Contacts of the helix formed by residues 120 - 137 (chain C) in PDB entry 4OE5
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 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C LEU 3.3 7.2 - - - +
119C LYS* 1.3 87.9 - - + +
121C ILE* 1.3 61.0 + - - +
122C ALA* 3.1 7.0 - - + +
123C ASP* 2.8 46.8 + - - +
124C ARG* 3.1 8.8 + - - +
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Residues in contact with ILE 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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119C LYS 3.5 2.2 + - - -
120C PRO* 1.3 71.0 - - - +
122C ALA* 1.3 57.2 + - + +
124C ARG* 3.2 22.5 + - - +
125C ALA* 2.8 33.0 + - + +
177C ALA* 3.7 38.1 - - + +
178C VAL* 4.3 9.2 - - + +
181C GLU* 3.6 44.2 - - + +
225C LEU* 3.6 32.1 - - + +
226C MET* 5.1 2.7 - - + -
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Residues in contact with ALA 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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120C PRO* 3.1 5.3 - - + +
121C ILE* 1.3 84.5 - - + +
123C ASP* 1.3 61.1 + - - +
125C ALA* 3.6 1.7 + - - +
126C GLN* 3.2 33.8 + - + +
178C VAL* 4.3 17.7 - - + -
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Residues in contact with ASP 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LYS* 5.2 5.2 - - + -
120C PRO* 2.8 40.3 + - + +
122C ALA* 1.3 78.3 - - - +
124C ARG* 1.3 66.3 + - - +
126C GLN* 3.5 14.9 + - - +
127C ILE* 3.7 16.6 + - - +
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Residues in contact with ARG 124 (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 TRP* 3.1 60.0 + - + +
117C ASP* 2.9 33.9 + - - +
119C LYS* 2.9 23.4 + - + +
120C PRO 3.1 10.0 + - - +
121C ILE* 3.6 32.5 - - + +
123C ASP* 1.3 73.9 - - - +
125C ALA* 1.3 66.0 + - - +
127C ILE* 3.2 15.2 + - - +
128C PHE* 3.2 18.0 - - - -
197C TYR 4.9 9.1 + - - -
225C LEU* 2.8 29.5 + - + +
226C MET* 3.7 14.3 + - - +
227C GLY* 3.6 7.9 - - - +
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Residues in contact with ALA 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 4.7 5.4 - - + -
121C ILE* 2.8 21.7 + - + +
122C ALA 3.8 4.7 - - - +
123C ASP 3.3 0.2 - - - -
124C ARG* 1.3 74.7 - - - +
126C GLN* 1.3 56.7 + - - +
128C PHE* 3.0 4.7 + - - +
129C LEU* 2.8 33.0 + - + +
174C ALA* 3.9 23.4 - - + +
178C VAL* 4.0 19.7 - - + -
225C LEU* 3.8 14.3 - - + +
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Residues in contact with GLN 126 (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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30C LEU* 5.0 7.3 - - - +
122C ALA* 3.2 24.0 + - + +
123C ASP* 3.7 11.9 - - - +
124C ARG 3.2 0.4 - - - -
125C ALA* 1.3 77.0 - - - +
127C ILE* 1.3 63.2 + - + +
129C LEU* 3.4 25.9 + - - +
130C LYS* 3.0 25.7 + - - +
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Residues in contact with ILE 127 (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 TRP* 3.9 31.9 - - + -
123C ASP 3.8 14.4 - - - +
124C ARG 3.2 7.4 + - - +
126C GLN* 1.3 77.6 - - + +
128C PHE* 1.3 66.1 + - + +
130C LYS* 3.6 2.8 - - - +
131C ALA* 3.0 26.2 + - - +
249C LEU* 4.2 11.7 - - + +
252C ALA* 3.7 16.2 - - + +
253C GLY* 3.5 24.9 - - - +
254C LEU* 3.6 27.4 - - + +
255C PRO* 4.1 1.6 - - + -
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Residues in contact with PHE 128 (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 TRP* 4.5 12.6 - + - -
124C ARG 3.2 18.2 - - - -
125C ALA* 3.0 7.6 + - - +
127C ILE* 1.3 79.3 - - + +
129C LEU* 1.3 60.3 + - - +
131C ALA* 3.8 4.3 - - - +
132C ALA* 3.0 28.2 + - - +
170C PHE* 3.7 44.1 - + + +
174C ALA* 4.9 1.3 - - + -
221C GLY* 3.6 35.7 - - - -
224C ALA* 4.0 11.2 - - + -
225C LEU* 3.8 35.4 - - + -
249C LEU* 3.9 20.4 - - + -
254C LEU* 4.6 14.1 - - + -
259C ILE* 5.4 1.3 - - + -
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Residues in contact with LEU 129 (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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30C LEU* 3.8 27.8 - - + -
