Contacts of the helix formed by residues 121 - 137 (chain C) in PDB entry 2OTD
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 THR 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C LEU* 5.6 4.0 - - - +
117C PRO* 4.1 1.8 - - - -
118C THR* 2.5 45.2 + - + +
119C THR 4.1 4.7 - - - +
120C GLY* 1.3 81.1 - - - +
122C GLY* 1.3 56.1 + - - +
123C PRO* 3.7 2.9 - - - -
124C LEU* 3.6 12.1 + - + +
125C THR* 2.6 47.9 + - - -
46D LYS* 4.1 12.3 - - - +
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Residues in contact with GLY 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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117C PRO* 4.0 17.9 - - - +
120C GLY 3.5 2.6 - - - +
121C THR* 1.3 75.1 - - - +
123C PRO* 1.3 75.5 - - - +
125C THR* 4.1 0.2 - - - -
126C GLY 3.1 18.2 + - - -
149C GLU* 5.5 1.6 - - - -
151C ASP* 4.0 18.8 - - - -
152C ALA* 3.3 13.3 - - - +
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Residues in contact with PRO 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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120C GLY 5.1 3.8 - - - +
121C THR* 3.9 1.1 - - - -
122C GLY* 1.3 86.5 - - - +
124C LEU* 1.3 66.8 + - - +
127C LYS* 3.1 22.2 + - - +
151C ASP* 3.5 27.8 - - + +
155C ALA* 3.3 18.9 - - + +
46D LYS* 6.1 0.7 - - - +
47D ASP* 3.6 32.1 - - + +
72D ASN* 5.1 3.4 - - - +
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 3.8 7.6 - - + -
121C THR* 3.6 14.4 + - + +
122C GLY 3.4 0.6 - - - -
123C PRO* 1.3 78.8 - - - +
125C THR* 1.3 63.8 + - - +
127C LYS* 3.7 2.9 - - + +
128C MSE 3.1 49.2 + - + +
44D LEU* 5.7 0.2 - - + -
46D LYS* 4.0 19.5 - - - +
47D ASP* 3.8 7.2 + - - +
48D GLY* 3.5 18.4 - - - +
124D LEU* 4.0 19.3 - - + -
128D MSE 2.5 37.0 - - + -
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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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42C ALA 4.4 0.7 - - - +
43C LYS* 4.3 16.4 - - - -
44C LEU* 3.4 23.6 + - + +
115C ILE* 3.7 18.2 - - + -
117C PRO* 3.6 23.2 - - + +
118C THR 4.7 0.3 + - - -
121C THR* 2.6 35.6 + - - -
122C GLY 4.1 0.7 - - - -
124C LEU* 1.3 77.2 - - - +
126C GLY* 1.3 56.6 + - - +
128C MSE 3.3 0.7 + - - +
129C VAL* 3.0 39.9 + - + +
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Residues in contact with GLY 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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115C ILE* 3.9 19.3 - - - +
122C GLY 3.1 14.8 + - - -
123C PRO 3.9 0.9 - - - -
125C THR* 1.3 74.0 - - - +
127C LYS* 1.3 64.7 + - - +
129C VAL* 4.5 0.6 - - - +
130C ALA* 3.3 24.8 + - - +
152C ALA* 3.6 17.7 - - - -
155C ALA* 3.9 5.2 - - - -
156C ALA* 3.6 7.5 - - - +
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Residues in contact with LYS 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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123C PRO 3.1 18.4 + - - +
124C LEU* 3.7 3.6 - - + +
126C GLY* 1.3 77.3 - - - +
128C MSE 1.3 67.0 + - + +
130C ALA* 3.8 1.9 - - - +
131C LEU* 3.2 50.7 + - + +
155C ALA* 3.6 19.1 - - + +
159C ALA* 3.9 9.3 - - + +
47D ASP 4.7 5.2 - - - +
48D GLY* 2.7 34.2 + - - +
49D GLU* 3.7 18.5 + - - +
50D ILE* 5.1 6.9 - - - +
128D MSE 5.2 6.9 - - - -
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Residues in contact with MSE 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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44C LEU* 3.0 48.0 - - + -
48C GLY* 4.1 13.2 - - - +
50C ILE* 3.4 11.6 - - + +
124C LEU* 3.1 31.9 + - + +
125C THR 4.0 2.2 - - - +
127C LYS* 1.3 84.1 - - + +
129C VAL* 1.3 61.4 + - - +
131C LEU* 3.6 8.6 + - + +
132C ALA* 2.9 30.5 + - - +
124D LEU* 3.8 19.5 - - + -
127D LYS* 5.6 7.0 - - - -
128D MSE 3.5 33.7 - - + +
131D LEU* 6.5 1.3 - - - -
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Residues in contact with VAL 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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42C ALA* 4.3 10.3 - - + -
44C LEU* 4.7 2.2 - - + -
