Contacts of the helix formed by residues 133 - 150 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128O GLU* 2.9 31.6 + - + +
131O ASP* 3.3 5.7 - - + -
132O GLY* 1.3 74.6 - - - +
134O LEU* 1.3 57.3 + - - +
135O LYS* 3.2 10.9 + - - +
136O MET* 2.6 42.1 + - + +
137O THR* 2.6 37.0 + - - -
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Residues in contact with LEU 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O GLU* 3.2 37.0 - - + +
48O ARG* 4.2 17.0 - - - -
69O ILE* 4.2 17.9 - - + -
70O GLU* 3.8 26.2 - - + +
132O GLY 3.2 5.4 + - - +
133O ASN* 1.3 71.5 + - - +
135O LYS* 1.3 66.7 + - - +
137O THR* 3.1 3.5 + - - -
138O LEU* 2.8 41.1 + - + +
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Residues in contact with LYS 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O TRP* 4.7 24.6 - - + -
44O GLU* 3.7 25.2 + - - +
133O ASN* 3.2 9.3 + - - +
134O LEU* 1.3 78.0 - - - +
136O MET* 1.3 58.7 + - + +
138O LEU* 3.6 5.8 + - - +
139O GLY* 2.9 25.6 + - - -
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Residues in contact with MET 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D VAL* 2.1 46.0 - - + +
55D GLY* 5.6 0.2 - - - -
123O SER 3.7 0.2 - - - -
124O ILE* 4.2 23.9 - - + +
128O GLU* 3.0 49.6 - - + +
129O ILE* 4.1 6.2 - - + +
133O ASN* 2.6 27.5 + - - +
135O LYS* 1.3 72.1 - - + +
137O THR* 1.3 59.8 + - - +
139O GLY* 3.3 1.5 + - - -
140O MET* 2.9 28.8 + - - +
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Residues in contact with THR 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69O ILE* 3.8 38.1 - - + +
70O GLU* 5.3 2.3 - - - -
73O PHE* 4.7 9.4 - - + -
129O ILE* 4.2 22.4 + - + +
132O GLY* 4.3 4.9 - - - -
133O ASN 2.6 29.3 + - - -
134O LEU* 3.7 6.5 - - - -
136O MET* 1.3 74.3 - - - +
138O LEU* 1.3 65.9 + - - +
140O MET* 3.2 16.0 + - + +
141O ILE* 3.0 23.2 + - + +
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Residues in contact with LEU 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ARG* 3.4 2.0 + - - -
43O TRP* 5.1 4.0 - - + -
44O GLU* 3.9 31.6 - - + +
47O GLN* 4.0 22.2 - - + +
48O ARG* 3.9 19.3 - - - +
51O PHE* 3.3 31.4 - - + -
69O ILE* 4.1 22.7 - - + -
134O LEU* 2.8 42.8 + - + +
135O LYS* 4.0 4.3 - - - +
137O THR* 1.3 74.3 - - - +
139O GLY* 1.3 63.1 + - - +
141O ILE* 4.5 0.7 - - - +
142O TRP 3.1 18.4 + - - -
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Residues in contact with GLY 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ASN* 2.7 45.8 + - - -
124O ILE* 4.0 4.9 - - - -
135O LYS 2.9 17.6 + - - -
136O MET* 3.7 2.2 - - - -
137O THR 3.2 0.2 - - - -
138O LEU* 1.3 78.5 - - - +
140O MET* 1.3 59.4 + - - +
142O TRP 3.4 0.2 + - - -
143O THR* 2.8 16.5 + - - -
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Residues in contact with MET 140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73O PHE* 4.9 4.7 - - + -
79O LEU* 3.5 46.4 - - + -
111O LEU* 3.8 23.1 - - + -
114O ILE* 4.5 6.1 - - + -
121O LEU* 5.3 2.2 - - + -
124O ILE* 3.8 15.6 - - + +
129O ILE* 3.8 30.3 - - + -
136O MET 2.9 14.4 + - - +
137O THR* 3.5 16.6 - - + +
139O GLY* 1.3 76.6 - - - +
141O ILE* 1.3 75.0 + - + +
143O THR* 3.1 8.3 + - - -
144O ILE* 3.0 28.3 + - + +
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Residues in contact with ILE 141 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O PHE* 4.0 17.0 - - + -
54O TRP* 4.7 2.2 - - + -
55O CYS* 3.8 24.0 - - - -
69O ILE* 4.3 15.5 - - + -
73O PHE* 3.7 27.6 - - + -
79O LEU* 4.3 10.3 - - + -
82O LEU* 4.3 6.7 - - + -
137O THR* 3.0 16.7 + - + +
138O LEU* 4.0 4.0 - - - +
139O GLY 3.4 0.2 - - - -
140O MET* 1.3 85.8 - - + +
142O TRP* 1.3 61.9 + - - +
144O ILE* 3.1 7.5 + - + +
145O ILE* 2.7 44.7 + - + +
