Contacts of the helix formed by residues 133 - 150 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128N GLU* 2.9 31.9 + - + +
131N ASP* 3.3 5.5 - - + -
132N GLY* 1.3 74.9 - - - +
134N LEU* 1.3 57.3 + - - +
135N LYS* 3.2 11.3 + - - +
136N MET* 2.6 40.8 + - - +
137N THR* 2.6 36.4 + - - -
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Residues in contact with LEU 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N GLU* 3.2 37.7 - - + +
48N ARG* 4.2 16.4 - - - -
69N ILE* 4.2 17.9 - - + -
70N GLU* 3.8 26.5 - - + -
132N GLY 3.2 6.2 + - - +
133N ASN* 1.3 71.7 + - - +
135N LYS* 1.3 67.3 + - - +
137N THR* 3.1 2.9 + - - -
138N LEU* 2.8 41.0 + - + +
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Residues in contact with LYS 135 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N TRP* 4.7 24.4 - - + -
44N GLU* 3.7 25.7 + - - +
133N ASN* 3.2 9.0 + - - +
134N LEU* 1.3 78.5 - - - +
136N MET* 1.3 58.8 + - + +
138N LEU* 3.6 5.7 + - - +
139N GLY* 2.9 25.6 + - - -
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Residues in contact with MET 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E VAL* 2.1 46.0 - - + +
55E GLY* 5.6 0.2 - - - -
124N ILE* 4.2 25.0 - - + +
128N GLU* 3.0 49.1 - - + +
129N ILE* 4.1 6.5 - - + +
133N ASN* 2.6 27.3 + - - +
135N LYS* 1.3 71.4 - - + +
137N THR* 1.3 59.3 + - - +
139N GLY* 3.3 2.2 + - - +
140N MET* 2.9 28.4 + - - +
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Residues in contact with THR 137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69N ILE* 3.8 38.7 + - + +
70N GLU* 5.3 2.3 - - - -
73N PHE* 4.7 9.9 - - + -
129N ILE* 4.2 22.6 + - + +
132N GLY* 4.3 4.7 - - - -
133N ASN 2.6 30.4 + - - -
134N LEU* 3.7 6.3 - - - -
136N MET* 1.3 73.9 - - - +
138N LEU* 1.3 66.1 + - - +
140N MET* 3.2 15.5 + - + +
141N ILE* 3.0 23.0 + - + +
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Residues in contact with LEU 138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ARG* 3.4 2.0 + - - -
43N TRP* 5.1 4.7 - - + -
44N GLU* 3.9 30.3 - - + +
47N GLN* 4.0 21.5 - - + +
48N ARG* 3.9 19.5 - - - +
51N PHE* 3.3 32.0 - - + -
69N ILE* 4.1 23.1 - - + -
134N LEU* 2.8 44.1 + - + +
135N LYS* 4.0 4.7 - - - +
137N THR* 1.3 73.5 - - - +
139N GLY* 1.3 62.4 + - - +
141N ILE* 3.4 0.8 + - - +
142N TRP 3.1 18.4 + - - -
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Residues in contact with GLY 139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E ASN* 2.7 45.7 + - - -
124N ILE* 4.0 5.4 - - - -
135N LYS 2.9 18.3 + - - -
136N MET 3.7 1.8 - - - -
138N LEU* 1.3 78.0 - - - +
140N MET* 1.3 59.4 + - - +
142N TRP* 3.4 0.4 + - - -
143N THR* 2.8 16.2 + - - -
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Residues in contact with MET 140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N PHE* 4.9 4.0 - - + -
79N LEU* 3.5 46.2 - - + -
111N LEU* 3.8 22.7 - - + -
114N ILE* 4.5 5.8 - - + -
121N LEU* 5.3 2.5 - - + -
124N ILE* 3.8 15.1 - - + +
129N ILE* 3.8 31.2 - - + -
136N MET 2.9 14.0 + - - +
137N THR* 3.2 15.9 + - + +
139N GLY* 1.3 76.1 - - - +
141N ILE* 1.3 76.3 + - + +
143N THR* 3.1 8.7 + - - -
144N ILE* 3.0 29.0 + - + +
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Residues in contact with ILE 141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N PHE* 4.0 16.6 - - + -
54N TRP* 4.7 1.8 - - + -
55N CYS* 3.8 23.3 - - - -
69N ILE* 4.3 14.8 - - + -
73N PHE* 3.7 28.7 - - + -
79N LEU* 4.3 9.9 - - + -
82N LEU* 4.3 6.7 - - + -
137N THR* 3.0 17.2 + - + +
138N LEU* 4.0 3.8 - - - +
139N GLY 3.4 0.2 - - - -
140N MET* 1.3 85.6 - - + +
142N TRP* 1.3 60.9 + - - +
144N ILE* 3.1 8.3 + - + +
145N ILE* 2.7 45.9 + - + +
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Residues in contact with TRP 142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E PHE 3.2 1.2 + - - -
