Contacts of the helix formed by residues 112 - 128 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197D GLY* 6.5 1.8 - - - -
73E HIS* 3.9 12.1 - - + -
75E ILE* 3.8 18.4 - - + -
110E LEU 3.6 1.8 - - - +
111E ASN* 1.3 96.4 - - - +
113E LYS* 1.3 64.3 + - - +
114E ALA* 3.4 2.5 - - + +
115E ASN* 3.0 32.2 + - - +
116E ARG* 3.3 5.7 + - - +
177E ARG* 2.8 13.2 - - - +
179E ASP* 5.0 4.3 - - - +
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Residues in contact with LYS 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D GLU 3.5 8.9 + - - +
196D ARG* 3.1 51.9 - - + +
197D GLY* 5.2 1.6 - - - +
111E ASN 3.5 2.5 + - - -
112E PRO* 1.3 69.1 - - - +
114E ALA* 1.3 63.2 + - + +
116E ARG* 3.2 19.9 + - - +
117E GLU* 3.2 19.0 + - - +
177E ARG* 4.8 0.2 - - - +
371E HIS* 3.5 33.9 - - + +
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Residues in contact with ALA 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E PRO* 3.4 1.9 - - + +
113E LYS* 1.3 77.1 - - + +
115E ASN* 1.3 62.9 + - - +
117E GLU* 3.7 12.4 - - - +
118E LYS* 2.8 29.0 + - - +
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Residues in contact with ASN 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E ILE* 3.3 28.7 - - - +
76E VAL* 3.5 19.0 + - - +
79E TRP* 4.1 19.6 - - + +
111E ASN* 3.2 24.0 + - - +
112E PRO* 3.0 23.2 + - - +
114E ALA* 1.3 78.1 + - - +
116E ARG* 1.3 64.6 + - - +
118E LYS* 3.0 3.5 + - - +
119E MET* 2.9 28.9 + - + +
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Residues in contact with ARG 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E GLU* 3.0 52.8 + - - +
111E ASN* 3.5 23.8 - - - +
112E PRO 3.3 4.0 + - - +
113E LYS* 3.2 12.9 + - - +
115E ASN* 1.3 74.8 - - - +
117E GLU* 1.3 61.9 + - - +
119E MET* 3.4 13.8 + - + +
120E THR* 2.9 28.5 + - - -
134E VAL* 4.4 8.6 + - + +
370E VAL* 3.2 35.0 + - + +
371E HIS* 3.8 20.9 + - + +
374E CYS* 3.0 36.6 + - - +
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Residues in contact with GLU 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E LYS* 3.2 16.7 + - - +
114E ALA* 3.8 11.8 - - - +
115E ASN 3.2 0.4 - - - -
116E ARG* 1.3 73.8 - - - +
118E LYS* 1.3 66.5 + - - +
120E THR* 2.9 3.5 + - - -
121E GLN* 2.9 26.0 + - - +
367E PRO* 3.9 29.5 - - + +
368E SER* 4.2 14.7 + - - -
370E VAL* 4.0 7.6 - - - -
371E HIS* 2.8 29.9 + - + +
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Residues in contact with LYS 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E TRP* 3.4 54.9 - - + +
80E ASP* 5.7 0.4 + - - -
83E GLU* 4.5 5.7 + - - -
114E ALA 2.8 23.1 + - - +
115E ASN 3.0 4.0 + - - +
117E GLU* 1.3 70.8 - - - +
119E MET* 1.3 57.7 + - - +
121E GLN* 3.1 17.3 - - + +
122E ILE* 3.0 50.7 + - + +
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Residues in contact with MET 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ASN* 5.7 0.7 - - - -
76E VAL* 6.4 1.8 - - + -
79E TRP* 4.2 13.4 - - + -
86E TRP* 4.2 21.1 - - + -
105E LEU* 3.5 28.3 - - + -
106E THR 4.7 5.2 - - - +
107E GLU* 4.4 7.9 - - + -
111E ASN* 3.5 28.7 - - - +
115E ASN* 2.9 18.6 + - + +
116E ARG* 3.5 11.4 - - - +
118E LYS* 1.3 76.7 - - - +
120E THR* 1.4 61.3 + - - +
122E ILE* 4.6 3.4 - - - +
123E MET* 3.2 30.8 + - - +
132E MET* 3.9 0.7 - - - +
134E VAL* 3.9 25.1 - - + -
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Residues in contact with THR 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ARG 2.9 14.5 + - - -
117E GLU 2.9 7.7 + - - -
