Contacts of the helix formed by residues 154 - 168 (chain B) in PDB entry 1JXH
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 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B ALA* 4.2 2.4 - - - +
153B ARG* 1.3 79.2 - - + +
155B GLU* 1.3 73.2 + - - +
156B GLN* 3.6 14.5 + - + +
157B GLU* 3.4 33.0 + - + +
158B MET* 3.1 22.9 + - - +
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Residues in contact with GLU 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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154B THR* 1.3 80.4 + - - +
156B GLN* 1.3 63.4 + - + +
158B MET* 3.2 24.5 + - + +
159B LEU* 2.8 48.4 + - + +
188B TRP* 3.6 25.5 + - - +
197B ARG* 5.3 4.9 + - - -
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Residues in contact with GLN 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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154B THR* 3.3 12.6 + - + +
155B GLU* 1.3 85.6 - - + +
157B GLU* 1.3 57.2 + - + +
159B LEU* 3.2 20.3 + - - +
160B ALA* 2.9 29.3 + - - +
163B ARG* 5.0 8.9 + - - +
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Residues in contact with GLU 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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151B HIS 4.4 1.0 - - - +
152B ALA* 3.7 11.9 - - + -
153B ARG* 2.6 48.6 + - - +
154B THR* 3.4 21.2 + - + +
155B GLU 3.3 0.4 - - - -
156B GLN* 1.3 77.0 - - + +
158B MET* 1.3 58.6 + - - +
160B ALA* 3.3 9.0 + - - +
161B GLN* 3.0 33.3 + - - +
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Residues in contact with MET 158 (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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140B LEU* 4.2 15.9 - - + -
152B ALA* 3.8 14.3 - - + +
154B THR 3.1 14.1 + - - +
155B GLU* 3.2 22.4 + - + +
157B GLU* 1.3 78.4 - - - +
159B LEU* 1.3 78.6 + - + +
161B GLN 3.3 1.0 + - - -
162B GLY* 3.1 17.2 + - - -
175B MET* 3.3 32.0 - - + +
188B TRP* 3.4 37.7 - - + +
190B PHE* 3.9 18.2 - - - -
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Residues in contact with LEU 159 (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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155B GLU* 2.8 35.6 + - + +
156B GLN* 3.2 24.0 + - - +
158B MET* 1.3 91.4 - - + +
160B ALA* 1.3 66.6 + - - +
162B GLY 3.3 0.7 + - - -
163B ARG* 3.1 52.0 + - - +
188B TRP* 4.1 23.8 - - + -
190B PHE* 3.4 26.6 - - + -
195B GLU* 4.2 7.2 - - + +
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Residues in contact with ALA 160 (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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156B GLN 2.9 14.3 + - - +
157B GLU* 3.4 13.0 - - - +
159B LEU* 1.3 77.2 - - - +
161B GLN* 1.3 57.3 + - + +
163B ARG* 3.3 13.0 + - - +
164B ALA* 2.9 28.7 + - - +
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Residues in contact with GLN 161 (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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140B LEU* 4.6 4.6 + - - +
143B ALA* 3.7 15.6 - - + +
144B ALA* 4.1 10.8 - - - +
147B LEU* 3.5 26.6 - - + +
149B ALA* 4.3 7.6 - - + +
150B PRO 3.1 24.6 - - - +
152B ALA* 3.9 19.6 + - - +
157B GLU* 3.0 17.4 + - - +
158B MET 3.7 5.8 - - - +
159B LEU 3.3 0.2 - - - -
160B ALA* 1.3 74.3 - - + +
162B GLY* 1.3 66.7 + - - +
164B ALA* 3.1 3.3 + - - +
165B LEU* 3.0 29.7 + - - +
175B MET* 3.6 21.0 - - + +
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Residues in contact with GLY 162 (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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158B MET 3.1 10.7 + - - -
159B LEU 3.3 4.2 + - - -
161B GLN* 1.3 78.0 - - - +
163B ARG* 1.3 61.0 + - - +
165B LEU* 3.3 4.8 + - - +
166B LEU* 3.3 22.2 + - - +
173B VAL* 3.7 8.7 - - - +
175B MET* 4.2 8.9 - - - +
190B PHE* 3.8 31.4 - - - -
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Residues in contact with ARG 163 (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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156B GLN* 5.0 8.3 + - - +
159B LEU* 3.1 44.9 + - - +
160B ALA* 3.7 8.9 - - - +
161B GLN 3.2 0.2 - - - -
162B GLY* 1.3 73.0 - - - +
164B ALA* 1.3 64.8 + - - +
166B LEU* 3.2 17.2 + - + +
167B ALA* 3.1 20.8 + - - +
190B PHE* 4.2 8.7 - - + -
195B GLU* 2.8 41.3 + - - +
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Residues in contact with ALA 164 (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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147B LEU* 3.9 20.4 - - + -
160B ALA 2.9 17.4 + - - +
161B GLN* 3.1 7.8 + - - +
163B ARG* 1.3 77.8 - - - +
165B LEU* 1.3 62.5 + - - +
167B ALA* 3.2 10.0 + - - +
168B MET* 3.1 26.6 + - - +
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Residues in contact with LEU 165 (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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130B LEU* 4.6 7.4 - - + -
136B ILE* 4.8 5.4 - - + -
138B PRO* 4.4 9.6 - - + -
143B ALA* 4.4 23.3 - - + -
146B LEU* 4.3 21.8 - - + -
147B LEU* 3.8 25.6 - - + -
161B GLN 3.0 20.4 + - - +
162B GLY* 3.6 7.9 - - - +
163B ARG 3.3 0.2 - - - -
164B ALA* 1.3 73.8 - - - +
166B LEU* 1.3 66.0 + - - +
168B MET* 3.3 25.4 + - - +
170B CYS* 3.5 21.2 + - - +
173B VAL* 3.7 29.6 - - + -
175B MET* 4.7 1.1 - - - -
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Residues in contact with LEU 166 (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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162B GLY 3.3 12.0 + - - +
163B ARG* 3.2 18.1 + - + +
164B ALA 3.2 0.2 - - - -
165B LEU* 1.3 72.3 - - - +
167B ALA* 1.3 62.7 + - - +
168B MET 3.0 1.3 - - - -
169B GLY* 2.8 21.0 + - - -
170B CYS 3.3 25.8 + - - +
171B GLU 3.5 17.0 - - - +
172B ALA* 3.6 15.5 - - - -
173B VAL* 3.9 8.1 - - + -
190B PHE* 3.9 19.1 - - + +
191B THR* 3.7 27.1 - - - +
192B ARG* 4.4 6.7 - - + +
195B GLU* 6.0 0.4 - - - +
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Residues in contact with ALA 167 (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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163B ARG 3.1 9.4 + - - +
164B ALA* 3.4 12.6 - - - +
166B LEU* 1.3 78.7 - - - +
168B MET* 1.3 60.9 + - + +
169B GLY* 3.1 1.8 + - - -
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Residues in contact with MET 168 (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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126B ARG* 3.6 45.1 - - + +
130B LEU* 3.7 19.8 - - + +
131B PRO* 3.9 17.8 - - - +
146B LEU 4.4 3.6 - - - +
147B LEU* 3.5 30.1 - - + -
164B ALA 3.1 12.1 + - - +
165B LEU* 3.4 22.2 - - - +
166B LEU 3.0 1.4 - - - -
167B ALA* 1.3 78.1 - - + +
169B GLY* 1.3 54.9 + - - +
170B CYS 3.7 1.1 - - - -
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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