91E TYR* 1.2 78.6 - + + +
92E ASN* 3.7 0.7 - - - +
95E ARG* 1.6 79.3 - - + +
96E VAL 2.8 36.3 - - - -
97E ALA* 4.6 0.4 - - + -
51N PHE* 5.0 0.4 - + - -
138N LEU 3.1 9.9 + - - +
139N GLY 3.8 1.8 - - - +
141N ILE* 1.3 74.9 - - - +
143N THR* 1.3 54.3 + - - +
145N ILE* 2.9 24.7 + - + +
146N LEU* 2.7 41.0 + - + +
150N ILE* 4.1 19.7 - - + -
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Residues in contact with THR 143 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E HIS* 4.1 16.2 + - + +
91E TYR* 4.6 3.7 - - + +
92E ASN* 3.3 12.0 + - - -
114N ILE* 4.4 6.7 - - + -
119N VAL* 3.1 36.1 - - + -
120N LYS 5.6 0.9 - - - +
121N LEU* 4.6 7.9 - - + -
124N ILE* 4.4 5.7 - - - +
139N GLY 2.8 19.2 + - - -
140N MET* 3.1 12.7 + - - -
142N TRP* 1.3 81.2 - - - +
144N ILE* 1.3 57.6 + - - +
146N LEU* 3.9 4.1 - - - +
147N ARG* 2.9 30.9 + - + +
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Residues in contact with ILE 144 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54N TRP* 4.2 11.9 - - + -
79N LEU* 3.9 24.2 - - + -
82N LEU* 4.9 6.1 - - + -
83N LEU* 3.8 14.1 - - + -
86N ILE* 3.5 28.0 - - + +
114N ILE* 3.4 39.5 - - + -
140N MET* 3.0 18.1 + - + +
141N ILE* 3.5 16.4 - - + +
142N TRP 3.1 0.2 - - - -
143N THR* 1.3 74.8 - - - +
145N ILE* 1.3 60.5 + - - +
147N ARG* 4.6 0.4 - - - -
148N PHE* 2.9 39.0 + - + +
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Residues in contact with ILE 145 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ARG* 3.9 0.9 - - - +
51N PHE* 3.7 35.9 - - + -
54N TRP* 3.6 54.5 - - + +
141N ILE* 2.7 31.7 + - + +
142N TRP* 2.9 24.4 + - + +
144N ILE* 1.3 71.2 - - - +
146N LEU* 1.3 63.1 + - - +
149N ALA* 3.0 27.4 + - + +
150N ILE* 3.5 10.5 + - + +
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Residues in contact with LEU 146 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E TYR* 1.0 93.1 - - + +
96E VAL 3.8 8.5 - - - +
97E ALA* 4.0 15.7 - - + -
98E PRO* 4.6 0.7 - - + -
99E GLU* 4.4 6.1 - - - +
142N TRP* 2.7 25.0 + - + +
143N THR 3.9 2.5 - - - +
145N ILE* 1.3 75.9 - - - +
147N ARG* 1.3 62.0 + - - +
150N ILE* 3.2 53.2 + - + +
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Residues in contact with ARG 147 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114N ILE* 5.7 0.2 - - + -
117N LYS* 3.3 43.5 + - + +
119N VAL* 3.6 26.0 - - + -
143N THR 2.9 20.7 + - - +
146N LEU* 1.3 80.1 - - - +
148N PHE* 1.3 85.6 + - + +
149N ALA 3.9 0.2 + - - -
150N ILE 4.8 2.3 + - - -
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Residues in contact with PHE 148 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54N TRP* 5.7 0.4 - - + -
83N LEU* 3.9 14.1 - - + -
86N ILE* 3.4 39.7 - - + +
87N SER* 3.8 32.5 - - - -
89N GLU* 5.4 0.2 - - - -
113N PHE* 3.7 16.2 - + - -
114N ILE* 4.6 11.9 - - + -
117N LYS* 3.5 36.3 - - + -
144N ILE* 2.9 26.2 + - + +
147N ARG* 1.3 92.3 - - + +
149N ALA* 1.3 59.6 + - + +
150N ILE 3.9 0.2 - - - -
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Residues in contact with ALA 149 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54N TRP* 4.2 26.5 - - + +
58N HIS* 5.8 1.1 - - - +
145N ILE* 3.0 17.3 + - + +
148N PHE* 1.3 79.5 - - - +
150N ILE* 1.3 69.7 + - + +
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Residues in contact with ILE 150 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ALA* 3.7 7.0 - - + -
99E GLU* 3.5 26.2 - - - +
100E GLU* 3.5 24.5 - - - +
142N TRP* 4.1 28.9 - - + -
145N ILE* 4.2 12.1 - - + +
146N LEU* 3.2 34.4 + - + +
147N ARG 5.3 2.0 - - - -
148N PHE 3.9 0.4 - - - -
149N ALA* 1.3 89.2 - - + +
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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