Contacts of the helix formed by residues 112 - 128 (chain D) 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 PRO 112 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197C GLY* 6.5 1.6 - - - -
73D HIS* 3.9 12.3 - - + -
75D ILE* 3.8 18.4 - - + -
110D LEU 3.6 1.6 - - - +
111D ASN* 1.3 96.3 - - - +
113D LYS* 1.3 65.4 + - - +
114D ALA* 3.4 2.5 - - + +
115D ASN* 3.0 32.5 + - - +
116D ARG* 3.3 5.7 + - - +
177D ARG* 2.8 14.1 - - - +
179D ASP* 5.0 5.2 - - - +
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Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C GLU 3.5 9.1 + - - +
196C ARG* 3.1 49.8 - - - +
197C GLY* 5.2 1.6 - - - +
111D ASN 3.5 2.1 + - - -
112D PRO* 1.3 70.3 - - - +
114D ALA* 1.3 64.9 + - + +
116D ARG* 3.2 20.1 + - - +
117D GLU* 3.2 18.4 + - - +
177D ARG* 4.8 0.4 - - - +
371D HIS* 3.5 33.9 - - + +
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Residues in contact with ALA 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D PRO* 3.4 1.9 - - + +
113D LYS* 1.3 76.8 - - + +
115D ASN* 1.3 63.5 + - - +
117D GLU* 3.7 11.8 - - - +
118D LYS* 2.8 29.4 + - - +
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Residues in contact with ASN 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ILE* 3.3 27.9 - - - +
76D VAL 3.5 18.6 + - - +
79D TRP* 4.1 21.1 - - + +
111D ASN* 3.2 24.1 + - - +
112D PRO* 3.0 23.6 + - - +
114D ALA* 1.3 79.1 + - - +
116D ARG* 1.3 65.1 + - - +
118D LYS* 3.0 2.9 + - - +
119D MET* 2.9 28.3 + - + +
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Residues in contact with ARG 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D GLU* 3.0 53.1 + - - +
111D ASN* 3.5 23.1 - - - +
112D PRO 3.3 4.0 + - - +
113D LYS* 3.2 12.9 + - - +
115D ASN* 1.3 76.0 - - - +
117D GLU* 1.3 61.3 + - - +
119D MET* 3.4 13.7 + - + +
120D THR* 2.9 27.9 + - - -
134D VAL* 4.4 8.6 - - + +
370D VAL* 3.2 35.7 + - + +
371D HIS* 3.8 21.5 + - + +
374D CYS* 3.0 36.8 + - - +
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Residues in contact with GLU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LYS* 3.2 16.9 + - - +
114D ALA* 3.8 11.0 - - - +
115D ASN 3.2 0.2 - - - -
116D ARG* 1.3 74.0 - - - +
118D LYS* 1.3 65.6 + - - +
120D THR* 2.9 4.0 + - - -
121D GLN* 2.9 24.8 + - - +
367D PRO* 3.9 29.6 - - + +
368D SER* 4.2 13.8 + - - -
370D VAL* 4.0 7.9 - - - -
371D HIS* 2.8 30.1 + - + +
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Residues in contact with LYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D TRP* 3.4 53.5 - - + +
80D ASP* 5.7 0.4 + - - -
83D GLU* 4.5 5.7 + - - -
114D ALA 2.8 22.2 + - - +
115D ASN 3.0 3.8 + - - +
117D GLU* 1.3 70.4 - - - +
119D MET* 1.3 57.4 + - - +
121D GLN* 3.1 16.5 - - + +
122D ILE* 3.0 51.6 + - + +
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Residues in contact with MET 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ASN* 5.7 0.7 - - - -
76D VAL* 6.4 1.8 - - + -
79D TRP* 4.2 14.5 - - + -
86D TRP* 4.2 22.7 - - + -
105D LEU* 3.5 27.4 - - + -
106D THR 4.7 4.9 - - - +
107D GLU* 4.4 7.9 - - + -
111D ASN* 3.5 28.7 - - - +
115D ASN* 2.9 19.5 + - + +
116D ARG* 3.5 11.2 - - - +
118D LYS* 1.3 76.9 - - - +
120D THR* 1.4 61.3 + - - +
122D ILE* 4.4 3.8 - - - +
123D MET* 3.2 31.0 + - - +
132D MET* 3.9 0.7 - - - +
134D VAL* 3.9 24.7 - - + -
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Residues in contact with THR 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ARG 2.9 14.7 + - - -
