Contacts of the helix formed by residues 137 - 145 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11J ASP* 4.3 5.1 - - - +
12J ASN 4.0 18.2 + - - -
13J GLY* 5.9 1.0 - - - -
74J GLY* 5.1 3.8 + - - -
106J THR* 3.8 12.7 + - - +
107J GLU* 3.0 35.9 + - - +
108J ALA* 3.3 10.7 - - - +
109J PRO* 4.7 1.1 - - + +
135J ALA 4.5 0.2 - - - -
136J ILE* 1.3 72.7 - - - +
138J ALA* 1.4 61.5 + - - +
140J LEU* 3.2 14.4 + - - +
141J SER 3.3 8.5 + - - -
154J ASP* 2.9 11.2 - - - +
156J GLY* 4.0 21.7 - - - -
157J ASP 5.6 2.0 - - - +
339J VAL* 3.4 39.7 - - + +
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Residues in contact with ALA 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J PRO* 4.8 0.7 - - + -
136J ILE* 3.5 9.1 - - + +
137J GLN* 1.4 70.1 - - - +
139J VAL* 1.3 61.7 + - - +
141J SER* 3.3 4.9 + - - -
142J LEU* 3.1 18.4 + - - +
152J VAL* 3.5 15.2 - - + +
154J ASP* 1.5 66.3 + - + +
161J HIS 4.7 3.6 - - - +
163J VAL* 5.0 7.2 - - + -
300J SER* 3.6 1.1 - - - +
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Residues in contact with VAL 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H VAL 4.9 6.8 - - - +
45H VAL* 3.1 18.4 - - - +
135J ALA* 6.1 1.3 - - + -
136J ILE* 3.5 24.8 + - + +
137J GLN 3.3 1.0 - - - -
138J ALA* 1.3 77.3 - - - +
140J LEU* 1.3 59.1 + - + +
142J LEU* 3.6 4.8 - - - +
143J TYR* 3.3 9.7 + - + +
163J VAL* 3.6 38.8 - - + -
165J ILE* 5.3 1.1 - - + -
170J ALA* 4.8 7.0 - - + -
375J PHE* 4.7 21.5 - - + -
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Residues in contact with LEU 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J VAL* 5.2 0.4 - - + -
104J LEU* 3.9 6.5 - - + -
106J THR* 3.2 30.7 - - + -
135J ALA* 3.4 22.4 - - + -
136J ILE 2.9 30.1 - - - +
137J GLN 3.2 4.6 + - - +
139J VAL* 1.3 77.9 - - + +
141J SER* 1.3 65.6 + - - +
142J LEU 3.3 0.2 - - - -
143J TYR* 4.5 3.8 - - - +
144J ALA* 3.1 19.8 + - - +
338J SER 4.2 1.1 - - - -
339J VAL* 3.3 25.6 - - + +
342J GLY* 3.1 14.8 - - - +
343J GLY* 3.6 27.4 - - - +
346J LEU* 5.7 4.9 - - + -
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Residues in contact with SER 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H VAL* 2.4 21.2 - - - +
137J GLN 3.3 2.4 + - - -
138J ALA 3.3 5.6 + - - -
140J LEU* 1.3 77.7 - - - +
142J LEU* 1.3 54.8 + - - -
144J ALA* 3.5 3.3 + - - +
145J SER* 3.4 15.4 + - - -
154J ASP* 3.4 1.0 + - - -
300J SER* 2.8 42.3 + - - -
338J SER* 3.6 22.9 + - - -
339J VAL* 3.2 23.9 - - - +
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Residues in contact with LEU 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H VAL 3.1 1.8 - - - +
44H MET* 2.1 22.4 - - - -
45H VAL* 0.9 384.2 - - + +
47H MET 3.2 7.1 - - - +
138J ALA 3.1 4.1 + - - +
139J VAL 3.6 4.9 - - - +
141J SER* 1.3 67.7 - - - +
143J TYR* 1.3 61.7 + - - -
145J SER* 2.8 13.7 + - - -
152J VAL* 2.1 28.5 - - + -
165J ILE* 1.5 53.8 - - + -
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Residues in contact with TYR 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H GLN* 5.4 2.0 - - + -
42H GLY 3.4 16.2 - - - -
43H VAL* 3.6 21.7 + - + +
45H VAL* 1.9 12.9 - - - +
47H MET 3.6 7.6 - - - +
48H GLY* 4.3 1.6 - - - -
49H GLN* 0.5 204.1 + - + +
139J VAL* 3.3 13.3 + - + +
140J LEU* 4.1 7.0 - - - +
142J LEU* 1.3 68.0 - - - +
144J ALA* 1.3 61.4 + - - +
145J SER 3.2 2.8 + - - -
168J GLY 4.7 0.2 - - - -
342J GLY 4.6 8.1 - - - +
345J ILE* 4.0 30.9 - - + +
346J LEU* 4.7 19.3 - - + -
349J LEU* 4.4 3.6 - - + -
101S PHE* 4.9 1.6 - - + +
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Residues in contact with ALA 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J LEU 3.1 19.1 + - - +
141J SER 3.8 5.6 - - - +
142J LEU 3.2 0.4 - - - -
143J TYR* 1.3 75.9 - - - +
145J SER* 1.3 56.3 + - - +
146J GLY 4.6 0.2 + - - -
338J SER* 4.1 10.8 - - - +
341J ILE* 4.0 9.6 - - + +
342J GLY* 3.4 22.6 - - - +
345J ILE* 4.0 16.5 - - + +
100S ARG* 5.9 2.9 - - - +
101S PHE* 4.9 4.9 - - - -
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Residues in contact with SER 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H VAL* 2.7 12.0 + - - -
46H GLY* 2.7 34.6 + - - -
47H MET 3.5 12.3 - - - -
48H GLY* 4.2 3.6 - - - -
141J SER 3.4 9.2 + - - -
142J LEU 2.8 8.1 + - - -
143J TYR 4.0 1.6 - - - -
144J ALA* 1.3 79.0 - - - +
146J GLY* 1.3 60.9 + - - +
147J ARG* 1.9 16.1 + - - -
298J VAL* 5.7 4.0 - - - -
100S ARG* 4.9 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