Contacts of the helix formed by residues 144 - 162 (chain E) in PDB entry 1JTY
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 144 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E ILE* 3.7 2.9 - - - -
143E ASN* 1.3 92.0 + - + +
145E VAL* 1.3 66.9 + - - +
146E ASN* 3.9 12.3 + - - +
147E ALA* 3.1 37.9 + - + +
148E VAL* 3.4 18.9 + - - +
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Residues in contact with VAL 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E HIS* 3.3 45.8 - - + +
131E PHE* 4.0 7.6 - - + -
132E LYS* 4.3 7.6 - - + +
135E ASN* 3.3 30.1 - - - +
142E ILE* 3.7 20.4 - - + +
143E ASN 4.0 0.8 + - - +
144E ASP* 1.3 68.0 + - - +
146E ASN* 1.3 56.3 + - - +
147E ALA 2.7 15.0 + - - -
148E VAL* 3.0 4.0 + - - +
149E SER* 3.0 32.7 + - - +
902E SO4 5.0 6.5 - - - +
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Residues in contact with ASN 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E ILE* 4.5 4.3 - - - +
128E HIS* 3.2 32.4 + - - +
144E ASP* 3.5 14.6 + - - +
145E VAL* 1.3 80.2 - - - +
147E ALA* 1.3 58.5 + - - +
149E SER* 4.1 3.5 - - - -
150E LYS* 3.7 24.9 + - - +
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Residues in contact with ALA 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D LYS* 6.2 4.3 - - - -
174D LEU* 4.0 17.9 - - + +
177D LYS* 5.4 8.7 - - + +
144E ASP* 3.1 24.6 + - + +
145E VAL 2.7 5.9 + - - -
146E ASN* 1.3 72.4 - - - +
148E VAL* 1.3 55.7 + - + +
149E SER 3.0 1.1 - - - -
150E LYS* 2.6 30.2 + - - +
151E ILE* 2.7 23.0 + - + +
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Residues in contact with VAL 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D LYS* 4.4 15.9 - - + +
181D ILE* 3.9 21.8 - - + -
131E PHE* 3.9 14.4 - - + -
142E ILE* 3.8 19.5 - - + -
143E ASN* 5.1 0.7 - - - +
144E ASP 3.4 16.2 - - - +
145E VAL 3.0 3.1 + - - +
147E ALA* 1.3 76.1 - - + +
149E SER* 1.3 53.6 + - - +
151E ILE* 4.0 8.1 - - + -
152E ALA* 2.7 34.3 + - - +
182E PHE* 3.4 31.6 - - + -
186E LEU* 4.7 8.3 - - + -
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Residues in contact with SER 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ILE* 3.0 25.5 - - - +
127E TYR* 3.8 14.7 - - - +
128E HIS* 3.2 41.2 - - - -
131E PHE* 3.2 11.8 - - - -
145E VAL* 3.0 19.5 + - - +
146E ASN* 4.1 5.6 - - - -
148E VAL* 1.3 77.9 - - - +
150E LYS* 1.3 59.7 + - - +
153E ALA* 3.3 15.4 + - - +
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Residues in contact with LYS 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D THR* 5.3 0.2 - - + -
166D GLN* 4.1 16.3 - - - +
170D GLU* 4.2 15.2 + - - +
174D LEU* 3.3 37.1 - - + +
124E ILE* 3.0 21.0 - - + +
146E ASN* 3.7 16.8 + - - +
147E ALA* 2.6 20.0 + - - +
149E SER* 1.3 74.9 - - - +
151E ILE* 1.3 60.3 + - - -
153E ALA* 3.7 2.6 + - - +
154E ASN* 3.3 37.7 + - - +
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Residues in contact with ILE 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ILE* 4.2 7.7 - - + +
174D LEU* 3.0 46.0 - - + +
177D LYS* 3.4 21.5 - - + -
178D PHE* 3.3 47.3 - - + +
181D ILE* 5.0 2.2 - - + -
147E ALA 2.7 15.9 + - - +
148E VAL* 3.1 13.0 + - - +
150E LYS* 1.3 73.8 - - - +
152E ALA* 1.3 66.9 + - - +
154E ASN* 3.1 6.9 + - - +
155E ALA* 2.9 21.4 + - + +
182E PHE* 3.8 12.3 - - + -
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Residues in contact with ALA 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E PHE* 4.2 4.5 - - + -
127E TYR* 3.5 27.6 - - + -
131E PHE* 4.1 3.8 - - + -
148E VAL 2.7 20.4 + - - +
151E ILE* 1.3 73.5 - - - +
153E ALA* 1.3 57.7 + - - +
155E ALA* 3.1 3.2 + - - +
156E VAL* 2.8 38.4 + - + +
178E PHE* 5.2 0.4 - - - -
182E PHE* 3.7 29.2 - - + -
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Residues in contact with ALA 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E TYR* 5.2 2.9 + - - +
123E TYR 5.9 0.2 - - - -
124E ILE* 4.3 16.4 - - + -
127E TYR* 3.7 25.9 - - + -
149E SER 3.3 19.6 + - - +
150E LYS* 3.9 4.7 - - - +
151E ILE 3.3 0.6 - - - -
152E ALA* 1.3 79.7 - - - +
154E ASN* 1.3 59.4 + - - +
156E VAL* 4.0 1.4 - - - +
157E ASN* 3.2 33.3 + - - +
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Residues in contact with ASN 154 (chain E).
