Contacts of the helix formed by residues 133 - 150 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M GLU* 2.9 33.0 + - + +
131M ASP* 3.3 5.1 - - + -
132M GLY* 1.3 74.7 - - - +
134M LEU* 1.3 57.0 + - - +
135M LYS* 3.2 10.9 + - - +
136M MET* 2.6 43.0 + - + +
137M THR* 2.6 36.4 + - - -
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Residues in contact with LEU 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M GLU* 3.2 38.4 - - + +
48M ARG* 4.2 16.8 - - - -
69M ILE* 4.2 17.7 - - + -
70M GLU* 3.8 26.0 - - + -
132M GLY 3.2 6.2 + - - +
133M ASN* 1.3 69.7 + - - +
135M LYS* 1.3 67.2 + - - +
137M THR* 3.1 4.1 + - - -
138M LEU* 2.8 41.0 + - + +
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Residues in contact with LYS 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M TRP* 4.7 23.7 - - + -
44M GLU* 3.7 25.5 + - - +
133M ASN* 3.2 9.3 + - - +
134M LEU* 1.3 78.7 - - - +
136M MET* 1.3 59.3 + - + +
138M LEU* 3.9 5.7 - - - +
139M GLY* 2.9 26.0 + - - -
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Residues in contact with MET 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 2.1 46.9 - - + +
57B GLU* 6.2 0.2 - - - -
124M ILE* 4.2 25.4 - - + +
128M GLU* 3.0 49.1 - - + +
129M ILE* 4.1 6.1 - - + +
133M ASN* 2.6 27.3 + - - +
135M LYS* 1.3 70.8 - - + +
137M THR* 1.3 59.4 + - - +
139M GLY* 3.3 1.7 + - - -
140M MET* 2.9 28.2 + - - +
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Residues in contact with THR 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69M ILE* 3.8 38.1 + - + +
70M GLU* 5.3 2.6 - - - -
73M PHE* 4.7 10.3 - - + -
129M ILE* 4.2 22.6 + - + +
132M GLY* 4.3 4.9 - - - -
133M ASN 2.6 28.8 + - - -
134M LEU* 3.7 6.1 - - - -
136M MET* 1.3 73.8 - - - +
138M LEU* 1.3 66.0 + - - +
140M MET* 3.2 15.8 + - + +
141M ILE* 3.0 23.3 + - + +
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Residues in contact with LEU 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ARG* 3.4 1.3 + - - -
43M TRP* 5.1 4.5 - - + -
44M GLU* 3.9 31.0 - - + +
47M GLN* 4.0 21.5 - - + +
48M ARG* 3.9 19.3 - - + +
51M PHE* 3.3 32.7 - - + -
69M ILE* 4.1 23.3 - - + -
134M LEU* 2.8 43.9 + - + +
135M LYS* 4.0 4.5 - - - +
137M THR* 1.3 72.7 - - - +
139M GLY* 1.3 63.9 + - - +
141M ILE* 3.4 1.2 + - - -
142M TRP 3.1 18.4 + - - -
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Residues in contact with GLY 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ASN* 2.7 44.9 + - - -
124M ILE* 4.0 5.2 - - - -
135M LYS 2.9 18.1 + - - -
136M MET* 3.7 2.2 - - - -
138M LEU* 1.3 79.4 - - - +
140M MET* 1.3 59.3 + - - +
142M TRP* 3.4 1.1 + - - -
143M THR* 2.8 15.9 + - - -
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Residues in contact with MET 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73M PHE* 4.9 3.8 - - + -
79M LEU* 3.5 45.5 - - + -
111M LEU* 3.8 23.3 - - + -
114M ILE* 4.5 6.2 - - + +
121M LEU* 5.3 2.9 - - + -
124M ILE* 3.8 14.3 - - + +
129M ILE* 3.8 31.0 - - + -
136M MET 2.9 13.6 + - - +
137M THR* 3.2 15.7 + - + +
139M GLY* 1.3 76.8 - - - +
141M ILE* 1.3 74.9 + - + +
143M THR* 3.1 8.0 + - - -
144M ILE* 3.0 29.5 + - + +
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Residues in contact with ILE 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51M PHE* 4.0 16.8 - - + -
54M TRP* 4.7 1.6 - - + -
55M CYS* 3.8 23.3 - - - -
69M ILE* 4.3 14.8 - - + -
73M PHE* 3.7 28.5 - - + -
79M LEU* 4.3 9.9 - - + -
82M LEU* 4.3 6.5 - - + -
137M THR* 3.0 16.5 + - + +
138M LEU* 4.0 3.6 - - - +
140M MET* 1.3 87.3 - - + +
142M TRP* 1.3 61.8 + - - +
144M ILE* 3.1 8.9 + - + +
145M ILE* 2.7 45.7 + - + +
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Residues in contact with TRP 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE 3.2 1.4 + - - -
91B TYR* 1.2 78.3 - + + +