119E MET* 1.4 75.1 - - - +
121E GLN* 1.3 60.6 + - - +
123E MET* 3.6 0.9 + - - +
124E PHE* 2.9 50.1 + - + -
132E MET* 4.1 15.0 - - - -
357E ILE* 5.3 2.2 - - + -
362E TYR* 3.7 25.8 - - + -
367E PRO* 4.2 10.5 - - + +
369E ILE* 4.9 6.3 - - + -
370E VAL* 3.0 28.4 - - + +
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Residues in contact with GLN 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E GLU* 2.9 12.1 + - - +
118E LYS* 3.1 25.7 - - + +
120E THR* 1.3 75.9 - - - +
122E ILE* 1.4 58.2 + - + +
124E PHE* 3.7 0.3 - - - +
125E GLU* 2.9 70.9 + - - +
362E TYR* 3.3 17.4 + - - -
367E PRO* 3.9 20.7 - - + +
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Residues in contact with ILE 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E TRP* 3.5 35.2 - - + -
83E GLU* 3.9 29.6 - - + +
86E TRP* 4.1 17.3 - - + -
118E LYS* 3.0 34.2 + - + +
119E MET* 4.4 3.1 - - - +
121E GLN* 1.4 75.2 - - + +
123E MET* 1.3 69.4 + - - +
126E THR* 2.8 38.2 + - - +
127E PHE* 2.9 32.7 + - + -
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Residues in contact with MET 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E TRP* 3.5 41.1 - - + -
90E PHE* 4.0 16.6 - - + -
103E VAL* 3.8 22.4 - - - -
105E LEU* 3.8 15.5 - - + -
119E MET 3.2 21.6 + - - +
120E THR 3.9 1.8 - - - +
122E ILE* 1.3 82.9 - - + +
124E PHE* 1.3 57.1 + - - +
127E PHE* 3.1 38.7 + - + +
128E ASN 3.2 3.1 + - - -
129E THR* 2.7 27.4 + - - +
132E MET* 3.8 25.8 - - + -
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Residues in contact with PHE 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E THR* 2.9 36.1 + - + +
121E GLN 3.2 0.2 + - - -
123E MET* 1.3 76.1 - - - +
125E GLU* 1.3 59.6 + - - +
128E ASN* 3.0 26.5 - - - +
129E THR* 3.0 33.7 - - - +
131E ALA* 4.0 4.7 - - - -
132E MET* 3.6 22.7 - - + -
357E ILE* 3.6 28.5 - - + -
358E SER 4.0 6.7 - - - -
359E LYS* 3.7 36.1 + - + +
362E TYR* 3.3 44.6 - + + -
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Residues in contact with GLU 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E GLN* 2.9 41.9 + - + +
124E PHE* 1.3 72.9 - - - +
126E THR* 1.3 66.1 + - - +
128E ASN* 4.4 4.7 + - - +
359E LYS* 4.7 6.1 - - - +
362E TYR* 2.8 31.5 + - + +
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Residues in contact with THR 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E GLU* 3.9 23.5 + - - +
122E ILE* 2.8 35.1 + - + +
125E GLU* 1.3 76.4 - - - +
127E PHE* 1.3 79.9 + - + +
128E ASN* 5.4 0.2 - - - +
120N LYS* 6.6 0.7 - - - -
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Residues in contact with PHE 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E TYR 5.8 0.2 - - - -
83E GLU* 4.0 11.4 - - + -
86E TRP* 3.9 16.6 - + + -
87E HIS* 3.7 41.5 - - + -
90E PHE* 4.2 8.3 - + + -
91E TYR* 4.1 24.7 + + - -
98E PRO* 3.3 32.6 - - + +
99E GLU* 3.8 6.4 - - - +
122E ILE* 2.9 34.4 + - + -
123E MET* 3.4 26.7 - - + +
126E THR* 1.3 89.7 - - + +
128E ASN* 1.3 72.8 + - - +
129E THR* 3.4 5.4 - - - +
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Residues in contact with ASN 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E GLU* 3.1 38.4 + - + +
123E MET 3.2 1.0 + - - -
124E PHE 3.0 19.8 + - - +
125E GLU 5.1 4.3 - - - +
126E THR 3.6 1.6 - - - +
127E PHE* 1.3 81.5 - - - +
129E THR* 1.3 61.9 + - - +
130E PRO 3.9 0.2 - - - -
359E LYS* 3.8 20.3 + - - +
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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