Contacts of the helix formed by residues 109 - 123 (chain C) in PDB entry 1E3O
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 GLU 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C SER 3.8 4.1 + - - +
108C ILE* 1.3 75.7 - - - +
110C THR* 1.3 80.0 + - - +
111C ASN* 3.1 26.4 - - - +
112C ILE* 3.1 29.9 + - + +
113C ARG* 3.0 23.9 + - - +
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Residues in contact with THR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ILE 3.7 1.4 + - - -
109C GLU* 1.3 85.7 + - - +
111C ASN* 1.3 62.5 + - - +
113C ARG* 3.4 27.5 + - - +
114C VAL* 3.4 14.7 + - + +
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Residues in contact with ASN 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLU* 3.1 22.6 - - - +
110C THR* 1.3 73.9 + - - +
112C ILE* 1.3 84.8 + - - +
114C VAL* 2.6 30.0 - - + +
115C ALA* 3.2 8.8 + - - +
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Residues in contact with ILE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ILE* 3.8 2.7 - - + -
109C GLU* 3.1 33.4 + - + +
111C ASN* 1.3 85.9 - - - +
113C ARG* 1.3 58.7 + - - +
115C ALA* 3.3 6.7 + - - +
116C LEU* 2.8 42.0 + - + +
138C LEU* 3.6 37.9 - - + +
140C MET* 3.4 47.8 - - + -
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Residues in contact with ARG 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A G 3.3 27.4 + - - -
204A C 2.8 32.5 + - - +
107C SER* 4.2 8.1 + - - -
108C ILE* 3.1 28.6 + - + +
109C GLU 3.0 16.6 + - - +
110C THR* 3.4 18.8 + - - +
111C ASN 3.2 0.2 - - - -
112C ILE* 1.3 76.2 - - - +
114C VAL* 1.3 53.0 + - + +
116C LEU* 2.9 13.3 + - - +
117C GLU* 2.7 41.6 + - + +
148C TRP* 4.5 8.0 - - + +
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C THR* 3.5 10.3 - - + +
111C ASN* 2.6 41.5 - - + +
113C ARG* 1.3 75.7 - - + +
115C ALA* 1.3 58.0 + - + +
117C GLU* 3.1 12.3 + - - +
118C LYS* 2.9 27.4 + - - +
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Residues in contact with ALA 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C ASN 3.2 7.8 + - - +
112C ILE* 3.7 7.9 - - - +
113C ARG 3.2 0.4 - - - -
114C VAL* 1.3 78.6 - - + +
116C LEU* 1.3 67.0 + - - +
118C LYS* 3.0 10.3 + - - +
119C SER* 2.8 23.4 + - - -
138C LEU* 4.4 21.1 - - + -
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ILE* 4.3 9.2 - - + -
112C ILE* 2.8 38.0 + - + +
113C ARG* 3.2 9.9 - - - +
115C ALA* 1.3 76.9 - - - +
117C GLU* 1.3 56.2 + - - +
119C SER* 3.1 7.1 + - - -
120C PHE 2.8 24.9 + - - -
134C ILE* 4.5 6.3 - - + -
138C LEU* 3.7 22.2 - - + -
145C ILE* 3.9 21.1 - - + -
148C TRP* 3.6 49.0 - - + +
149C PHE* 4.2 21.5 - - + -
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Residues in contact with GLU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ARG* 2.7 24.1 + - + +
114C VAL* 3.1 11.4 + - - +
116C LEU* 1.3 71.5 - - - +
118C LYS* 1.3 66.1 + - - +
120C PHE* 3.2 6.4 + - - +
121C MET* 3.0 21.8 + - - +
148C TRP* 3.5 18.8 - - + -
152C ARG* 2.9 39.7 + - - -
155C LYS* 5.6 3.1 + - - -
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Residues in contact with LYS 118 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C VAL 2.9 12.7 + - - +
115C ALA* 3.2 14.1 - - - +
117C GLU* 1.3 75.1 - - - +
119C SER* 1.3 63.2 + - - +
121C MET* 3.0 22.9 - - - +
122C GLU* 3.2 15.6 + - - +
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Residues in contact with SER 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ALA 2.8 12.5 + - - -
116C LEU* 3.1 11.0 + - - -
118C LYS* 1.3 76.6 - - - +
120C PHE* 1.3 65.2 + - - +
122C GLU* 2.7 27.8 + - - +
123C ASN* 2.9 15.3 + - - +
126C PRO* 5.6 0.7 - - - +
134C ILE* 4.2 20.2 - - - +
149C PHE* 3.4 19.6 - - - -
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Residues in contact with PHE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU 2.8 15.4 + - - +
117C GLU* 3.4 10.3 - - - +
119C SER* 1.3 72.7 + - - +
121C MET* 1.3 64.3 - - - +
123C ASN 3.2 22.1 - - - -
124C GLN* 3.3 68.8 + - + +
148C TRP* 4.0 11.4 - - + -
149C PHE* 3.8 13.1 - + - -
152C ARG* 3.4 66.2 - - + -
153C ARG* 3.9 13.9 - - + -
156C GLU* 4.3 9.0 - - + -
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Residues in contact with MET 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C GLU 3.0 11.9 + - - +
118C LYS* 3.0 17.0 - - - +
120C PHE* 1.3 81.7 - - - +
122C GLU* 1.3 61.5 + - + +
124C GLN* 5.8 0.3 - - - +
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Residues in contact with GLU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LYS* 3.8 10.9 - - - +
119C SER* 2.7 25.9 + - - +
121C MET* 1.3 77.3 - - + +
123C ASN* 1.3 62.1 + - + +
124C GLN 4.4 0.3 + - - -
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Residues in contact with ASN 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C SER* 2.9 17.5 + - - +
120C PHE* 3.2 12.5 - - - +
122C GLU* 1.3 76.5 - - + +
124C GLN* 1.3 62.8 + - - +
125C LYS* 2.9 27.1 + - - +
126C PRO* 3.6 27.7 - - + +
127C THR* 6.1 0.2 - - - +
130C ASP* 4.3 9.3 + - - -
149C PHE* 3.7 2.4 - - - -
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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