Contacts of the helix formed by residues 133 - 150 (chain Q) 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 ASN 133 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128Q GLU* 2.9 33.0 + - + +
131Q ASP* 3.3 5.3 - - + -
132Q GLY* 1.3 75.6 - - - +
134Q LEU* 1.3 56.5 + - - +
135Q LYS* 3.2 11.4 + - - +
136Q MET* 2.6 42.3 + - - +
137Q THR* 2.6 37.0 + - - -
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Residues in contact with LEU 134 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Q GLU* 3.2 37.5 - - + +
48Q ARG* 4.2 17.3 - - - -
69Q ILE* 4.2 17.5 - - + -
70Q GLU* 3.8 26.0 - - + -
132Q GLY 3.2 5.8 + - - +
133Q ASN* 1.3 70.1 + - - +
135Q LYS* 1.3 67.9 + - + +
137Q THR* 3.1 4.0 + - - -
138Q LEU* 2.8 40.7 + - + +
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Residues in contact with LYS 135 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Q TRP* 4.7 23.9 - - + -
44Q GLU* 3.7 25.9 + - - +
133Q ASN* 3.2 8.8 + - - +
134Q LEU* 1.3 78.5 - - - +
136Q MET* 1.3 58.6 + - + +
138Q LEU* 3.9 5.7 - - - +
139Q GLY* 2.9 25.5 + - - -
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Residues in contact with MET 136 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F VAL* 2.1 46.7 - - + +
55F GLY* 5.6 0.2 - - - -
57F GLU* 6.2 0.2 - - - -
124Q ILE* 4.2 25.0 - - + +
128Q GLU* 3.0 48.5 - - + +
129Q ILE* 4.1 5.8 - - + +
133Q ASN* 2.6 28.1 + - - +
135Q LYS* 1.3 70.6 - - + +
137Q THR* 1.3 58.9 + - - +
139Q GLY* 3.3 1.7 + - - -
140Q MET* 2.9 28.4 + - - +
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Residues in contact with THR 137 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Q ILE* 3.8 38.0 + - + +
70Q GLU* 5.3 2.2 - - - -
73Q PHE* 4.7 10.1 - - + -
129Q ILE* 4.2 22.6 + - + +
132Q GLY* 4.3 5.0 - - - -
133Q ASN 2.6 29.6 + - - -
134Q LEU* 3.7 6.3 - - - -
136Q MET* 1.3 74.1 - - - +
138Q LEU* 1.3 66.3 + - - +
140Q MET* 3.2 15.8 + - + +
141Q ILE* 3.0 23.3 + - + +
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Residues in contact with LEU 138 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F ARG* 3.4 1.7 + - - -
43Q TRP* 5.1 4.3 - - + -
44Q GLU* 3.9 31.0 - - + +
47Q GLN* 4.0 21.1 - - + +
48Q ARG* 3.9 18.8 - - + +
51Q PHE* 3.3 32.3 - - + -
69Q ILE* 4.0 23.6 - - + -
134Q LEU* 2.8 43.3 + - + +
135Q LYS* 4.0 4.7 - - - +
137Q THR* 1.3 73.1 - - - +
139Q GLY* 1.3 63.1 + - - +
141Q ILE* 3.4 1.2 + - - -
142Q TRP 3.1 18.9 + - - -
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Residues in contact with GLY 139 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ASN* 2.7 47.1 + - - -
124Q ILE* 4.0 5.6 - - - -
135Q LYS 2.9 17.9 + - - -
136Q MET* 3.3 2.4 + - - -
138Q LEU* 1.3 78.1 - - - +
140Q MET* 1.3 59.0 + - - +
142Q TRP 3.4 0.2 + - - -
143Q THR* 2.8 15.8 + - - -
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Residues in contact with MET 140 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73Q PHE* 4.9 4.0 - - + -
79Q LEU* 3.5 45.5 - - + -
111Q LEU* 3.8 23.6 - - + -
114Q ILE* 4.5 6.2 - - + +
121Q LEU* 5.3 2.9 - - + -
124Q ILE* 3.8 14.9 - - + +
129Q ILE* 3.8 30.5 - - + -
136Q MET 2.9 13.6 + - - +
137Q THR* 3.2 15.7 + - + +
139Q GLY* 1.3 77.0 - - - +
141Q ILE* 1.3 74.8 + - + +
143Q THR* 3.1 7.8 + - - -
144Q ILE* 3.0 29.7 + - + +
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Residues in contact with ILE 141 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Q PHE* 4.0 16.4 - - + -
54Q TRP* 4.7 1.6 - - + -
55Q CYS* 3.8 23.3 - - - -
69Q ILE* 4.3 15.0 - - + -
73Q PHE* 3.7 29.2 - - + -
79Q LEU* 4.3 9.9 - - + -
82Q LEU* 4.3 6.5 - - + -
137Q THR* 3.0 17.1 + - + +
138Q LEU* 4.0 3.8 - - - +
140Q MET* 1.3 86.9 - - + +
142Q TRP* 1.3 60.8 + - - +
144Q ILE* 3.1 9.1 + - + +
145Q ILE* 2.7 45.4 + - + +
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Residues in contact with TRP 142 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F PHE 3.2 1.8 + - - -
