Contacts of the helix formed by residues 108 - 123 (chain C) in PDB entry 1EN5
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 SER 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C ILE* 4.2 0.4 - - - +
103C GLU* 3.9 16.5 + - - +
106C PHE* 3.2 5.1 + - - +
107C GLY* 1.3 79.9 - - - +
109C VAL* 1.3 64.6 + - - +
110C ASP* 3.7 10.5 + - - +
111C ASN* 3.3 29.0 + - - +
112C PHE* 3.1 21.5 + - - +
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Residues in contact with VAL 109 (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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94C LEU* 3.9 31.6 - - + -
99C LYS* 4.4 17.3 - - + -
102C ILE* 4.2 10.8 - - + -
103C GLU* 4.4 19.1 + - + +
108C SER* 1.3 74.3 - - - +
110C ASP* 1.3 62.8 + - - +
112C PHE* 3.2 7.1 + - + +
113C LYS* 2.9 47.2 + - + +
194C TRP* 6.2 0.4 - - + -
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Residues in contact with ASP 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 SER* 3.2 9.9 + - - +
109C VAL* 1.3 80.5 - - - +
111C ASN* 1.3 64.3 + - - +
113C LYS* 3.3 12.2 + - - +
114C ALA* 3.0 24.6 + - - +
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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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106C PHE* 3.0 31.1 + - + +
107C GLY* 4.5 3.2 - - - -
108C SER* 3.3 23.1 + - - +
110C ASP* 1.3 76.9 - - - +
112C PHE* 1.3 62.6 + - - +
114C ALA* 3.3 6.9 + - - +
115C GLU* 2.9 29.7 + - - +
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Residues in contact with PHE 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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94C LEU* 5.6 0.2 - - + -
102C ILE* 3.6 34.1 - - + -
106C PHE* 3.8 33.1 - + + +
108C SER 3.1 3.7 + - - +
109C VAL* 3.4 13.9 - - + +
111C ASN* 1.3 80.0 - - - +
113C LYS* 1.3 63.4 + - + +
115C GLU* 3.1 3.5 + - - +
116C PHE* 2.8 32.9 + + + +
131C LEU* 3.7 39.0 - - + -
140C VAL* 3.9 14.1 - - + -
164C MET* 3.9 12.6 - - + -
189C TRP* 3.9 22.4 - + - -
194C TRP* 4.0 19.3 - + - -
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Residues in contact with LYS 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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109C VAL* 2.9 33.1 + - + +
110C ASP* 3.7 13.0 - - - +
112C PHE* 1.3 79.5 - - + +
114C ALA* 1.3 58.9 + - - +
116C PHE* 3.3 1.6 + - - +
117C GLU* 2.8 42.3 + - - +
189C TRP* 3.6 68.8 - - + +
194C TRP* 5.4 5.4 - - - -
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Residues in contact with ALA 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 ASP 3.0 17.0 + - - +
111C ASN* 3.5 8.3 - - - +
113C LYS* 1.3 76.2 - - - +
115C GLU* 1.3 60.3 + - - +
117C GLU* 3.8 8.6 - - - +
118C LYS* 3.0 30.8 + - - +
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Residues in contact with GLU 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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106C PHE* 4.4 22.4 - - + -
111C ASN* 2.9 16.7 + - - +
112C PHE* 3.4 11.7 - - - +
114C ALA* 1.3 78.4 - - - +
116C PHE* 1.3 61.4 + - - +
118C LYS* 3.2 36.1 + - - +
119C ALA* 3.1 23.0 + - - +
140C VAL* 3.9 11.9 - - + +
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Residues in contact with PHE 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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112C PHE* 2.8 28.4 + + + +
113C LYS 3.6 3.8 - - - +
115C GLU* 1.3 74.3 - - - +
117C GLU* 1.3 61.9 + - - +
119C ALA* 3.2 2.9 + - - +
120C ALA* 2.9 29.9 + - + +
129C ALA* 3.7 32.1 - - + -
130C TRP 3.9 13.9 - - - -
131C LEU 4.2 0.4 - - - -
140C VAL* 4.1 23.3 - - + +
164C MET* 3.9 24.5 - - - -
166C LEU* 3.8 27.1 - - + -
185C ILE* 5.2 2.2 - - + -
188C PHE* 3.8 20.2 - + - -
189C TRP* 3.7 26.5 - + + -
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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 LYS* 2.8 28.1 + - - +
114C ALA* 3.8 6.5 - - - +
116C PHE* 1.3 76.4 - - - +
118C LYS* 1.3 57.6 + - - +
120C ALA* 3.3 1.4 + - - +
121C ALA* 2.8 34.1 + - - +
185C ILE* 3.5 30.7 - - + +
186C LYS* 2.9 35.4 + - - +
189C TRP* 2.9 29.8 + - + +
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Residues in contact with LYS 118 (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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114C ALA 3.0 16.3 + - - +
115C GLU* 3.2 38.1 + - - +
117C GLU* 1.3 77.4 - - - +
119C ALA* 1.3 51.2 + - - +
121C ALA* 3.8 3.6 - - - +
122C SER* 2.7 44.9 + - - +
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Residues in contact with ALA 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 GLU 3.1 7.8 + - - +
116C PHE 3.2 3.6 + - - +
118C LYS* 1.3 76.7 - - - +
120C ALA* 1.3 62.3 + - - +
122C SER* 3.4 7.2 + - - -
123C ARG* 3.3 23.0 + - - +
129C ALA* 4.5 5.6 - - + -
140C VAL* 3.4 33.2 - - + -
141C VAL* 4.9 2.2 - - - +
142C SER* 4.3 18.1 + - - -
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Residues in contact with ALA 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 PHE* 2.9 18.2 + - + +
117C GLU* 3.7 2.9 - - - +
119C ALA* 1.3 79.8 - - - +
121C ALA* 1.3 58.9 + - - +
123C ARG* 3.7 4.4 + - - +
129C ALA* 3.7 22.6 - - + +
166C LEU* 4.4 7.6 - - + -
168C VAL* 3.9 13.8 - - + +
181C ARG* 2.9 26.2 + - - -
185C ILE* 3.6 24.7 - - + -
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Residues in contact with ALA 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 2.8 21.4 + - - +
118C LYS* 4.0 4.5 - - - +
120C ALA* 1.3 74.5 - - - +
122C SER* 1.3 61.2 + - - +
123C ARG 3.3 1.1 + - - +
181C ARG* 3.8 15.0 + - - +
182C PRO* 5.3 11.0 - - + -
185C ILE* 3.7 14.1 - - + +
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Residues in contact with SER 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* 2.7 27.8 + - - +
119C ALA* 3.4 10.9 + - - -
120C ALA 3.4 0.2 - - - -
121C ALA* 1.3 75.9 - - - +
123C ARG* 1.3 58.8 + - - +
124C PHE* 3.0 12.9 + - - +
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Residues in contact with ARG 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 ALA 3.3 16.3 + - - +
120C ALA* 3.9 8.3 - - - +
121C ALA 3.3 1.9 - - - +
122C SER* 1.3 75.2 - - - +
124C PHE* 1.3 73.2 + - - +
125C GLY 3.6 0.4 + - - +
126C SER 4.0 8.5 - - - +
127C GLY* 4.0 10.8 - - - +
128C TRP 4.5 1.8 - - - +
142C SER* 3.1 40.9 + - - +
143C THR* 3.4 20.6 + - - +
144C ALA* 3.6 21.0 - - - +
168C VAL* 3.9 21.1 - - + -
181C ARG* 2.7 30.2 + - - +
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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
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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