32C VAL* 4.7 8.3 - - + -
125C ALA* 2.8 21.5 + - + +
126C GLN* 3.7 30.5 - - - +
127C ILE 3.4 0.2 - - - -
128C PHE* 1.3 75.2 - - - +
130C LYS* 1.3 57.8 + - - +
132C ALA* 3.3 5.4 + - - +
133C ASP* 3.0 37.8 + - - +
171C ARG* 3.9 41.5 - - + +
174C ALA* 4.0 10.3 - - + -
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Residues in contact with LYS 130 (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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126C GLN* 3.0 19.2 + - - +
127C ILE 3.6 4.7 - - - +
129C LEU* 1.3 74.9 - - - +
131C ALA* 1.3 60.2 + - - +
133C ASP* 3.2 9.0 + - - +
134C MET* 2.9 37.4 + - + +
252C ALA* 4.0 18.2 - - + +
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Residues in contact with ALA 131 (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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127C ILE 3.0 17.8 + - - +
128C PHE 3.8 4.7 - - - +
129C LEU 3.4 0.2 - - - -
130C LYS* 1.3 75.4 - - - +
132C ALA* 1.3 57.1 + - - +
134C MET* 3.3 2.9 + - - +
135C LEU* 3.0 35.5 + - - +
170C PHE* 4.0 8.7 - - + -
248C ILE* 3.9 15.7 - - + +
249C LEU* 3.8 27.1 - - + -
252C ALA* 3.7 14.3 - - + +
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Residues in contact with ALA 132 (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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128C PHE 3.0 18.3 + - - +
129C LEU 3.4 6.1 - - - +
130C LYS 3.2 0.2 - - - -
131C ALA* 1.3 76.5 - - - +
133C ASP* 1.3 52.8 + - - +
135C LEU* 3.4 7.0 + - - +
136C SER* 2.8 34.7 + - - -
167C ILE* 3.8 12.5 - - + +
170C PHE* 3.8 18.5 - - + -
171C ARG* 3.6 32.7 + - + +
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Residues in contact with ASP 133 (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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129C LEU* 3.0 23.3 + - - +
130C LYS* 3.2 7.9 + - - +
132C ALA* 1.3 72.5 - - - +
134C MET* 1.3 66.5 + - + +
136C SER* 3.2 6.0 + - - -
137C GLY* 3.0 19.2 + - - -
138C PRO* 3.8 5.1 - - - +
171C ARG* 2.9 29.1 + - - -
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Residues in contact with MET 134 (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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130C LYS* 2.9 24.0 + - + +
131C ALA 3.6 3.8 - - - +
133C ASP* 1.3 75.3 - - + +
135C LEU* 1.3 61.8 + - - +
137C GLY 3.2 6.2 + - - -
138C PRO* 3.3 13.6 - - + +
139C ARG* 2.8 61.4 + - + +
248C ILE* 3.9 19.3 - - + -
251C GLU* 4.0 21.3 - - + +
252C ALA* 3.8 25.8 - - - -
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Residues in contact with LEU 135 (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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131C ALA 3.0 20.6 + - - +
132C ALA 3.6 4.3 - - - +
134C MET* 1.3 75.8 - - - +
136C SER* 1.3 57.0 + - - +
139C ARG* 4.2 4.7 - - - +
140C ARG* 3.1 30.8 - - - +
143C ILE* 4.0 26.6 - - + +
166C LEU* 3.7 39.3 - - + -
167C ILE* 3.8 17.4 - - + +
170C PHE* 3.9 22.7 - - + -
245C VAL* 4.6 7.2 - - + -
248C ILE* 3.5 31.2 - - + -
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Residues in contact with SER 136 (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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35C GLU* 2.5 30.1 + - - -
132C ALA 2.8 18.5 + - - -
133C ASP* 3.5 6.1 - - - -
134C MET 3.1 0.2 - - - -
135C LEU* 1.3 79.4 - - - +
137C GLY* 1.3 56.6 + - - +
140C ARG* 2.9 27.0 + - - +
167C ILE* 3.7 9.4 - - - -
171C ARG* 3.5 16.4 + - - -
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Residues in contact with GLY 137 (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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133C ASP 3.0 10.0 + - - -
134C MET 3.2 1.0 + - - -
136C SER* 1.3 76.9 - - - +
138C PRO* 1.3 72.0 - - - +
139C ARG 3.1 2.7 + - - -
140C ARG* 3.3 14.9 + - - +
141C ALA 4.8 1.0 + - - -
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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