Contacts of the helix formed by residues 167 - 185 (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 ASN 167 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E GLN* 1.3 71.3 - - - +
168E ILE* 1.3 83.1 + - - +
169E ASN* 2.8 35.6 + - - +
170E GLU* 3.0 22.5 + - + +
171E ARG* 3.2 11.1 + - - +
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Residues in contact with ILE 168 (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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2A ASN* 5.8 5.8 - - - +
87E LEU* 6.0 3.6 - - + +
88E THR* 5.2 10.5 - - + -
166E GLN 3.2 6.8 + - - +
167E ASN* 1.3 85.2 - - - +
169E ASN* 1.3 71.5 + - - +
171E ARG* 3.4 11.7 + - + +
172E ILE* 3.1 41.0 + - + +
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Residues in contact with ASN 169 (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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167E ASN* 2.8 24.4 + - - +
168E ILE* 1.3 81.1 - - - +
170E GLU* 1.3 66.0 + - - +
172E ILE* 2.8 22.0 + - - +
173E LYS* 3.0 32.2 + - - +
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Residues in contact with GLU 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D LYS* 4.3 9.9 - - - -
166E GLN* 2.6 46.3 + - - +
167E ASN* 3.0 16.6 + - + +
169E ASN* 1.3 77.9 - - - +
171E ARG* 1.3 53.5 + - - +
173E LYS* 2.8 18.3 + - + +
174E LEU* 2.7 61.5 + - + +
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Residues in contact with ARG 171 (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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87E LEU* 3.4 51.3 + - + +
159E ILE* 5.4 1.4 - - - +
160E VAL* 3.0 12.9 + - - +
163E THR* 2.8 67.6 + - - +
164E HIS* 2.9 29.6 + - - +
166E GLN* 3.8 20.5 + - + +
167E ASN 3.3 15.3 - - - +
168E ILE* 3.4 11.5 - - + +
170E GLU* 1.3 78.6 - - - +
172E ILE* 1.3 58.1 + - + +
173E LYS 3.0 0.2 + - - -
174E LEU* 3.1 10.1 + - - +
175E MET* 2.8 30.8 + - - +
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Residues in contact with ILE 172 (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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84E GLU* 3.3 43.5 - - + +
87E LEU* 3.5 19.7 - - + -
88E THR* 4.7 8.1 - - + -
168E ILE* 3.1 29.6 - - + +
169E ASN* 2.8 13.6 + - - +
171E ARG* 1.3 72.6 - - - +
173E LYS* 1.3 58.6 + - + +
175E MET* 3.9 1.1 - - - +
176E ASN* 3.1 37.5 + - - +
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Residues in contact with LYS 173 (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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169E ASN* 3.0 36.4 + - - +
170E GLU* 2.8 18.0 + - + +
172E ILE* 1.3 77.2 - - + +
174E LEU* 1.3 65.0 + - + +
176E ASN* 3.0 9.7 + - - +
177E LYS* 2.9 23.4 + - - +
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Residues in contact with LEU 174 (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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147D ALA* 4.1 25.6 - - + +
150D LYS* 4.2 24.9 - - + -
151D ILE* 3.6 34.6 - - + +
154D ASN* 5.6 0.7 - - - +
159E ILE* 5.2 9.0 - - + -
163E THR* 4.9 13.2 - - + -
166E GLN* 4.6 3.8 - - - +
170E GLU* 2.7 46.3 + - + +
171E ARG* 3.6 9.9 - - - +
173E LYS* 1.3 73.1 - - + +
175E MET* 1.3 57.5 + - - +
177E LYS* 3.4 2.0 + - - -
178E PHE* 3.0 26.6 + - - +
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Residues in contact with MET 175 (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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80E TYR 5.4 0.2 - - - +
83E ASN* 3.0 55.4 - - + +
84E GLU* 3.9 5.6 - - + +
87E LEU* 3.5 23.1 - - + -
156E VAL* 3.6 13.9 - - + -
159E ILE* 3.8 25.5 - - + +
160E VAL* 3.5 28.3 - - + -
171E ARG 2.8 15.6 + - - +
172E ILE 4.0 3.8 - - - +
174E LEU* 1.3 76.0 - - - +
176E ASN* 1.3 60.6 + - - +
178E PHE* 3.8 5.4 - - - +
179E SER* 2.9 31.5 + - - -
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Residues in contact with ASN 176 (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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80E TYR* 3.6 28.0 - - + +
84E GLU* 4.9 5.9 - - - +
172E ILE* 3.1 38.7 + - - +
173E LYS* 3.0 10.1 + - - +
175E MET* 1.3 75.1 - - - +
177E LYS* 1.3 61.9 + - - +
179E SER* 3.4 4.1 - - - -
180E GLN* 2.8 30.3 + - - +
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Residues in contact with LYS 177 (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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142D ILE* 6.1 1.4 - - - +
