Contacts of the helix formed by residues 137 - 145 (chain D) in PDB entry 3LUE
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 GLN 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D ASP* 4.3 6.6 - - - +
12D ASN 4.0 18.1 + - - -
13D GLY* 5.9 1.8 - - - -
74D GLY* 5.1 3.8 + - - -
106D THR* 3.8 13.1 + - - +
107D GLU* 3.0 34.5 + - - +
108D ALA* 3.3 10.7 - - - +
109D PRO* 4.7 1.3 - - + +
136D ILE* 1.3 73.0 - - - +
138D ALA* 1.4 61.8 + - - +
140D LEU* 3.2 15.5 + - - +
141D SER 3.3 8.3 + - - -
154D ASP* 2.9 10.7 - - - +
156D GLY* 4.0 22.0 - - - -
157D ASP 5.0 2.1 + - - +
339D VAL* 3.4 37.6 - - + +
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D PRO* 4.8 0.7 - - + -
136D ILE* 3.5 9.2 - - + +
137D GLN* 1.4 69.5 - - - +
139D VAL* 1.3 62.9 + - - +
141D SER* 3.3 5.0 + - - -
142D LEU* 3.1 18.2 + - - +
152D VAL* 3.5 15.4 - - + +
154D ASP* 1.5 67.8 + - + +
161D HIS* 4.7 3.4 - - + +
163D VAL* 5.0 8.3 - - + -
300D SER* 3.6 1.1 - - - +
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Residues in contact with VAL 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL 4.9 7.3 - - - +
45B VAL* 3.1 18.5 - - - +
135D ALA* 6.1 1.6 - - + -
136D ILE* 3.5 24.8 + - + +
137D GLN 3.3 0.6 - - - -
138D ALA* 1.3 77.0 - - - +
140D LEU* 1.3 60.2 + - + +
142D LEU* 3.6 4.6 - - - +
143D TYR* 3.3 10.1 + - + +
163D VAL* 3.6 39.3 - - + -
165D ILE* 5.3 0.9 - - + -
170D ALA* 4.8 7.6 - - + -
375D PHE* 4.7 21.8 - - + -
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 5.2 0.4 - - + -
104D LEU* 3.9 7.0 - - + -
106D THR* 3.3 30.5 - - + -
135D ALA* 3.4 20.9 - - + -
136D ILE 2.9 30.5 - - - +
137D GLN 3.2 5.0 + - - +
139D VAL* 1.3 76.1 - - + +
141D SER* 1.3 65.6 + - - +
142D LEU 3.3 0.2 - - - -
143D TYR* 4.5 4.0 - - - +
144D ALA* 3.1 19.6 + - - +
338D SER 4.2 1.6 - - - -
339D VAL* 3.3 25.6 - - + +
342D GLY* 3.1 14.9 - - - +
343D GLY* 3.6 27.4 - - - +
346D LEU* 5.7 5.4 - - + -
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Residues in contact with SER 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B VAL* 2.4 21.8 - - - +
137D GLN 3.3 1.8 + - - -
138D ALA 3.3 6.7 + - - -
140D LEU* 1.3 77.7 - - - +
142D LEU* 1.3 54.0 + - - -
144D ALA* 3.5 3.3 + - - +
145D SER* 3.4 14.7 + - - -
152D VAL* 4.4 0.2 - - - -
154D ASP* 3.4 1.6 + - - -
300D SER* 2.8 40.9 + - - -
338D SER* 3.6 22.8 + - - -
339D VAL* 3.2 24.1 - - - +
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL 3.1 2.0 - - - +
44B MET* 2.1 22.4 - - - -
45B VAL* 0.9 385.4 - - + +
47B MET 3.2 7.4 - - - +
138D ALA 3.1 4.9 + - - +
139D VAL 3.6 5.8 - - - +
141D SER* 1.3 66.7 - - - +
143D TYR* 1.3 62.0 + - - -
145D SER* 2.8 13.5 + - - -
152D VAL* 2.1 28.5 - - + -
165D ILE* 1.5 55.2 - - + -
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Residues in contact with TYR 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLN* 5.4 2.2 - - + -
42B GLY 3.4 16.6 - - - -
43B VAL* 3.6 22.3 + - + +
45B VAL* 1.9 12.7 - - - +
47B MET 3.6 7.8 - - - +
48B GLY* 4.3 1.0 - - - -
49B GLN* 0.5 205.6 + - + +
139D VAL* 3.3 13.9 + - + +
140D LEU* 4.1 7.0 - - - +
142D LEU 1.3 68.0 - - - +
144D ALA* 1.3 62.1 + - - +
145D SER 3.2 2.3 + - - -
168D GLY 4.7 0.2 - - - -
342D GLY 4.6 8.3 - - - +
345D ILE* 4.0 30.2 - - + +
346D LEU* 4.7 18.4 - - + -
349D LEU* 4.4 4.9 - - + -
101M PHE* 4.9 2.0 - - + +
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Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D LEU 3.1 19.9 + - - +
141D SER* 3.8 4.9 - - - +
142D LEU 3.2 0.2 - - - -
143D TYR* 1.3 75.9 - - - +
145D SER* 1.3 56.1 + - - +
338D SER* 4.1 10.5 - - - +
341D ILE* 4.0 9.4 - - + +
342D GLY* 3.4 22.8 - - - +
345D ILE* 4.0 16.8 - - + +
100M ARG* 5.8 3.3 - - - +
101M PHE* 4.9 4.3 - - + -
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Residues in contact with SER 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B VAL* 2.7 12.3 - - - -
46B GLY* 2.7 34.8 + - - -
47B MET 3.5 12.3 - - - -
48B GLY* 4.2 2.9 - - - -
141D SER 3.4 9.6 + - - -
142D LEU 2.8 7.7 + - - -
143D TYR 4.0 1.8 - - - -
144D ALA* 1.3 79.2 - - - +
146D GLY* 1.3 62.7 + - - +
147D ARG* 1.9 16.9 + - - -
298D VAL* 5.7 4.3 - - - -
100M ARG* 4.8 2.9 - - - -
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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