Contacts of the helix formed by residues 143 - 157 (chain B) in PDB entry 2EX4
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 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B THR* 3.7 12.1 - - - +
6B ILE* 3.9 22.2 - - + -
9B GLU* 3.9 31.5 + - + +
12B PHE* 4.1 1.5 - - + -
13B TYR* 3.1 15.2 + - + +
142B LEU* 1.3 75.5 - - - +
144B ASP* 1.3 60.5 + - - +
145B GLN* 3.6 5.9 + - - +
146B HIS* 3.1 29.8 + - - -
147B LEU* 2.8 26.9 + - - +
186B ARG* 3.3 0.9 - - - +
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Residues in contact with ASP 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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0B GLY 4.8 0.3 - - - +
1B SER* 3.3 15.9 - - - -
2B THR* 2.9 43.6 + - - +
3B SER 4.7 0.2 + - - -
143B THR* 1.3 71.1 - - - +
145B GLN* 1.3 58.3 + - - +
147B LEU* 3.2 1.8 + - - +
148B ALA* 2.9 29.6 + - - +
175B VAL* 5.4 0.2 - - - +
186B ARG* 2.9 34.1 + - - +
190B VAL* 4.6 5.7 - - - +
194B ILE* 3.5 22.6 - - + +
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Residues in contact with GLN 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 THR* 3.2 5.8 + - - +
144B ASP* 1.3 78.9 - - - +
146B HIS* 1.3 68.0 + - + +
148B ALA* 3.4 5.5 + - + +
149B GLU* 2.8 58.8 + - + +
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Residues in contact with HIS 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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9B GLU* 3.1 31.8 + - - -
13B TYR* 2.6 36.6 + + - +
121B GLN* 3.7 29.8 + - + +
142B LEU* 4.1 4.9 - - + -
143B THR* 3.1 18.4 + - - +
145B GLN* 1.3 80.1 - - + +
147B LEU* 1.3 59.0 + - - +
149B GLU* 3.9 17.3 - - - +
150B PHE* 2.8 32.4 + - - +
153B ARG* 5.1 1.6 + - - -
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Residues in contact with LEU 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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135B ILE* 5.9 0.9 - - + -
139B ILE* 3.9 39.0 - - + +
142B LEU* 3.9 22.6 - - + +
143B THR 2.8 18.3 + - - +
144B ASP 3.5 4.5 - - - +
146B HIS* 1.3 74.5 - - - +
148B ALA* 1.3 65.4 + - - +
150B PHE* 3.7 4.6 - - + +
151B LEU* 2.9 48.2 + - + +
166B ILE* 5.3 1.8 - - + -
186B ARG* 3.9 29.6 - - - +
191B VAL* 6.0 3.1 - - + -
194B ILE* 3.9 23.1 - - + -
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Residues in contact with ALA 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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144B ASP 2.9 19.3 + - - +
145B GLN* 3.8 6.7 - - + +
147B LEU* 1.3 73.2 - - - +
149B GLU* 1.3 59.6 + - + +
151B LEU* 3.3 0.6 + - - -
152B ARG* 3.0 34.2 + - + +
194B ILE* 3.9 13.6 - - + +
197B SER* 3.9 22.0 - - - +
198B ALA* 3.6 10.9 - - + +
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Residues in contact with GLU 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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145B GLN* 2.8 54.2 + - + +
146B HIS* 3.9 20.5 - - - +
148B ALA* 1.3 73.7 - - + +
150B PHE* 1.3 61.1 + - - +
152B ARG* 3.2 12.5 + - - +
153B ARG* 2.9 47.3 + - - +
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Residues in contact with PHE 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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67B LEU* 5.1 0.7 - - + -
69B CYS* 3.8 18.8 - - - -
120B LEU* 3.4 53.2 - - + +
123B PHE* 3.9 25.8 - + - -
125B PRO* 4.4 4.3 - - + -
135B ILE* 3.8 22.2 - - + -
142B LEU* 4.1 11.9 - - + -
146B HIS 2.8 19.6 + - - +
147B LEU* 3.7 7.4 - - + +
149B GLU* 1.3 75.5 - - - +
151B LEU* 1.3 55.6 + - + +