50C ILE* 3.5 32.1 - - + -
97C LEU* 4.6 4.4 - - + +
113C ILE* 3.8 25.6 - - + -
115C ILE* 3.7 30.3 - - + -
125C THR* 3.0 34.3 + - + +
126C GLY 4.5 0.4 - - - +
128C MSE 1.3 73.7 - - - +
130C ALA* 1.3 57.9 + - - +
132C ALA* 4.0 0.7 - - - +
133C ALA* 2.9 28.6 + - + +
145C LEU* 5.1 2.2 - - + -
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Residues in contact with ALA 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 GLY 3.3 18.9 + - - +
127C LYS 3.8 3.4 - - - +
128C MSE 3.2 0.6 - - - -
129C VAL* 1.3 75.8 - - - +
131C LEU* 1.3 68.3 + - - +
133C ALA* 3.2 3.4 + - - +
134C ARG* 2.8 23.7 + - - +
145C LEU* 4.1 15.7 - - + +
156C ALA* 3.9 23.3 - - + -
159C ALA* 4.1 3.8 - - + -
160C ALA* 4.1 18.8 - - + -
163C LEU* 3.7 3.1 - - - +
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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
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127C LYS* 3.2 46.9 + - + +
128C MSE 3.8 9.6 - - + +
130C ALA* 1.3 79.6 - - - +
132C ALA* 1.3 61.7 + - - +
134C ARG* 3.2 20.1 + - - +
135C GLN* 3.2 19.2 + - - +
159C ALA* 3.6 31.0 - - + +
160C ALA* 5.3 0.4 - - - -
128D MSE 6.0 2.7 - - - -
131D LEU* 6.1 11.9 - - + -
135D GLN* 4.8 12.1 - - - +
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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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50C ILE* 3.7 20.9 - - + -
97C LEU* 4.1 10.3 - - + -
128C MSE 2.9 21.9 + - - +
129C VAL 4.0 1.6 - - - +
131C LEU* 1.3 73.5 - - - +
133C ALA* 1.3 58.2 + - - +
135C GLN* 3.2 5.7 + - - +
136C LEU* 2.8 42.9 + - + +
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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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97C LEU* 4.5 1.7 - - - +
113C ILE* 3.9 24.0 - - + -
129C VAL 2.9 20.6 + - - +
130C ALA 3.5 3.8 - - - +
132C ALA* 1.3 72.8 - - - +
134C ARG* 1.3 67.4 + - - +
137C TRP* 2.9 40.6 + - - +
143C PRO* 4.1 7.6 - - + +
145C LEU* 4.3 5.2 - - + -
163C LEU* 4.0 14.4 - - + -
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Residues in contact with ARG 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 ALA 2.8 13.4 + - - +
131C LEU* 3.2 20.3 + - - +
133C ALA* 1.3 77.6 - - - +
135C GLN* 1.3 62.9 + - - +
137C TRP 4.2 0.9 - - - -
138C ALA* 3.6 16.6 + - - +
159C ALA 3.4 17.4 + - - -
160C ALA* 3.4 15.8 - - + +
161C PRO* 3.6 7.5 - - - +
162C GLU* 2.9 39.6 + - - +
163C LEU* 3.7 14.9 - - + +
135D GLN* 4.2 22.8 + - - +
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Residues in contact with GLN 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 LEU 3.2 9.7 + - - +
132C ALA* 4.0 6.5 - - - +
134C ARG* 1.3 80.7 - - + +
136C LEU* 1.3 76.9 + - + +
138C ALA* 3.5 18.6 - - - +
131D LEU* 5.8 4.9 - - - +
134D ARG* 4.7 14.1 - - - +
159D ALA 5.6 2.0 + - - -
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Residues in contact with LEU 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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97C LEU* 3.8 24.9 - - + +
98C SER* 3.5 48.5 - - - +
101C ALA* 4.0 10.4 - - + +
105C ARG* 4.0 5.9 + - - -
132C ALA* 2.8 26.7 + - + +
135C GLN* 1.3 91.4 - - + +
137C TRP* 1.3 69.9 + - + +
138C ALA* 3.2 2.4 + - - +
140C MSE 3.2 16.5 - - - +
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Residues in contact with TRP 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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40C PHE* 4.1 13.2 - + - -
97C LEU* 4.1 17.9 - - + -
101C ALA* 3.7 38.4 - - + -
104C CYS* 4.4 10.3 - - - +
109C MSE 5.4 2.2 + - - -
110C MSE 5.9 0.4 - - - +
111C ALA* 3.6 31.9 - - + +
113C ILE* 3.9 21.8 - - + -
133C ALA* 2.9 25.9 + - - +
134C ARG 4.2 2.2 - - - -
136C LEU* 1.3 84.7 - - + +
138C ALA* 1.3 66.9 + - - +
140C MSE 3.1 44.6 + - + +
141C THR 3.6 19.5 - - - -
142C PRO* 5.5 0.3 - - - +
143C PRO* 3.3 31.2 - - + -
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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