91F TYR* 1.2 78.5 - + + +
92F ASN* 3.7 0.9 - - - +
95F ARG* 1.6 80.2 - - + +
96F VAL* 2.8 35.2 - - - -
97F ALA* 5.2 0.2 - - + -
51Q PHE* 5.0 1.3 - + - -
138Q LEU 3.1 10.4 + - - +
139Q GLY* 3.8 1.6 - - - +
141Q ILE* 1.3 76.7 - - - +
143Q THR* 1.3 53.8 + - - +
145Q ILE* 2.9 24.1 + - + -
146Q LEU* 2.7 41.2 + - + +
150Q ILE* 4.1 20.0 - - + -
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Residues in contact with THR 143 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F HIS* 4.1 17.4 + - + +
91F TYR* 4.5 4.1 - - + +
92F ASN* 3.3 11.1 + - - -
114Q ILE* 4.4 7.2 - - + -
119Q VAL* 3.1 35.7 - - + -
120Q LYS 5.6 0.9 - - - +
121Q LEU* 4.6 8.3 - - + -
124Q ILE* 4.4 5.7 - - - +
139Q GLY 2.8 20.7 + - - -
140Q MET* 3.2 12.1 - - - -
142Q TRP* 1.3 79.8 - - - +
144Q ILE* 1.3 57.2 + - - +
146Q LEU* 3.9 4.6 - - - +
147Q ARG* 2.9 31.2 + - - +
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Residues in contact with ILE 144 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q TRP* 4.2 11.8 - - + -
79Q LEU* 3.9 24.2 - - + -
82Q LEU* 4.9 6.7 - - + -
83Q LEU* 3.8 13.9 - - + -
86Q ILE* 3.5 27.5 - - + +
114Q ILE* 3.4 39.0 - - + -
140Q MET* 3.0 17.3 + - + +
141Q ILE* 3.5 15.7 - - + +
143Q THR* 1.3 76.8 - - - +
145Q ILE* 1.3 60.9 + - - +
147Q ARG* 4.6 0.4 - - - -
148Q PHE* 2.9 38.9 + - + +
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Residues in contact with ILE 145 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F ARG* 3.9 1.6 - - - +
50Q THR* 6.4 0.2 - - + -
51Q PHE* 3.7 35.4 - - + -
54Q TRP* 3.6 55.2 - - + +
141Q ILE* 2.7 30.6 + - + +
142Q TRP* 3.4 24.2 - - + +
144Q ILE* 1.3 72.0 - - - +
146Q LEU* 1.3 64.5 + - - +
149Q ALA* 3.0 26.9 + - + +
150Q ILE* 3.5 10.7 + - + +
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Residues in contact with LEU 146 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F TYR* 1.0 94.4 - - + +
96F VAL 3.8 8.5 - - - +
97F ALA* 4.0 16.4 - - + -
98F PRO* 4.6 0.9 - - + -
99F GLU* 4.4 5.8 - - - +
142Q TRP* 2.7 25.4 + - + +
143Q THR 3.9 2.0 - - - +
145Q ILE* 1.3 76.6 - - - +
147Q ARG* 1.3 62.8 + - - +
150Q ILE* 3.2 53.9 + - + +
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Residues in contact with ARG 147 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117Q LYS* 3.3 42.4 + - + +
118Q GLY 5.8 0.2 - - - -
119Q VAL* 3.6 26.2 - - + -
143Q THR 2.9 18.8 + - - +
144Q ILE* 4.6 0.2 - - - -
146Q LEU* 1.3 79.9 - - - +
148Q PHE* 1.3 85.5 + - + +
149Q ALA 3.9 0.2 + - - -
150Q ILE 4.8 2.3 + - - -
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Residues in contact with PHE 148 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Q TRP* 5.7 0.7 - - + -
83Q LEU* 3.9 14.4 - - + -
86Q ILE* 3.4 39.6 - - + +
87Q SER* 3.8 33.2 - - - -
113Q PHE* 3.7 15.9 - + - -
114Q ILE* 4.6 11.7 - - + -
117Q LYS* 3.5 37.7 - - + -
144Q ILE* 2.9 26.6 + - + +
147Q ARG* 1.3 92.8 - - + +
149Q ALA* 1.3 60.8 + - + +
150Q ILE 3.9 0.2 - - - -
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Residues in contact with ALA 149 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Q TRP* 4.2 26.2 - - + +
58Q HIS* 5.8 0.7 - - - +
145Q ILE* 3.0 17.7 + - + +
148Q PHE* 1.3 79.3 - - - +
150Q ILE* 1.3 68.7 + - + +
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Residues in contact with ILE 150 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F ALA* 3.7 7.0 - - + -
99F GLU* 3.5 26.1 - - - +
100F GLU* 3.5 24.5 - - - +
142Q TRP* 4.1 29.6 - - + -
145Q ILE* 3.5 12.3 + - + +
146Q LEU* 3.2 34.3 + - + +
147Q ARG 4.7 2.4 - - - -
148Q PHE 3.9 0.2 - - - -
149Q ALA* 1.3 88.5 - - + +
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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
------------------------------------------------------------
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