92B ASN* 3.7 0.9 - - - +
95B ARG* 1.6 79.6 - - + +
96B VAL 2.8 34.5 - - - -
97B ALA* 5.2 0.2 - - + -
51M PHE* 5.0 1.1 - + - -
138M LEU 3.1 10.2 + - - +
139M GLY 3.8 1.6 - - - +
141M ILE* 1.3 76.0 - - - +
143M THR* 1.3 53.4 + - - +
145M ILE* 2.9 25.6 + - + +
146M LEU* 2.7 41.2 + - + +
150M ILE* 4.1 19.5 - - + -
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Residues in contact with THR 143 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B HIS* 4.2 16.9 + - + +
91B TYR* 4.6 4.1 - - + +
92B ASN* 3.3 11.1 + - - -
114M ILE* 4.4 7.2 - - + -
119M VAL* 3.1 36.1 - - + -
120M LYS 5.6 0.9 - - - +
121M LEU* 4.6 8.1 - - + -
124M ILE* 4.4 5.5 - - - +
139M GLY 2.8 20.1 + - - -
140M MET* 3.1 12.7 + - - -
142M TRP* 1.3 79.8 - - - +
144M ILE* 1.3 56.8 + - - +
146M LEU* 3.6 5.0 + - - +
147M ARG* 2.9 31.4 + - - +
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Residues in contact with ILE 144 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M TRP* 4.2 11.8 - - + -
79M LEU* 3.9 24.7 - - + -
82M LEU* 4.9 6.7 - - + -
83M LEU* 3.8 13.7 - - + -
86M ILE* 3.5 27.8 - - + +
114M ILE* 3.4 39.0 - - + -
140M MET* 3.0 17.5 + - + +
141M ILE* 3.5 16.2 - - + +
142M TRP 3.1 0.2 - - - -
143M THR* 1.3 75.9 - - - +
145M ILE* 1.3 61.0 + - - +
147M ARG* 4.6 0.4 - - - -
148M PHE* 2.9 38.5 + - + +
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Residues in contact with ILE 145 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ARG* 3.9 1.1 - - - +
51M PHE* 3.7 35.9 - - + -
54M TRP* 3.6 55.0 - - + +
141M ILE* 2.7 29.8 + - + +
142M TRP* 3.4 23.8 - - + +
144M ILE* 1.3 72.2 - - - +
146M LEU* 1.3 65.4 + - - +
149M ALA* 3.0 27.1 + - + +
150M ILE* 3.5 10.3 + - + +
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Residues in contact with LEU 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B TYR* 1.0 94.2 - - + +
96B VAL 3.8 7.9 - - - +
97B ALA* 4.0 16.4 - - + -
98B PRO* 4.2 0.4 - - + -
99B GLU* 4.4 6.3 - - - +
142M TRP* 2.7 24.9 + - + +
143M THR 3.9 2.0 - - - +
145M ILE* 1.3 75.8 - - - +
147M ARG* 1.3 63.1 + - - +
150M ILE* 3.2 53.4 + - + +
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Residues in contact with ARG 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M ILE* 5.7 0.2 - - + -
117M LYS* 3.3 42.5 + - + +
118M GLY 5.8 0.2 - - - -
119M VAL* 3.6 26.5 - - + -
143M THR 2.9 18.8 + - - +
144M ILE* 4.6 0.2 - - - -
146M LEU* 1.3 79.7 - - - +
148M PHE* 1.3 85.4 + - + +
149M ALA 3.9 0.2 + - - -
150M ILE 4.8 2.1 + - - -
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Residues in contact with PHE 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M TRP* 5.7 0.7 - - + -
83M LEU* 3.9 14.6 - - + -
86M ILE* 3.4 40.2 - - + +
87M SER* 3.8 33.0 - - - -
113M PHE* 3.7 16.6 - + - -
114M ILE* 4.6 11.7 - - + -
117M LYS* 3.5 36.6 - - + -
144M ILE* 2.9 26.0 + - + +
147M ARG* 1.3 93.3 - - + +
149M ALA* 1.3 59.6 + - + +
150M ILE 3.9 0.2 - - - -
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Residues in contact with ALA 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M TRP* 4.2 26.0 - - + +
58M HIS* 5.8 0.9 - - - +
145M ILE* 3.0 17.7 + - + +
148M PHE* 1.3 78.6 - - - +
150M ILE* 1.3 68.1 + - + +
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Residues in contact with ILE 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA* 3.7 7.9 - - + -
99B GLU* 3.5 25.7 - - - +
100B GLU* 3.5 24.2 - - - +
142M TRP* 4.1 29.6 - - + -
145M ILE* 3.5 12.3 + - + +
146M LEU* 3.2 32.9 + - + +
147M ARG 4.7 2.7 - - - -
148M PHE 3.9 0.2 - - - -
149M ALA* 1.3 89.0 - - + +
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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
------------------------------------------------------------
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