Contacts of the helix formed by residues 122 - 137 (chain C) in PDB entry 1E3S
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 LEU 122 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ILE* 3.0 19.3 + - + +
121C ASN* 1.3 74.9 - - - +
123C ILE* 1.3 67.9 + - + +
124C GLY 3.3 0.9 - - - -
125C THR* 3.4 2.8 + - - -
126C PHE* 3.2 21.1 + - - +
170C ALA 4.8 1.8 - - - +
171C SER* 3.9 16.4 - - - +
174C GLY* 3.6 41.3 - - - +
175C ILE* 3.7 7.4 - - + +
178C MET* 4.0 19.9 - - + +
114D PHE* 4.5 6.7 - - + -
118D ILE* 4.0 24.0 - - + -
122D LEU* 4.3 17.5 - - + -
170D ALA* 4.2 6.1 - - + +
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Residues in contact with ILE 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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66C THR* 5.8 6.7 - - + +
118C ILE* 3.0 20.3 + - + +
119C ASN* 3.3 27.6 - - + +
122C LEU* 1.3 73.6 - - + +
124C GLY* 1.3 63.5 + - - +
126C PHE* 3.4 2.9 + - - +
127C ASN* 3.0 22.5 + - + +
111D LEU* 3.8 26.8 - - + +
114D PHE* 4.1 24.5 - - + -
115D GLN* 2.9 49.8 - - + +
118D ILE* 4.4 8.1 - - + -
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Residues in contact with GLY 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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65C VAL* 3.6 32.2 - - - +
66C THR* 4.6 2.2 - - - -
119C ASN 2.9 13.1 + - - -
120C VAL 3.6 13.1 + - - -
122C LEU 3.3 0.4 - - - -
123C ILE* 1.3 76.4 - - - +
125C THR* 1.3 60.2 + - - +
127C ASN* 3.4 2.4 + - - +
128C VAL* 3.2 27.9 + - - +
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Residues in contact with THR 125 (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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90C ASN* 3.8 26.5 - - + +
92C ALA 4.9 7.3 + - - -
120C VAL 4.1 1.4 + - - -
121C ASN 3.1 22.9 + - - -
122C LEU* 3.4 4.6 + - - -
123C ILE 3.4 0.4 - - - -
124C GLY* 1.3 76.0 - - - +
126C PHE* 1.3 61.1 + - - +
128C VAL* 3.4 3.6 + - - +
129C ILE* 3.1 28.5 + - + +
152C ASN* 3.8 28.7 - - + +
153C THR 5.7 0.3 + - - -
175C ILE* 4.5 9.8 - - + +
178C MET* 4.0 12.1 - - + -
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Residues in contact with PHE 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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122C LEU 3.2 8.2 + - - +
123C ILE 3.4 3.6 + - - +
125C THR* 1.3 72.9 - - - +
127C ASN* 1.3 60.9 + - - +
129C ILE* 3.3 5.7 + - + +
130C ARG* 2.8 55.1 + - + +
178C MET* 4.2 6.9 - - + +
182C ILE* 4.0 23.1 - - + -
100D THR* 3.9 24.7 - - + -
109D HIS* 3.8 34.1 - + + -
110D THR 4.7 0.2 - - - -
111D LEU* 4.9 2.9 - - + -
114D PHE* 3.4 68.0 - + + -
166D ALA* 4.2 5.6 - - + -
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Residues in contact with ASN 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C VAL 3.0 21.4 + - - +
66C THR* 4.2 3.6 - - - -
67C SER 3.7 3.8 + - - -
68C GLU* 3.6 27.1 - - - +
71C VAL* 3.9 7.5 - - - +
123C ILE 3.0 17.9 + - - +
124C GLY 3.6 5.2 - - - +
125C THR 3.3 0.2 - - - -
126C PHE* 1.3 76.9 - - - +
128C VAL* 1.3 61.4 + - - +
130C ARG* 2.8 47.6 + - - +
131C LEU* 3.3 28.0 + - - +
111D LEU* 3.9 16.7 - - + +
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Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 5.9 3.4 - - + -
16C THR* 3.9 23.8 - - + -
40C LEU* 5.4 2.2 - - + -
65C VAL* 4.0 15.3 - - + -
71C VAL* 4.4 23.3 - - + -
75C LEU* 4.9 7.0 - - + +
88C ALA* 5.1 8.3 - - + -
89C VAL 6.3 0.2 - - - -
90C ASN* 3.4 28.0 - - - +
124C GLY 3.2 14.0 + - - +
125C THR 3.8 1.8 - - - +
126C PHE 3.3 0.2 - - - -
127C ASN* 1.3 77.2 - - - +
129C ILE* 1.3 61.1 + - - +
131C LEU* 4.1 0.5 - - - +
132C VAL* 3.0 34.3 + - + +
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Residues in contact with ILE 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ASN* 3.8 13.7 - - - +
125C THR* 3.1 25.0 + - + +
126C PHE* 3.3 8.3 + - + +
128C VAL* 1.3 77.0 - - - +