143D ASN* 5.8 2.8 - - - +
144D ASP* 4.7 23.6 + - - +
147D ALA* 5.2 7.4 - - + +
148D VAL* 5.2 7.1 - - + +
151D ILE* 3.5 24.7 - - + -
173E LYS 2.9 12.0 + - - +
174E LEU* 3.6 3.6 - - - +
175E MET 3.3 0.2 - - - -
176E ASN* 1.3 72.9 - - - +
178E PHE* 1.3 68.8 + - - +
180E GLN* 2.9 30.3 + - - +
181E ILE* 2.9 40.0 + - + +
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Residues in contact with PHE 178 (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* 3.2 34.2 - - + +
155D ALA* 4.0 17.7 - - + -
178D PHE* 4.0 14.4 - + - -
182D PHE* 4.4 10.8 - + - -
79E PHE* 4.6 7.2 - + - -
83E ASN* 4.7 2.2 - - - -
152E ALA* 5.1 0.9 - - - -
155E ALA* 3.5 18.2 - - + -
156E VAL* 4.1 23.6 - - + -
159E ILE* 3.4 19.3 - - + -
174E LEU 3.0 10.7 + - - +
175E MET* 3.8 6.7 - - - +
177E LYS* 1.3 75.5 - - - +
179E SER* 1.3 71.0 + - - +
181E ILE* 2.9 7.1 + - - +
182E PHE* 2.9 61.0 + + + +
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Residues in contact with SER 179 (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* 3.4 22.1 - - - -
80E TYR* 3.4 35.9 - - - -
83E ASN* 3.0 23.5 + - - +
175E MET 2.9 20.5 + - - -
176E ASN* 3.4 3.4 - - - -
178E PHE* 1.3 80.9 - - - +
180E GLN* 1.3 63.9 + - - +
183E LEU* 3.3 22.3 + - - +
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Residues in contact with GLN 180 (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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76E ARG* 5.2 3.8 + - - +
80E TYR* 3.1 25.7 + - - +
176E ASN 2.8 16.8 + - - +
177E LYS* 2.9 39.1 + - - +
179E SER* 1.3 72.6 - - - +
181E ILE* 1.3 70.9 + - - +
183E LEU* 3.5 2.0 + - - +
184E ASN* 3.0 24.3 + - + +
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Residues in contact with ILE 181 (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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148D VAL* 4.2 15.7 - - + -
151D ILE* 5.0 1.8 - - + -
182D PHE* 3.6 57.0 - - + +
185D GLY* 3.8 17.0 - - - +
186D LEU* 3.8 19.3 - - + -
177E LYS* 2.9 38.7 + - + +
178E PHE* 2.9 6.0 + - - +
180E GLN* 1.3 75.9 - - - +
182E PHE* 1.3 68.7 + - - +
184E ASN* 2.7 21.1 + - - +
185E GLY 2.8 11.4 + - - -
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Residues in contact with PHE 182 (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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178D PHE* 4.4 9.9 - + - -
181D ILE* 3.4 26.1 - - + +
182D PHE* 5.0 3.5 - + - -
79E PHE* 3.7 13.7 - + + -
131E PHE* 3.8 16.8 - + - -
148E VAL* 3.4 33.9 - - + -
151E ILE* 3.8 22.7 - - + -
152E ALA* 3.7 20.6 - - + -
155E ALA* 5.2 0.2 - - + -
178E PHE* 2.9 49.0 + + + +
179E SER 4.2 2.9 - - - +
181E ILE* 1.3 79.0 - - - +
183E LEU* 1.3 62.7 + - + +
185E GLY 3.5 1.2 + - - -
186E LEU* 3.1 29.9 - - + +
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Residues in contact with LEU 183 (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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76E ARG* 3.4 63.3 - - - +
79E PHE* 3.3 42.4 - - + -
80E TYR* 4.5 5.2 - - + -
131E PHE* 4.3 10.3 - - + -
140E TRP* 3.9 22.8 - - + +
179E SER 3.3 12.9 + - - +
180E GLN* 3.8 2.9 - - - +
181E ILE 2.8 4.0 + - - -
182E PHE* 1.3 80.1 - - + +
184E ASN* 1.3 64.4 + - - +
186E LEU* 2.9 26.8 + - + +
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Residues in contact with ASN 184 (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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184D ASN* 3.6 6.6 - - - +
185D GLY* 3.4 20.7 - - - +
187D SER 4.5 19.5 + - - +
76E ARG* 4.9 7.8 - - - +
180E GLN* 3.0 18.7 + - + +
181E ILE* 2.7 14.9 + - - +
183E LEU* 1.3 68.4 - - - +
185E GLY* 1.3 53.8 + - - +
186E LEU 2.6 17.8 + - - -
187E SER* 3.4 11.4 + - - -
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Residues in contact with GLY 185 (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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181D ILE* 3.7 15.0 - - - +
184D ASN* 2.8 46.3 - - - +
185D GLY* 3.4 8.9 - - - -
181E ILE 2.8 14.9 + - - -
182E PHE 3.5 2.0 + - - -
183E LEU 3.3 0.6 - - - -
184E ASN* 1.3 70.2 + - - +
186E LEU* 1.3 66.5 + - - +
187E SER 3.7 0.5 + - - -
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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