Contacts of the helix formed by residues 143 - 154 (chain B) in PDB entry 2G73
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 ASP 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B GLY 5.6 0.4 - - - -
45B GLN* 3.6 23.7 + - - +
142B CYS* 1.3 77.7 - - - +
144B LEU* 1.3 67.2 + - - +
145B ALA* 3.2 6.3 + - + +
146B ASP* 3.2 32.8 + - - +
147B VAL* 3.3 11.8 + - - +
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B TRP* 4.8 2.2 - - + -
40B PHE* 4.7 8.7 - - + -
44B GLY 5.2 1.4 + - - -
46B LEU* 4.2 25.6 - - + +
142B CYS 3.6 3.4 + - - -
143B ASP* 1.3 72.6 - - - +
145B ALA* 1.3 64.9 + - - +
147B VAL* 3.0 7.1 + - + +
148B LEU* 2.8 49.0 + - + +
172B ARG 4.8 0.2 - - - +
175B LEU* 3.6 24.7 - - + -
176B SER* 3.5 42.2 - - - +
179B THR* 3.7 21.9 - - + +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ASP* 3.2 4.8 + - + +
144B LEU* 1.3 78.9 - - - +
146B ASP* 1.3 55.6 + - - +
148B LEU* 3.1 9.4 + - - +
149B HIS* 2.7 57.4 + - + +
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Residues in contact with ASP 146 (chain B).
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* 3.4 29.7 - - - +
154A THR* 3.6 5.0 - - + +
156A TRP* 6.2 0.4 - - - +
142B CYS* 5.4 3.1 - - + +
143B ASP* 3.2 28.3 + - - +
145B ALA* 1.3 80.2 - - - +
147B VAL* 1.3 52.8 + - + +
149B HIS* 2.9 15.5 + - - +
150B GLY 2.7 32.4 + - - -
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A THR* 3.8 7.5 - - + +
156A TRP* 3.8 18.6 - - + -
38B TRP* 5.0 2.0 - - + -
46B LEU* 4.1 17.3 - - + -
48B VAL* 4.1 9.2 - - + -
142B CYS* 3.7 29.8 - - + -
143B ASP 3.3 3.8 + - - +
144B LEU* 3.0 12.6 + - + +
146B ASP* 1.3 76.8 - - + +
148B LEU* 1.3 59.5 + - + +
150B GLY* 3.1 1.0 + - - -
151B ILE* 2.9 37.9 + - + +
158B PHE* 5.2 1.3 - - + -
162B MET* 3.8 28.3 - - + -
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B TRP* 5.7 0.4 - - + -
144B LEU* 2.8 50.9 + - + +
145B ALA* 3.6 7.0 - - - +
147B VAL* 1.3 79.1 - - + +
149B HIS* 1.3 61.5 + - + +
151B ILE* 3.5 8.9 + - + +
152B ASP* 3.0 27.5 + - - +
166B ALA* 3.8 21.1 - - + +
172B ARG* 3.5 62.9 + - + +
175B LEU* 5.1 3.1 - - + -
176B SER* 5.1 2.9 - - - +
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Residues in contact with HIS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A HIS* 5.6 0.3 - - - +
153A ALA* 3.8 13.7 - - + +
145B ALA* 2.7 35.0 + - + +
146B ASP* 3.4 14.7 + - - +
148B LEU* 1.3 79.4 - - + +
150B GLY* 1.3 65.5 + - - +
152B ASP* 3.4 6.2 + - + +
153B ALA* 3.0 24.4 + - - +
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Residues in contact with GLY 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLY* 4.5 7.9 - - - -
153A ALA* 3.7 7.1 - - - +
154A THR* 3.9 22.0 - - - -
146B ASP 2.7 17.4 + - - -
147B VAL 3.1 2.4 + - - -
149B HIS* 1.3 73.9 - - - +
151B ILE* 1.3 58.0 + - - +
153B ALA 4.5 0.2 - - - -
154B THR* 2.7 34.8 + - - -
158B PHE* 3.6 8.3 - - - -
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B TRP* 4.9 0.9 - - + -
147B VAL* 2.9 34.1 + - + +
148B LEU* 3.9 7.6 - - + +
150B GLY* 1.3 76.0 - - - +
152B ASP* 1.3 64.0 + - - +
155B PRO* 3.3 23.6 - - - +
158B PHE* 3.9 27.1 - - + -
162B MET* 4.0 22.4 - - + +
163B VAL* 3.9 31.2 - - + -
166B ALA* 3.8 25.4 - - + -
167B THR* 4.5 13.2 - - + -
172B ARG* 5.2 2.5 - - - +
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Residues in contact with ASP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B LEU 3.0 18.1 + - - +
149B HIS* 3.6 8.3 - - + +
151B ILE* 1.3 82.1 - - - +
153B ALA* 1.3 65.2 + - - +
155B PRO* 3.9 5.5 - - - +
172B ARG* 6.4 0.4 - - - +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ASP* 3.4 43.1 - - - +
149A HIS* 3.7 14.4 - - + +
150A GLY* 3.6 15.5 - - - +
149B HIS 3.0 16.7 + - - +
152B ASP* 1.3 83.2 - - - +
154B THR* 1.3 63.9 + - - +
155B PRO* 3.7 3.4 - - - +
156B TRP* 4.7 2.8 + - - -
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Residues in contact with THR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ASP* 3.7 17.5 - - + +
147A VAL* 4.0 11.7 - - + +
150A GLY* 4.1 6.5 - - - -
158A PHE* 3.5 23.6 - - + -
150B GLY 2.7 20.4 + - - -
153B ALA* 1.3 80.4 - - - +
155B PRO* 1.3 66.0 - - - +
156B TRP* 3.1 39.9 - - + +
157B ALA* 3.1 10.9 + - - +
158B PHE* 3.2 13.3 - - - -
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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