153B ARG* 3.0 20.8 + - - +
154B CYS* 2.7 60.2 + - - -
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Residues in contact with LEU 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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135B ILE* 3.8 28.9 - - + -
147B LEU* 2.9 40.2 + - + +
148B ALA 3.7 4.3 - - - +
150B PHE* 1.3 77.0 - - + +
152B ARG* 1.3 56.8 + - - +
154B CYS* 3.3 5.5 + - - +
155B LYS* 2.9 29.1 + - - +
164B ILE* 4.1 15.7 - - + +
166B ILE* 4.0 27.8 - - + -
194B ILE* 4.3 13.0 - - + -
195B ILE* 4.5 9.2 - - + -
198B ALA* 3.9 13.9 - - + -
200B LEU* 3.9 18.1 - - + +
223B LEU* 4.8 0.2 - - + -
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Residues in contact with ARG 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 ALA* 3.0 21.0 + - - +
149B GLU* 3.2 13.9 + - - +
151B LEU* 1.3 74.3 - - - +
153B ARG* 1.3 65.7 + - + +
155B LYS* 3.3 10.3 + - - +
156B GLY* 3.1 18.2 + - - -
197B SER 2.7 28.0 + - - -
198B ALA* 3.2 33.9 + - - +
199B GLY* 3.7 8.9 - - - +
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Residues in contact with ARG 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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120B LEU 3.0 19.0 + - - -
121B GLN* 3.5 18.5 + - - +
122B ASP 5.4 0.2 - - - -
123B PHE 2.7 30.3 + - - +
124B THR* 3.2 31.3 + - + -
125B PRO* 3.8 19.9 - - + +
146B HIS 5.1 0.8 + - - -
149B GLU* 2.9 36.3 + - - +
150B PHE* 3.4 20.5 - - - +
152B ARG* 1.3 75.9 - - + +
154B CYS* 1.3 63.2 + - - +
156B GLY* 3.1 12.2 + - - -
157B SER* 3.2 9.0 + - - -
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Residues in contact with CYS 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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67B LEU* 5.3 0.2 - - - -
125B PRO* 3.9 5.8 - - - +
133B ILE* 3.5 34.0 - - + +
135B ILE* 4.5 4.3 - - - -
150B PHE* 2.7 57.8 + - - +
151B LEU* 3.5 11.2 - - + +
153B ARG* 1.3 72.7 - - - +
155B LYS* 1.3 62.9 + - - +
157B SER* 2.7 25.7 + - - -
158B LEU* 3.4 5.5 + - - +
164B ILE* 3.7 13.7 - - + -
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Residues in contact with LYS 155 (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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151B LEU 2.9 13.7 + - - +
152B ARG* 3.5 13.9 - - - +
153B ARG 3.3 0.2 - - - -
154B CYS* 1.3 74.7 - - - +
156B GLY* 1.3 63.1 - - - +
157B SER 3.1 1.2 + - - -
158B LEU* 3.3 22.4 + - + +
164B ILE* 3.9 7.8 - - - +
198B ALA 4.2 9.0 - - - +
199B GLY* 3.0 28.7 + - - +
200B LEU* 3.7 18.2 - - + -
224B ARG 3.7 23.3 + - - -
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Residues in contact with GLY 156 (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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125B PRO 5.4 0.9 - - - -
127B PRO* 3.4 22.2 - - - +
128B ASP 3.8 2.6 + - - -
152B ARG 3.1 9.6 + - - -
153B ARG* 3.1 10.2 + - - -
155B LYS* 1.3 76.7 - - - +
157B SER* 1.3 56.5 + - - +
158B LEU 3.5 1.9 - - - +
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Residues in contact with SER 157 (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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125B PRO* 3.5 31.7 - - - +
126B GLU 3.3 23.8 - - - -
127B PRO* 4.0 0.2 - - - -
128B ASP 3.8 3.1 - - - +
129B SER 2.8 26.2 + - - -
130B TYR* 3.1 11.8 + - - -
133B ILE* 3.3 16.7 - - - +
153B ARG 3.2 1.6 + - - -
154B CYS 2.7 19.8 + - - -
156B GLY* 1.3 76.0 - - - +
158B LEU* 1.3 59.8 + - - +
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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