Contacts of the helix formed by residues 121 - 137 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C LYS* 5.2 3.4 - - - +
44D LEU* 6.1 1.1 - - - +
117D PRO* 4.1 0.9 - - - -
118D THR* 2.6 38.6 + - + +
119D THR 3.9 5.6 - - - +
120D GLY* 1.3 84.2 - - - +
122D GLY* 1.3 62.1 + - - +
123D PRO* 3.6 4.7 - - - -
124D LEU* 3.6 14.1 + - + +
125D THR* 2.7 41.0 + - - -
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Residues in contact with GLY 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D PRO* 3.9 18.9 - - - +
120D GLY* 3.7 1.0 - - - -
121D THR* 1.3 78.2 - - - +
123D PRO* 1.4 66.4 - - - +
125D THR* 3.5 2.1 - - - -
126D GLY* 2.9 28.1 + - - -
149D GLU* 5.5 0.7 - - - -
151D ASP* 3.5 16.5 + - - -
152D ALA* 3.8 10.7 - - - +
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Residues in contact with PRO 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ASP* 3.9 29.4 - - + +
120D GLY 5.5 1.6 - - - +
121D THR* 3.8 2.5 - - - -
122D GLY* 1.4 86.8 - - - +
124D LEU* 1.3 62.7 + - - +
127D LYS* 3.0 24.1 + - - +
151D ASP* 3.9 24.2 - - + +
155D ALA* 3.3 21.3 - - + +
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Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LYS 4.2 15.9 - - - +
47C ASP* 3.8 14.5 + - - +
48C GLY* 3.8 15.0 - - - +
124C LEU* 4.0 22.2 - - + -
128C MSE 3.8 24.5 - - + -
44D LEU* 3.8 17.0 - - + -
121D THR* 3.6 14.7 + - + +
122D GLY 3.4 0.8 - - - -
123D PRO* 1.3 80.3 - - - +
125D THR* 1.3 57.5 + - - +
127D LYS* 3.6 4.5 - - + +
128D MSE 2.9 49.4 + - + +
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Residues in contact with THR 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ALA 4.4 0.4 - - - +
43D LYS* 4.3 14.1 - - - -
44D LEU* 3.7 22.2 + - + +
115D ILE* 3.6 21.3 - - + -
117D PRO* 3.4 22.2 - - + +
118D THR 4.6 0.5 + - - -
121D THR* 2.7 35.0 + - - -
122D GLY 3.5 3.6 - - - -
124D LEU* 1.3 78.0 - - - +
126D GLY* 1.3 55.2 + - - +
128D MSE 3.1 1.6 + - - +
129D VAL* 2.7 47.7 + - + +
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Residues in contact with GLY 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ILE* 4.0 18.5 - - - +
122D GLY 2.9 17.9 + - - -
123D PRO 4.0 0.4 - - - -
125D THR* 1.3 73.0 - - - +
127D LYS* 1.3 61.7 + - - +
130D ALA* 3.0 26.9 + - - +
152D ALA* 3.6 20.0 - - - -
155D ALA* 4.0 5.2 - - - -
156D ALA* 3.9 6.5 - - - +
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Residues in contact with LYS 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ASP 4.9 4.5 - - - +
48C GLY* 2.7 31.6 + - - +
49C GLU* 4.1 23.0 + - - +
50C ILE* 5.0 6.5 - - - +
128C MSE 5.6 6.9 - - - -
123D PRO 3.0 18.6 + - - +
124D LEU* 3.6 7.0 - - + +
126D GLY* 1.3 75.9 - - - +
128D MSE 1.3 66.4 + - + +
130D ALA* 3.3 2.9 + - - +
131D LEU* 3.1 47.6 + - + +
155D ALA* 3.6 17.9 - - + +
159D ALA* 4.2 9.9 - - + -
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Residues in contact with MSE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C LEU* 2.5 42.0 - - + -
127C LYS* 5.2 8.5 - - + -
128C MSE 3.5 29.6 - - + +
131C LEU* 6.0 2.7 - - - -
44D LEU* 3.7 25.6 - - + -
48D GLY* 4.0 18.2 - - - +
50D ILE* 3.4 12.9 - - + +
124D LEU* 2.9 42.8 + - + +
125D THR 3.5 2.9 - - - +
127D LYS* 1.3 79.4 - - + +
129D VAL* 1.3 62.7 + - - +
131D LEU* 3.7 8.0 + - - +
132D ALA* 3.1 18.7 + - - +
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Residues in contact with VAL 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ALA* 4.5 9.9 - - + +
44D LEU* 4.3 4.3 - - + -
50D ILE* 3.7 28.5 - - + -
97D LEU* 4.7 5.5 - - + +
113D ILE* 3.9 26.7 - - + -