130C ARG* 1.3 61.6 + - - +
132C VAL* 3.7 7.8 - - - +
133C ALA* 3.2 24.6 + - - +
150C ILE* 4.0 21.3 - - + +
152C ASN* 3.4 26.9 - - - +
178C MET* 4.4 6.3 - - + -
182C ILE* 4.0 42.2 - - + -
186C LEU* 5.0 1.6 - - + -
193C VAL* 5.3 1.1 - - + -
100D THR* 4.2 10.5 - - + -
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Residues in contact with ARG 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLU* 2.8 38.2 + - - +
126C PHE* 2.8 45.4 + - + +
127C ASN* 2.8 37.0 + - - +
129C ILE* 1.3 74.0 - - - +
131C LEU* 1.3 79.6 + - + +
133C ALA* 3.8 10.7 + - - +
134C GLY 4.1 3.5 + - - -
100D THR* 4.1 17.0 - - + +
101D TYR* 5.2 0.9 - - - +
108D VAL* 3.6 34.1 + - + +
109D HIS 3.0 25.0 + - - +
110D THR* 4.0 2.8 - - - +
111D LEU* 3.8 21.4 - - - +
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Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLU* 4.1 14.1 - - + +
71C VAL* 3.7 26.5 - - + -
72C GLN* 3.8 30.0 - - - +
75C LEU* 3.8 14.5 - - + +
127C ASN* 3.3 30.9 + - - +
128C VAL 4.3 0.4 - - - +
130C ARG* 1.3 106.5 - - + +
132C VAL* 1.3 63.5 + - - +
133C ALA 3.5 0.5 + - - -
134C GLY* 3.7 8.1 + - - -
135C VAL* 3.7 14.9 + - - +
108D VAL* 4.8 7.2 - - + -
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 5.6 1.1 - - + -
75C LEU* 3.7 25.5 - - + +
85C ILE* 3.9 32.1 - - + -
88C ALA* 4.0 20.2 - - + -
128C VAL* 3.0 24.3 + - + +
129C ILE* 3.7 7.2 - - - +
131C LEU* 1.3 75.2 - - - +
133C ALA* 1.3 66.4 + - - +
135C VAL* 3.1 4.8 + - + +
136C MET* 3.0 29.8 + - + +
150C ILE* 3.9 20.6 - - + -
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Residues in contact with ALA 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 ILE 3.2 18.4 + - - +
130C ARG* 3.9 7.9 - - - +
131C LEU 3.3 0.6 - - - -
132C VAL* 1.3 79.8 - - - +
134C GLY* 1.3 57.4 + - - +
136C MET* 3.4 1.7 + - - -
137C GLY* 3.0 25.5 + - - -
150C ILE* 5.0 1.6 - - + -
186C LEU* 4.3 32.8 - - + -
189C ILE* 4.3 3.3 - - - +
191C ILE* 3.7 16.5 - - + +
100D THR* 5.0 1.6 - - + -
101D TYR* 4.4 11.4 - - + -
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Residues in contact with GLY 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 ARG 4.1 4.6 + - - -
131C LEU 3.7 7.1 + - - -
132C VAL 3.3 0.6 - - - -
133C ALA* 1.3 79.1 - - - +
135C VAL* 1.3 60.9 + - - +
137C GLY* 3.4 9.6 + - - -
138C GLN* 3.6 19.4 + - - +
101D TYR* 4.2 30.3 + - - -
108D VAL* 5.5 3.1 - - - -
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Residues in contact with VAL 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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72C GLN* 5.3 5.4 - - - +
75C LEU* 4.8 12.3 - - + +
79C LYS* 4.3 24.0 - - + -
84C ARG* 5.7 0.2 - - - -
85C ILE* 3.9 40.3 + - + +
131C LEU 3.7 15.0 + - - +
132C VAL* 3.1 10.1 + - - +
134C GLY* 1.3 74.2 - - - +
136C MET* 1.3 64.0 + - - +
138C GLN* 3.2 32.0 + - - +
139C ASN* 4.1 6.1 + - - +
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Residues in contact with MET 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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85C ILE* 3.8 16.2 - - + +
86C ASP 3.8 13.2 - - - +
87C VAL 3.8 3.6 - - - -
88C ALA* 3.7 22.9 - - + +
132C VAL* 3.0 27.6 + - + +
133C ALA 3.8 0.2 - - - +
135C VAL* 1.3 74.6 - - - +
137C GLY* 1.3 62.8 + - - +
139C ASN* 3.0 30.0 + - - +
147C ARG* 3.7 19.1 - - - +
148C GLY* 4.0 6.7 - - - -
149C VAL 3.7 21.5 - - - +
150C ILE* 3.9 25.1 - - + -
191C ILE* 3.7 29.8 - - + -
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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 ALA 3.0 16.2 + - - -
134C GLY* 3.4 6.0 + - - -
135C VAL 3.2 1.0 - - - -
136C MET* 1.3 76.8 - - - +
138C GLN* 1.3 58.8 + - - +
139C ASN 3.3 0.9 + - - +
147C ARG* 3.5 25.3 + - - -
189C ILE* 4.3 16.5 - - - +
191C ILE* 4.5 0.4 - - - +
101D TYR* 5.5 4.3 - - - -
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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