Contacts of the helix formed by residues 146 - 162 (chain D) in PDB entry 1JUM
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 ASN 146 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ILE* 5.1 3.6 - - - +
128D HIS* 3.4 26.3 + - - -
144D ASP* 2.9 14.0 + - - +
145D VAL* 1.3 83.2 - - - +
147D ALA* 1.3 59.3 + - - +
148D VAL 3.5 0.2 - - - -
149D SER* 3.8 5.4 - - - -
150D LYS* 3.1 41.6 + - - +
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Residues in contact with ALA 147 (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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144D ASP* 3.5 26.7 + - + +
146D ASN* 1.3 77.4 - - - +
148D VAL* 1.3 57.2 + - + +
150D LYS* 3.8 4.2 - - - +
151D ILE* 2.7 45.7 + - + +
174E LEU* 4.0 19.7 - - + -
177E LYS* 5.2 8.3 - - + -
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Residues in contact with VAL 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D PHE* 3.4 34.8 - - + -
142D ILE* 4.4 18.6 - - + -
144D ASP 3.4 15.5 + - - +
145D VAL* 5.1 0.2 - - - -
147D ALA* 1.3 78.0 - - + +
149D SER* 1.3 58.5 + - - +
151D ILE* 3.7 8.4 - - + +
152D ALA* 2.9 30.7 + - - +
182D PHE* 3.9 14.3 - - + -
186D LEU* 4.3 8.3 - - + -
177E LYS* 4.7 11.9 - - - -
181E ILE* 4.2 24.7 - - + -
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Residues in contact with SER 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D ILE* 3.1 14.9 + - - +
127D TYR* 3.0 12.6 + - - +
128D HIS* 2.9 39.2 + - - -
131D PHE* 3.6 9.8 - - - -
145D VAL 2.9 22.9 + - - -
146D ASN* 3.8 6.7 - - - -
148D VAL* 1.3 81.3 - - - +
150D LYS* 1.3 56.7 + - - +
153D ALA* 3.0 27.4 + - - +
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Residues in contact with LYS 150 (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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121D ASN* 5.9 3.0 - - - +
124D ILE* 3.8 25.6 - - + +
146D ASN* 3.1 31.5 + - - +
147D ALA* 3.9 6.5 - - - +
148D VAL 3.2 0.4 - - - -
149D SER* 1.3 73.8 - - - +
151D ILE* 1.3 67.2 + - - +
153D ALA* 3.3 3.2 + - - +
154D ASN* 3.0 37.7 + - - +
163E THR* 5.7 3.6 - - + -
166E GLN* 4.4 19.5 + - + +
174E LEU* 4.2 22.4 - - + -
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Residues in contact with ILE 151 (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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147D ALA 2.7 31.3 + - - +
148D VAL* 3.7 8.1 - - + +
150D LYS* 1.3 76.1 - - - +
152D ALA* 1.3 59.4 + - - +
154D ASN* 3.1 3.1 + - - -
155D ALA* 2.8 27.6 + - + +
182D PHE* 4.7 9.0 - - + -
159E ILE* 3.6 13.2 - - + +
174E LEU* 3.7 29.8 - - + +
177E LYS* 3.6 38.1 - - + -
178E PHE* 3.5 41.5 - - + +
181E ILE* 5.2 2.2 - - + -
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Residues in contact with ALA 152 (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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79D PHE* 4.3 7.2 - - + -
127D TYR* 4.3 11.9 - - + -
131D PHE* 4.2 12.3 - - + -
148D VAL 2.9 17.1 + - - +
149D SER 4.2 1.8 - - - +
151D ILE* 1.3 73.4 - - - +
153D ALA* 1.3 69.0 + - - +
154D ASN 2.9 1.4 + - - -
155D ALA* 4.6 4.3 - - - +
156D VAL* 3.1 31.3 + - + +
178D PHE* 5.3 1.8 - - - -
182D PHE* 4.0 26.7 - - + -
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Residues in contact with ALA 153 (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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123D TYR* 3.5 12.7 + - + -
124D ILE* 3.3 31.9 - - + -
127D TYR* 3.5 26.1 - - + -
149D SER 3.0 20.0 + - - +
150D LYS 3.4 4.3 - - - +
152D ALA* 1.3 80.8 - - - +
154D ASN* 1.3 61.8 + - - +
156D VAL* 4.1 1.0 - - - +
157D ASN* 3.3 20.4 + - - +
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Residues in contact with ASN 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D TYR* 5.1 3.8 - - - -
124D ILE* 4.6 8.3 - - - +
150D LYS* 3.0 26.5 + - - +
151D ILE* 3.7 2.8 - - - +
152D ALA 2.9 0.8 + - - -
153D ALA* 1.3 84.8 + - - +
155D ALA* 1.3 65.6 + - - +
157D ASN* 3.5 7.1 - - - +
158D GLY 2.9 18.5 + - - -
158E GLY* 3.7 8.8 - - - -
159E ILE* 4.1 22.3 - - + +
162E PHE* 3.6 26.2 + - + +
163E THR* 3.4 23.0 - - - +
174E LEU* 5.2 1.9 - - - +
