 9.4 - - - +
140A ILE* 3.2 8.8 - - + -
141A THR* 3.1 28.1 + - - +
143A GLU* 1.3 75.8 - - + +
145A LEU* 1.3 68.7 + - - +
147A ARG* 3.4 16.5 + - - +
148A LEU* 3.5 15.9 - - - +
193A CA 2.5 29.9 - - - -
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LYS* 4.1 2.5 - - + +
21A LEU* 3.8 34.8 - - + +
140A ILE* 4.4 4.3 - - + +
141A THR 3.0 6.4 + - - +
142A ASN 3.0 8.5 + - - +
144A GLU* 1.3 74.9 - - - +
146A GLY* 1.3 64.1 + - - +
148A LEU* 3.1 29.0 + - + +
149A PHE* 3.5 27.1 - - + -
154A VAL* 3.9 9.4 - - + -
158A THR* 4.0 24.5 - - + -
159A TRP* 3.7 35.0 - - + -
162A VAL* 4.1 13.0 - - + -
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Residues in contact with GLY 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ASN 2.9 12.1 + - - -
143A GLU 3.6 3.6 - - - -
144A GLU 3.2 0.2 - - - -
145A LEU* 1.3 76.5 - - - +
147A ARG* 1.3 55.9 + - - +
149A PHE* 2.8 19.9 + - - -
151A VAL* 2.9 36.4 + - - +
153A GLU 4.3 4.7 - - - -
154A VAL* 3.7 18.5 - - - +
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Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLN 2.9 27.9 + - - -
132A PHE* 4.2 4.4 + - - +
134A SER* 3.6 27.1 + - - -
143A GLU 2.9 13.3 + - - +
144A GLU* 3.6 12.2 + - - +
145A LEU 3.3 0.4 - - - -
146A GLY* 1.3 73.4 - - - +
148A LEU* 1.3 86.1 + - - +
150A GLY* 3.2 13.1 + - - +
151A VAL 3.1 9.0 + - - +
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.7 0.9 - - + -
24A ALA* 3.7 26.5 - - + -
132A PHE* 3.6 47.1 - - + -
144A GLU 3.5 12.8 - - - +
145A LEU* 3.1 23.5 + - + +
147A ARG* 1.3 101.8 - - - +
149A PHE* 1.3 68.8 + - + +
150A GLY 3.4 1.4 + - - -
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Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LYS* 3.2 45.3 - - + -
23A GLN* 3.9 20.4 - - - -
24A ALA* 3.9 16.8 - - + -
100A ARG* 4.2 11.9 - - - -
145A LEU* 3.5 34.5 - - + -
146A GLY* 2.8 7.8 + - - +
148A LEU* 1.3 80.7 - - + +
150A GLY* 1.3 62.5 + - - +
151A VAL* 3.3 20.1 + - + +
154A VAL* 5.3 4.5 - - + -
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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