115D ILE* 3.8 31.0 - - + -
125D THR* 2.7 38.7 + - + +
128D MSE 1.3 71.4 - - - +
130D ALA* 1.3 60.3 + - - +
132D ALA* 3.3 1.2 + - - +
133D ALA* 2.8 29.8 + - + +
145D LEU* 5.2 2.2 - - + -
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Residues in contact with ALA 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ILE* 5.0 0.6 - - + +
126D GLY 3.0 22.4 + - - +
127D LYS 3.5 3.8 - - - +
129D VAL* 1.3 76.7 - - - +
131D LEU* 1.3 56.9 + - - +
133D ALA* 3.2 2.9 + - - +
134D ARG* 3.0 25.6 + - - +
145D LEU* 4.4 14.8 - - + -
156D ALA* 3.8 24.2 - - + -
159D ALA* 4.1 5.6 - - + -
160D ALA* 3.9 18.2 - - + -
163D LEU* 3.6 6.9 - - - +
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C MSE 6.5 1.1 - - - -
131C LEU* 6.1 12.6 - - + -
135C GLN* 5.8 4.9 - - - +
127D LYS* 3.1 40.6 + - + +
128D MSE 3.9 9.0 - - - +
130D ALA* 1.3 77.7 - - - +
132D ALA* 1.3 62.8 + - - +
134D ARG* 3.4 16.2 - - - +
135D GLN* 3.3 21.1 + - - +
159D ALA* 3.2 42.2 - - + +
160D ALA* 5.1 0.9 - - + -
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Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ILE* 3.2 35.4 - - + -
97D LEU* 4.2 7.2 - - + -
128D MSE 3.1 5.4 + - - +
129D VAL 3.3 1.3 + - - +
131D LEU* 1.3 76.4 - - - +
133D ALA* 1.3 61.6 + - - +
135D GLN* 3.2 7.5 + - - +
136D LEU* 2.9 41.2 + - + +
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Residues in contact with ALA 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 4.6 1.5 - - - +
113D ILE* 4.0 23.6 - - + -
129D VAL 2.8 14.5 + - - +
130D ALA 3.3 9.9 - - - +
132D ALA* 1.3 73.1 - - - +
134D ARG* 1.3 68.1 + - - +
135D GLN 3.1 0.2 + - - -
136D LEU 3.2 0.5 + - - -
137D TRP* 2.9 41.4 + - - +
143D PRO* 4.2 9.6 - - + -
145D LEU* 4.4 5.6 - - + -
163D LEU* 4.1 12.6 - - + -
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Residues in contact with ARG 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C GLN* 4.7 13.9 - - - +
130D ALA 3.0 9.2 + - - +
131D LEU* 3.4 18.4 - - - +
133D ALA* 1.3 80.0 - - - +
135D GLN* 1.3 62.3 + - + +
137D TRP* 4.0 2.4 - - - +
138D ALA* 3.5 18.4 + - - +
159D ALA 3.5 15.5 + - - -
160D ALA* 3.4 16.5 - - + +
161D PRO* 3.5 9.5 - - - +
162D GLU* 2.7 43.7 + - - +
163D LEU* 3.9 13.5 - - + +
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Residues in contact with GLN 135 (chain D).
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* 4.8 12.9 - - - +
134C ARG* 4.2 20.7 + - - +
159C ALA 5.8 0.2 + - - -
131D LEU 3.3 9.6 + - - +
132D ALA* 3.2 9.6 + - - +
133D ALA 3.1 0.8 - - - -
134D ARG* 1.3 83.2 - - + +
136D LEU* 1.3 69.6 + - + +
138D ALA* 3.5 18.0 - - + +
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 4.0 22.4 - - + +
98D SER* 3.6 46.9 - - - +
101D ALA* 3.9 12.6 - - + +
105D ARG* 4.1 4.9 + - - -
132D ALA* 2.9 25.4 + - + +
135D GLN* 1.3 83.3 - - + +
137D TRP* 1.3 70.1 - - + +
138D ALA 3.3 1.9 + - - +
140D MSE 2.8 19.2 - - - +
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Residues in contact with TRP 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D PHE* 4.2 9.0 - + - -
97D LEU* 4.0 30.5 - - + -
101D ALA* 3.7 35.7 - - + -
104D CYS* 4.3 14.1 - - + +
109D MSE 5.5 2.2 + - - -
110D MSE 5.7 1.0 - - - +
111D ALA* 3.5 33.5 - - + +
113D ILE* 4.1 8.7 - - + -
133D ALA* 2.9 26.4 + - - +
134D ARG* 4.0 4.3 - - - +
136D LEU* 1.3 86.8 - - + +
138D ALA* 1.3 62.7 + - - +
139D GLY 3.2 0.7 + - - -
140D MSE 3.2 44.4 + - + +
141D THR 3.3 23.3 + - - +
142D PRO* 5.3 0.9 - - - +
143D PRO* 3.7 29.1 - - + +
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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