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Residues in contact with ALA 155 (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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151D ILE* 2.8 18.8 + - + +
152D ALA* 4.1 1.1 - - - +
154D ASN* 1.3 72.2 - - - +
156D VAL* 1.3 64.9 + - - +
158D GLY* 3.0 3.6 + - - -
159D ILE* 2.9 26.5 + - - +
178D PHE* 4.0 16.8 - - + -
182D PHE* 6.2 0.2 - - + -
155E ALA* 3.4 38.8 - - + +
159E ILE* 3.9 7.7 - - + +
178E PHE* 4.2 7.6 - - + -
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Residues in contact with VAL 156 (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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79D PHE* 5.2 0.4 - - + -
83D ASN* 3.5 22.0 - - - +
86D SER* 4.6 6.3 - - - +
93D TYR* 4.8 4.0 - - - +
127D TYR* 3.3 30.3 - - + +
152D ALA* 3.1 16.4 + - + +
153D ALA 4.1 2.2 - - - +
155D ALA* 1.3 76.0 - - - +
157D ASN* 1.3 55.4 + - - +
159D ILE* 2.7 33.3 + - - +
160D VAL* 2.8 20.8 + - + +
175D MET* 3.7 19.5 - - + -
178D PHE* 3.5 23.8 - - + -
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Residues in contact with ASN 157 (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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92D TYR* 4.8 1.0 - - - -
93D TYR* 4.1 12.3 - - - -
96D GLN* 3.1 47.1 - - - +
123D TYR* 3.8 27.3 + - - +
153D ALA 3.3 15.4 + - - +
154D ASN* 3.5 9.4 - - - +
156D VAL* 1.3 80.4 - - - +
158D GLY* 1.3 62.3 + - - +
160D VAL* 3.3 8.0 + - - +
161D THR* 3.0 24.8 + - - +
162E PHE* 3.4 14.3 - - + -
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Residues in contact with GLY 158 (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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154D ASN 2.9 11.5 + - - -
155D ALA 3.0 3.3 + - - -
157D ASN* 1.3 77.4 - - - +
159D ILE* 1.3 57.6 + - - +
162D PHE* 2.9 53.5 + - - +
154E ASN 3.4 12.9 - - - +
158E GLY* 3.6 13.5 - - - -
162E PHE* 4.1 2.0 - - - -
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Residues in contact with ILE 159 (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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87D LEU* 5.2 3.3 - - + +
155D ALA 2.9 17.2 + - - +
156D VAL* 2.7 12.5 + - - +
158D GLY* 1.3 78.0 - - - +
160D VAL* 1.3 56.7 + - - +
163D THR* 2.5 41.8 + - + +
171D ARG* 4.4 1.4 + - - +
174D LEU* 5.5 5.2 - - + -
175D MET* 3.9 28.9 - - + +
178D PHE* 3.4 50.5 - - + -
151E ILE* 4.4 10.8 - - + +
154E ASN* 4.0 8.3 - - + -
155E ALA* 4.2 15.5 - - + +
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Residues in contact with VAL 160 (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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86D SER* 4.1 28.3 - - - +
87D LEU* 4.4 18.2 - - + -
93D TYR* 4.3 19.5 - - + -
156D VAL* 2.8 27.6 + - + +
157D ASN* 3.7 9.0 - - - +
158D GLY 3.2 0.2 - - - -
159D ILE* 1.3 78.4 - - - +
161D THR* 1.3 66.4 + - + +
164D HIS* 3.8 6.2 + - - +
171D ARG* 3.3 23.9 + - - +
175D MET* 3.6 20.9 - - + -
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Residues in contact with THR 161 (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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93D TYR* 4.0 11.7 - - + +
96D GLN* 3.5 34.5 - - + -
97D ASN* 6.0 0.2 - - - -
157D ASN* 3.0 18.5 + - - +
160D VAL* 1.3 84.8 - - + +
162D PHE* 1.3 70.2 + - - +
163D THR 3.4 2.2 + - - -
164D HIS* 3.8 14.2 - - - +
100E ILE* 3.6 28.4 - - - +
162E PHE* 4.0 12.6 - - - -
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Residues in contact with PHE 162 (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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158D GLY* 2.9 40.5 + - - +
161D THR* 1.3 86.8 - - - +
163D THR* 1.3 60.9 + - - +
164D HIS 3.5 2.7 - - - -
165D GLU* 2.9 16.5 - - - +
96E GLN* 3.6 32.5 - - + -
97E ASN* 5.8 0.4 - - - -
100E ILE* 4.0 32.8 - - + -
120E GLU* 5.0 2.4 - - - +
154E ASN* 3.2 24.2 + - - +
157E ASN* 3.6 31.4 - - + +
158E GLY* 4.1 0.9 - - - -
161E THR* 3.6 24.5 - - + -
162E PHE* 4.3 5.8 - + - -
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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
------------------------------------------------------------
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