Contacts of the helix formed by residues 144 - 159 (chain A) in PDB entry 2DOS
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 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A GLN* 5.2 6.2 - - - +
130A TRP* 4.5 1.6 - - - +
142A LEU* 5.4 2.0 - - - +
143A ILE* 1.3 78.0 - - - +
145A ASP* 1.3 59.3 + - - +
146A THR* 3.3 19.5 - - - -
147A TYR* 3.3 8.7 + - - +
148A LEU* 2.7 36.0 + - - +
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Residues in contact with ASP 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ILE* 3.0 50.1 - - + +
125A LYS* 6.3 0.9 - - - -
128A LYS* 3.4 27.7 + - - +
130A TRP* 4.1 10.6 - - + +
144A SER* 1.3 73.5 + - - +
146A THR* 1.3 80.1 + - - +
148A LEU* 3.2 14.0 + - - -
149A ALA* 3.2 6.4 + - - +
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Residues in contact with THR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ILE* 5.2 0.4 - - - -
144A SER* 4.1 15.5 - - - -
145A ASP* 1.3 89.0 + - - +
147A TYR* 1.3 65.3 + - + +
149A ALA* 4.3 4.5 + - - +
150A LEU* 3.7 25.5 + - - +
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Residues in contact with TYR 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ILE* 3.6 24.7 - - + -
144A SER* 3.3 15.8 + - - +
145A ASP 3.1 0.4 - - - -
146A THR* 1.3 82.4 - - + +
148A LEU* 1.3 56.1 + - - +
149A ALA 3.4 0.7 - - - -
150A LEU* 3.5 9.8 + - + +
151A PHE* 2.7 56.6 + + + +
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A PRO* 3.5 25.8 - - + +
107A ILE* 3.8 4.5 - - + +
112A PHE* 5.5 4.7 - - + -
123A VAL* 4.3 10.8 - - + -
130A TRP* 3.0 60.6 - - + +
132A ASN* 5.2 2.0 - - - +
143A ILE* 3.9 8.3 - - + +
144A SER 2.7 18.4 + - - +
145A ASP 3.2 3.6 + - - +
147A TYR* 1.3 75.1 - - - +
149A ALA* 1.3 65.0 + - - +
151A PHE* 3.4 20.4 - - + +
152A LEU* 2.9 40.6 + - + +
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A PRO* 3.9 21.3 - - + -
107A ILE* 4.3 4.7 - - + -
145A ASP 3.2 12.6 + - - +
146A THR* 4.5 5.6 - - - +
148A LEU* 1.3 79.6 - - - +
150A LEU* 1.3 58.6 + - + +
152A LEU* 3.2 14.6 - - - +
153A ALA* 3.0 29.9 + - - +
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A THR* 3.7 18.8 + - - +
147A TYR* 3.5 12.9 + - + +
148A LEU 3.2 0.2 - - - -
149A ALA* 1.3 79.3 - - + +
151A PHE* 1.3 66.7 + - - +
153A ALA* 3.5 7.2 - - + +
154A GLN* 2.9 31.6 + - + +
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Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 5.8 3.1 - + - -
114A CYS* 4.5 10.8 - - + -
121A PHE* 5.7 10.8 - + - -
123A VAL* 4.9 5.8 - - + -
132A ASN* 4.2 23.8 - - - -
143A ILE* 5.1 8.1 - - + -
147A TYR* 2.7 45.7 + + + +
148A LEU* 3.1 24.7 + - + +
150A LEU* 1.3 75.4 - - - +
152A LEU* 1.3 80.5 + - + +
154A GLN* 3.4 9.5 + - - +
155A LEU* 3.1 52.2 - - + +
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TYR* 5.3 5.4 - - - +
106A PRO* 3.4 37.0 - - + -
112A PHE* 3.9 30.7 - - + -
114A CYS* 5.6 0.4 - - - -
148A LEU* 2.9 39.0 + - + +
149A ALA 3.2 8.3 - - - +
151A PHE* 1.3 85.2 - - + +
153A ALA* 1.3 80.2 + - + +
155A LEU* 2.9 21.4 + - + +
156A GLN* 3.0 30.2 + - - +
162A ILE* 3.8 9.9 - - + +
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ALA 3.0 21.9 + - - +
150A LEU* 3.3 13.4 + - + +
152A LEU* 1.3 78.1 - - + +
154A GLN* 1.3 57.0 + - - +
156A GLN* 2.9 35.2 - - - +
157A GLN* 3.0 23.4 + - - +
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Residues in contact with GLN 154 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A LEU* 2.9 19.7 + - + +
151A PHE* 3.5 9.8 - - - +
152A LEU 3.1 0.2 - - - -
153A ALA* 1.3 77.3 - - - +
155A LEU* 1.3 63.2 + - + +
157A GLN* 3.2 24.1 - - - +
158A GLU* 2.9 45.1 + - + +
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A CYS* 3.4 32.5 - - + -
151A PHE* 3.1 43.7 - - + +
152A LEU* 2.9 9.2 + - - +
154A GLN* 1.3 80.5 - - + +
156A GLN* 1.3 60.5 + - - +
158A GLU* 3.1 0.4 + - - -
159A GLY 2.8 29.5 + - - -
160A TYR* 3.0 44.4 + - + -
162A ILE* 3.7 6.1 - - + -
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Residues in contact with GLN 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A PHE* 3.5 41.6 - - + +
99A TYR* 5.4 7.6 + - - -
152A LEU* 3.0 33.8 + - - +
153A ALA* 2.9 31.7 + - - +
155A LEU* 1.3 76.8 - - - +
157A GLN* 1.3 65.5 + - + +
158A GLU 3.3 1.0 + - - -
159A GLY* 4.0 6.9 + - - -
160A TYR 4.6 1.1 - - - +
162A ILE* 3.2 22.2 - - + +
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Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ALA* 3.0 21.0 + - - +
154A GLN* 3.2 42.6 + - - +
156A GLN* 1.3 77.3 - - + +
158A GLU* 1.3 65.6 + - + +
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Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLN* 2.9 33.0 + - + +
155A LEU* 3.1 3.5 + - + +
156A GLN 4.2 0.9 - - - -
157A GLN* 1.3 89.0 - - + +
159A GLY* 1.3 60.2 + - - +
160A TYR* 3.8 18.3 - - + -
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Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 5.7 2.4 - - - -
117A LYS* 4.5 15.8 + - - +
155A LEU 2.8 10.5 + - - -
156A GLN 4.0 4.4 + - - -
158A GLU* 1.3 78.6 - - - +
160A TYR* 1.3 66.5 + - - -
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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