117D GLU 2.9 7.5 + - - -
119D MET* 1.4 73.5 - - - +
121D GLN* 1.3 59.4 + - - +
123D MET* 3.6 1.2 + - - +
124D PHE* 2.9 50.5 + - + +
132D MET* 4.1 15.5 - - - -
357D ILE* 5.3 1.6 - - + -
362D TYR* 3.7 26.2 - - + -
367D PRO* 4.2 10.5 - - - +
369D ILE* 4.9 6.5 - - + -
370D VAL* 3.0 28.2 - - + +
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Residues in contact with GLN 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D GLU* 2.9 12.6 + - - +
118D LYS* 3.1 25.5 - - + +
120D THR* 1.3 76.9 - - - +
122D ILE* 1.4 57.8 + - + +
124D PHE* 3.7 0.3 - - - +
125D GLU* 2.9 71.1 + - - +
362D TYR* 3.3 16.7 + - - -
367D PRO* 3.9 20.1 - - + +
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Residues in contact with ILE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D TRP* 3.5 35.9 - - + -
83D GLU* 3.9 30.7 - - + +
86D TRP* 4.1 17.0 - - + -
118D LYS* 3.0 34.2 + - + +
119D MET* 4.4 3.4 - - - +
121D GLN* 1.4 74.2 - - + +
123D MET* 1.3 70.7 + - - +
126D THR* 2.8 38.7 + - - +
127D PHE* 2.9 30.9 + - + -
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Residues in contact with MET 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D TRP* 3.5 41.3 - - + -
90D PHE* 4.0 17.0 - - + -
103D VAL* 3.8 22.7 - - - -
105D LEU* 3.8 15.3 - - + -
119D MET 3.2 20.7 + - - +
120D THR 3.9 1.8 - - - +
122D ILE* 1.3 81.9 - - + +
124D PHE* 1.3 56.6 + - - +
127D PHE* 3.1 37.2 + - + +
128D ASN 3.2 3.3 + - - -
129D THR* 2.7 27.0 + - - +
132D MET* 3.8 26.0 - - + -
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Residues in contact with PHE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D THR* 2.9 36.4 + - + +
123D MET* 1.3 77.5 - - - +
125D GLU* 1.3 58.3 + - - +
128D ASN* 3.0 26.0 - - - +
129D THR* 3.0 33.4 - - - +
131D ALA* 4.0 6.1 - - - -
132D MET* 3.6 23.3 - - + -
357D ILE* 3.6 28.9 - - + -
358D SER 4.0 6.7 - - - -
359D LYS* 3.7 36.7 + - + +
362D TYR* 3.3 44.6 - + + -
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D GLN* 2.9 41.9 + - - +
124D PHE* 1.3 73.1 - - - +
126D THR* 1.4 65.7 + - - +
128D ASN* 4.4 4.9 + - - +
359D LYS* 4.7 6.7 - - - +
362D TYR* 2.8 31.4 + - + +
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Residues in contact with THR 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D GLU* 3.9 22.7 + - - +
122D ILE* 2.8 35.8 + - + +
125D GLU* 1.4 77.1 - - - +
127D PHE* 1.3 79.0 + - + +
128D ASN* 5.4 0.3 - - - +
120O LYS* 6.6 0.2 - - - -
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Residues in contact with PHE 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D TYR 5.8 0.2 - - - -
83D GLU* 4.0 11.2 - - + -
86D TRP* 3.9 16.6 - + + -
87D HIS* 3.7 40.4 - - + -
90D PHE* 4.2 7.6 - + + -
91D TYR* 4.1 24.3 + + - -
98D PRO* 3.3 31.3 - - + +
99D GLU* 3.8 6.4 - - - +
122D ILE* 2.9 34.4 + - + -
123D MET* 3.4 26.5 - - + +
126D THR* 1.3 89.5 - - + +
128D ASN* 1.3 73.7 + - - +
129D THR* 3.4 5.4 - - - +
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Residues in contact with ASN 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D GLU* 3.1 37.8 + - + +
123D MET 3.2 0.8 + - - -
124D PHE 3.0 20.2 + - - +
125D GLU 5.1 3.6 - - - +
126D THR 3.6 1.6 - - - +
127D PHE* 1.3 81.7 - - - +
129D THR* 1.3 61.6 + - - +
130D PRO 3.9 0.2 - - - -
359D LYS* 3.8 20.5 + - - +
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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
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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