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* 3.1 24.9 - - - +
159D ILE* 3.7 22.6 + - + +
162D PHE* 3.4 21.1 - - - +
163D THR* 2.8 36.3 - - - +
174D LEU* 5.4 1.6 - - - +
150E LYS* 3.3 25.7 + - - +
151E ILE* 3.1 6.1 + - - +
153E ALA* 1.3 76.9 - - - +
155E ALA* 1.3 66.1 + - - +
157E ASN* 3.7 6.4 + - - +
158E GLY 3.2 7.1 + - - -
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Residues in contact with ALA 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ALA* 3.4 33.8 - - + +
159D ILE* 4.4 2.6 - - + +
178D PHE* 4.3 11.4 - - + -
151E ILE* 2.9 17.3 + - + +
152E ALA* 3.6 4.0 - - - +
154E ASN* 1.3 75.2 - - - +
156E VAL* 1.3 69.7 + - - +
158E GLY 3.2 2.4 + - - -
159E ILE* 3.1 18.2 + - - +
178E PHE* 3.5 26.9 - - + -
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Residues in contact with VAL 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E PHE* 5.3 0.2 - - + -
83E ASN* 3.1 33.2 - - + +
86E SER* 3.9 11.4 - - - +
93E TYR* 4.8 3.8 - - + +
127E TYR* 3.1 20.0 - - + +
152E ALA* 2.8 18.8 + - + +
153E ALA 4.0 2.2 - - - +
155E ALA* 1.3 75.4 - - - +
157E ASN* 1.3 55.5 + - - +
159E ILE* 2.8 32.6 + - - +
160E VAL* 2.9 20.6 + - + +
175E MET* 3.6 24.2 - - + -
178E PHE* 4.1 13.5 - - + -
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Residues in contact with ASN 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D PHE* 3.3 29.2 - - + -
92E TYR* 4.1 12.1 + - - -
93E TYR* 3.7 20.7 + - - -
96E GLN* 3.1 41.0 + - - +
153E ALA* 3.2 20.0 + - - +
154E ASN* 3.7 9.0 + - - +
156E VAL* 1.3 78.8 - - - +
158E GLY* 1.3 57.5 + - - +
160E VAL* 3.6 6.6 - - - +
161E THR* 2.8 35.5 + - - -
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Residues in contact with GLY 158 (chain E).
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 3.6 8.3 - - - -
158D GLY* 3.5 20.1 - - - -
162D PHE* 4.5 0.2 - - - -
154E ASN 3.2 8.3 + - - -
155E ALA 3.8 0.7 - - - -
156E VAL 3.1 0.8 - - - -
157E ASN* 1.3 75.8 - - - +
159E ILE* 1.3 59.2 + - - +
162E PHE* 2.8 56.6 + - - +
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Residues in contact with ILE 159 (chain E).
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* 3.7 15.0 - - + +
154D ASN* 3.9 10.3 + - + -
155D ALA* 3.9 15.0 - - + +
87E LEU* 4.7 3.9 - - + +
155E ALA 3.1 13.4 + - - +
156E VAL* 2.8 13.5 + - - +
158E GLY* 1.3 72.3 - - - +
160E VAL* 1.3 52.2 + - - +
163E THR* 2.6 37.6 + - + +
171E ARG* 5.4 0.9 - - - +
174E LEU* 5.2 8.3 - - + -
175E MET* 3.8 33.7 - - + +
178E PHE* 3.4 50.7 - - + -
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Residues in contact with VAL 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E SER* 3.7 37.9 - - - +
87E LEU* 4.0 15.9 - - + -
93E TYR* 4.4 14.8 - - + +
156E VAL* 2.9 20.9 + - + +
157E ASN* 3.6 8.1 - - - +
159E ILE* 1.3 76.6 - - - +
161E THR* 1.3 68.0 + - - +
163E THR 3.6 0.5 + - - -
164E HIS* 3.3 21.9 - - + +
171E ARG* 3.0 24.1 + - - +
175E MET* 3.5 22.7 - - + -
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Residues in contact with THR 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ILE* 3.4 41.2 - - + +
162D PHE* 3.5 20.4 - - + -
93E TYR 4.6 2.3 + - - -
96E GLN* 3.7 19.8 - - + +
97E ASN 5.7 0.7 - - - +
157E ASN* 2.8 23.6 + - - -
160E VAL* 1.3 75.7 - - - +
162E PHE* 1.3 69.1 + - + +
163E THR 3.2 4.7 + - - -
164E HIS* 3.7 23.3 + - + +
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Residues in contact with PHE 162 (chain E).
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* 5.7 0.2 - - - -
96D GLN* 3.4 23.8 - - + -
99D ILE* 6.5 0.7 - - + -
100D ILE* 4.7 16.6 - - + -
120D GLU* 5.7 0.9 - - - +
123D TYR* 5.1 1.6 - + - -
154D ASN* 3.1 29.7 + - - +
157D ASN* 3.2 46.9 - - + -
161D THR* 3.8 11.2 - - + -
162D PHE* 4.2 15.3 - + - -
158E GLY* 2.8 47.4 + - - +
161E THR* 1.3 76.8 - - + +
163E THR* 1.3 66.9 + - - +
164E HIS 3.8 0.2 - - - -
165E GLU* 3.2 11.3 - - - +
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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