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Residues in contact with TRP 142 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D PHE 3.2 1.2 + - - -
91D TYR* 1.2 77.7 - + + +
92D ASN* 3.7 0.7 - - - +
95D ARG* 1.6 79.6 - - + +
96D VAL 2.8 35.2 - - - -
97D ALA* 4.6 0.7 - - + -
51O PHE* 5.0 1.3 - + - -
138O LEU 3.1 10.8 + - - +
139O GLY 3.8 1.6 - - - +
140O MET 3.3 0.2 - - - -
141O ILE* 1.3 75.6 - - - +
143O THR* 1.3 55.2 + - - +
145O ILE* 2.9 24.8 + - + -
146O LEU* 2.7 42.0 + - + +
150O ILE* 4.1 19.3 - - + -
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Residues in contact with THR 143 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D HIS* 4.1 16.7 + - + +
91D TYR* 4.6 4.2 - - + +
92D ASN* 3.3 11.1 + - - -
114O ILE* 4.4 6.7 - - + -
119O VAL* 3.1 35.4 - - + -
120O LYS 5.6 0.9 - - - +
121O LEU* 4.6 8.3 - - + -
124O ILE* 4.4 5.7 - - - +
139O GLY 2.8 20.3 + - - -
140O MET* 3.1 13.1 + - - -
142O TRP* 1.3 80.6 - - - +
144O ILE* 1.3 56.5 + - - +
146O LEU* 3.9 3.9 - - - +
147O ARG* 2.9 31.9 + - + +
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Residues in contact with ILE 144 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54O TRP* 4.2 11.4 - - + -
79O LEU* 3.9 24.9 - - + -
82O LEU* 4.9 5.4 - - + -
83O LEU* 3.8 14.1 - - + -
86O ILE* 3.5 28.0 - - + +
114O ILE* 3.4 38.6 - - + -
140O MET* 3.0 17.8 + - + +
141O ILE* 3.5 16.8 - - + +
143O THR* 1.3 74.2 - - - +
145O ILE* 1.3 59.9 + - - +
147O ARG* 4.6 0.7 - - - -
148O PHE* 2.9 38.2 + - + +
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Residues in contact with ILE 145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ARG* 3.9 1.1 - - - +
51O PHE* 3.7 35.7 - - + -
54O TRP* 3.6 55.2 - - + +
141O ILE* 2.7 31.0 + - + +
142O TRP* 3.4 23.8 - - + +
144O ILE* 1.3 72.0 - - - +
146O LEU* 1.3 64.9 + - - +
149O ALA* 3.0 27.1 + - + +
150O ILE* 3.5 10.5 + - + +
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Residues in contact with LEU 146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D TYR* 1.0 92.7 - - + +
96D VAL 3.8 8.5 - - - +
97D ALA* 4.0 15.7 - - + -
98D PRO* 4.2 0.7 - - + -
99D GLU* 4.4 6.1 - - - +
142O TRP* 2.7 24.3 + - + +
143O THR 3.9 2.5 - - - +
145O ILE* 1.3 74.7 - - - +
147O ARG* 1.3 61.7 + - - +
150O ILE* 3.2 53.2 + - + +
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Residues in contact with ARG 147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117O LYS* 3.3 42.7 + - + +
118O GLY 5.8 0.2 - - - -
119O VAL* 3.6 25.6 - - + -
143O THR 2.9 20.7 + - - +
144O ILE* 4.6 0.2 - - - -
146O LEU* 1.3 80.4 - - - +
148O PHE* 1.3 84.9 + - + +
150O ILE 4.8 2.6 + - - -
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Residues in contact with PHE 148 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54O TRP* 5.7 0.4 - - + -
83O LEU* 3.9 13.5 - - + -
86O ILE* 3.4 41.4 - - + +
87O SER* 3.8 33.4 - - - -
89O GLU* 5.4 0.2 - - - -
113O PHE* 3.7 16.6 - + - -
114O ILE* 4.6 12.3 - - + -
117O LYS* 3.5 35.7 - - + -
144O ILE* 2.9 26.0 + - + +
147O ARG* 1.3 93.7 - - + +
149O ALA* 1.3 59.5 + - + +
150O ILE 3.9 0.2 - - - -
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Residues in contact with ALA 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54O TRP* 4.2 25.4 - - + +
58O HIS* 5.8 1.3 - - - +
145O ILE* 3.0 16.5 + - + +
148O PHE* 1.3 80.4 - - - +
150O ILE* 1.3 68.6 + - + +
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Residues in contact with ILE 150 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ALA* 3.7 7.0 - - + -
99D GLU* 3.5 26.9 - - - +
100D GLU* 3.5 24.0 - - - +
142O TRP* 4.1 29.2 - - + -
145O ILE* 3.5 13.4 + - + +
146O LEU* 3.2 33.7 + - + +
147O ARG 4.7 2.9 + - - -
149O ALA* 1.3 87.5 - - + +
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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