Contacts of the helix formed by residues 137 - 145 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E ASP* 4.3 6.1 - - - +
12E ASN 4.0 17.5 + - - -
13E GLY* 5.9 1.7 - - - -
74E GLY* 5.1 3.8 + - - -
106E THR* 3.8 13.3 + - - +
107E GLU* 3.0 35.0 + - - +
108E ALA* 3.3 10.3 - - - +
109E PRO* 4.7 1.3 - - - +
136E ILE* 1.3 74.3 - - - +
138E ALA* 1.4 62.9 + - - +
140E LEU* 3.2 15.0 + - - +
141E SER 3.3 8.7 + - - -
154E ASP* 2.9 10.7 - - - +
156E GLY* 4.0 21.9 - - - -
157E ASP 5.0 2.5 + - - +
339E VAL* 3.4 37.6 - - + +
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Residues in contact with ALA 138 (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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109E PRO* 4.8 0.7 - - + -
136E ILE* 3.5 9.3 - - + +
137E GLN* 1.4 69.7 - - - +
139E VAL* 1.3 62.9 + - - +
141E SER* 3.3 5.8 + - - -
142E LEU* 3.1 17.7 + - - +
152E VAL* 3.5 14.8 - - + +
154E ASP* 1.5 65.7 + - + +
161E HIS* 4.7 3.8 - - + +
163E VAL* 5.0 7.0 - - + -
300E SER* 3.6 1.3 - - - +
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Residues in contact with VAL 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C VAL 4.9 7.1 - - - +
45C VAL* 3.1 18.5 - - - +
135E ALA* 6.1 1.3 - - + -
136E ILE* 3.5 25.5 + - + +
137E GLN 3.3 1.0 - - - -
138E ALA* 1.3 77.7 - - - +
140E LEU* 1.3 59.3 + - + +
142E LEU* 3.6 4.3 - - - +
143E TYR* 3.3 9.8 + - + +
152E VAL* 5.9 0.2 - - - -
163E VAL* 3.6 38.1 - - + -
165E ILE* 5.3 1.1 - - + -
170E ALA* 4.8 7.4 - - + -
375E PHE* 4.7 21.1 - - + -
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Residues in contact with LEU 140 (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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9E VAL* 5.2 0.4 - - + -
104E LEU* 3.9 6.5 - - + -
106E THR* 3.2 30.5 - - + -
135E ALA* 3.4 21.8 - - + -
136E ILE 2.9 29.8 - - - +
137E GLN 3.2 4.2 + - - +
139E VAL* 1.3 76.3 - - + +
141E SER* 1.3 65.2 + - - +
142E LEU 3.3 0.2 - - - -
143E TYR* 4.5 4.5 - - - +
144E ALA* 3.1 19.4 + - - +
338E SER 4.2 1.3 - - - -
339E VAL* 3.3 24.9 - - + +
342E GLY* 3.1 15.1 - - - +
343E GLY* 3.6 27.1 - - - +
346E LEU* 5.7 5.4 - - + -
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Residues in contact with SER 141 (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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45C VAL* 2.4 21.5 - - - +
137E GLN 3.3 2.2 + - - -
138E ALA 3.3 5.8 + - - -
140E LEU* 1.3 78.1 - - - +
142E LEU* 1.3 53.9 + - - -
144E ALA* 3.5 3.1 + - - +
145E SER* 3.4 15.2 + - - -
154E ASP* 3.4 1.4 + - - -
300E SER* 2.8 41.2 + - - -
338E SER* 3.6 21.9 + - - -
339E VAL* 3.2 23.3 - - - +
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Residues in contact with LEU 142 (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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43C VAL 3.1 2.2 - - - +
44C MET* 2.1 21.8 - - - -
45C VAL* 0.9 383.9 - - + +
47C MET 3.2 6.8 - - - +
138E ALA 3.1 4.4 + - - +
139E VAL 3.6 5.6 - - - +
141E SER* 1.3 66.5 - - - +
143E TYR* 1.3 61.6 + - - -
145E SER* 2.8 13.9 + - - -
152E VAL* 2.1 28.3 - - + -
165E ILE* 1.5 54.7 - - + -
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Residues in contact with TYR 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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41C GLN* 5.4 2.5 - - + -
42C GLY 3.4 15.7 - - - -
43C VAL* 3.6 21.4 + - + +
45C VAL* 1.9 12.5 - - - +
47C MET 3.6 7.3 - - - +
48C GLY* 4.3 1.2 - - - -
49C GLN* 0.5 205.1 + - + +
139E VAL* 3.3 12.6 + - + +
140E LEU* 4.1 7.2 - - - +
142E LEU 1.3 68.0 - - - +
144E ALA* 1.3 62.0 + - - +
145E SER 3.2 2.8 + - - -
168E GLY 4.7 0.2 - - - -
342E GLY 4.6 8.1 - - - +
345E ILE* 4.0 30.8 - - + +
346E LEU* 4.7 18.8 - - + -
349E LEU* 4.0 4.7 - - + +
101L PHE* 4.9 1.6 - - + +
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Residues in contact with ALA 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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140E LEU 3.1 19.5 + - - +
141E SER 3.8 5.2 - - - +
142E LEU 3.2 0.2 - - - -
143E TYR* 1.3 75.2 - - - +
145E SER* 1.3 57.4 + - - +
338E SER* 4.1 10.5 - - - +
341E ILE* 4.0 9.4 - - + +
342E GLY* 3.4 22.6 - - - +
345E ILE* 4.0 16.7 - - + +
100L ARG* 5.8 2.9 - - - +
101L PHE* 4.9 4.7 - - + -
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Residues in contact with SER 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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45C VAL* 2.7 13.2 - - - -
46C GLY* 2.7 34.7 + - - -
47C MET 3.5 13.2 - - - -
48C GLY* 4.2 3.4 - - - -
141E SER 3.4 9.0 + - - -
142E LEU 2.8 7.7 + - - -
143E TYR 4.0 1.3 - - - -
144E ALA* 1.3 79.0 - - - +
146E GLY* 1.3 62.3 + - - +
147E ARG* 1.9 15.7 + - - -
298E VAL* 5.7 4.0 - - - -
100L ARG* 4.8 2.5 - - - -
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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