Contacts of the helix formed by residues 139 - 148 (chain A) in PDB entry 2QNJ
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 GLU 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A GLY 4.0 0.5 + - - +
138A GLY* 1.3 74.0 - - - -
140A VAL* 1.3 67.4 + - - +
141A PHE* 4.4 1.5 - - - +
142A ASP* 3.1 35.2 + - - +
143A TYR* 3.0 21.1 + - - +
181A ALA* 3.9 12.9 - - + +
182A GLU* 3.3 40.1 + - - +
184A LEU 3.4 6.7 - - - +
185A LEU* 3.8 17.4 - - + +
186A LEU* 4.7 1.1 - - - -
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Residues in contact with VAL 140 (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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138A GLY 3.8 0.8 + - - -
139A GLU* 1.3 71.8 - - - +
141A PHE* 1.3 58.7 + - - +
143A TYR* 2.9 6.6 + - - +
144A LEU* 2.8 37.1 + - + +
150A MET* 4.9 8.5 - - + -
158A LYS* 6.5 0.4 - - + -
162A ILE* 5.9 0.2 - - + -
181A ALA 4.6 0.4 + - - +
184A LEU* 2.9 49.0 + - + +
185A LEU 4.0 3.6 - - - +
186A LEU* 3.6 33.9 - - + -
192A ILE* 4.2 10.8 - - + -
242A ILE* 6.0 0.4 - - + -
245A THR* 5.6 0.9 - - - +
246A LEU* 3.9 28.0 - - + -
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Residues in contact with PHE 141 (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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139A GLU* 3.2 1.9 - - + +
140A VAL* 1.3 79.2 - - - +
142A ASP* 1.3 62.6 + - - +
144A LEU* 3.1 11.2 + - + +
145A VAL* 2.8 49.6 + - + +
181A ALA* 3.7 29.8 + - + +
218A TYR* 4.2 8.1 - - - +
245A THR* 4.0 36.1 - - + -
249A GLY 4.7 3.8 - - - -
250A SER* 4.5 14.6 - - - -
251A LEU* 4.3 24.5 - - + -
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Residues in contact with ASP 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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139A GLU* 3.1 41.0 + - + +
141A PHE* 1.3 82.5 - - - +
143A TYR* 1.3 56.2 + - - +
145A VAL* 3.1 7.8 + - - +
146A ALA* 2.8 32.0 + - - +
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Residues in contact with TYR 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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137A GLY 5.2 5.8 - - - +
139A GLU 3.0 6.6 + - - +
140A VAL 2.9 9.7 + - - +
142A ASP* 1.3 74.5 - - - +
144A LEU* 1.3 63.5 + - + +
146A ALA* 4.6 1.1 - - - -
147A HIS* 2.9 65.2 + + + +
148A GLY 4.7 4.5 - - - -
150A MET* 4.0 32.1 - - + -
154A GLU* 3.9 10.1 + - - -
186A LEU* 3.7 26.2 - - + -
190A MET* 3.5 29.7 - - + +
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Residues in contact with LEU 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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140A VAL* 2.8 34.8 + - + +
141A PHE* 3.1 17.9 + - + +
143A TYR* 1.3 78.0 - - + +
145A VAL* 1.3 58.2 + - - +
148A GLY* 2.8 48.9 + - - +
149A ARG* 4.0 2.9 - - - -
150A MET* 4.0 19.7 - - + +
245A THR* 3.5 47.1 - - - +
246A LEU* 3.8 16.8 - - - +
249A GLY* 4.4 13.6 - - - +
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Residues in contact with VAL 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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141A PHE* 2.8 54.1 + - + +
142A ASP* 3.8 7.4 - - - +
144A LEU* 1.3 72.7 - - - +
146A ALA* 1.3 66.3 + - - +
148A GLY* 4.0 3.1 + - - -
249A GLY 4.9 8.1 - - - +
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Residues in contact with ALA 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 ASP 2.8 20.4 + - - +
143A TYR* 3.9 2.9 - - - +
145A VAL* 1.3 79.7 - - - +
147A HIS* 1.3 83.5 + - + +
148A GLY 3.6 0.5 + - - -
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Residues in contact with HIS 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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143A TYR* 2.9 63.3 + + + +
146A ALA* 1.3 89.0 + - + +
148A GLY* 1.3 61.9 + - - +
149A ARG 4.6 1.9 - - - +
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Residues in contact with GLY 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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143A TYR* 4.2 5.2 - - - +
144A LEU* 2.8 34.8 + - - +
145A VAL 4.0 2.1 + - - -
146A ALA 3.5 3.8 + - - -
147A HIS* 1.3 75.3 - - - +
149A ARG* 1.3 66.6 + - - -
150A MET 3.8 0.9 + - - -
249A GLY* 4.9 1.6 - - - -
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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