Contacts of the helix formed by residues 167 - 185 (chain B) in PDB entry 1JT0
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B GLU 4.1 0.4 + - - -
166B GLN* 1.3 71.7 - - - +
168B ILE* 1.3 55.9 + - - +
169B ASN* 2.7 14.6 + - - +
170B GLU* 2.5 47.9 + - + +
171B ARG* 3.0 7.9 + - - -
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Residues in contact with ILE 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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87B LEU* 2.9 34.1 - - + +
88B THR* 4.3 12.8 - - + -
166B GLN 3.6 3.8 + - - -
167B ASN* 1.3 71.4 - - - +
169B ASN* 1.3 72.2 + - + +
171B ARG* 3.0 24.0 + - - +
172B ILE* 2.8 37.4 + - + +
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Residues in contact with ASN 169 (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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167B ASN* 2.7 16.1 + - - +
168B ILE* 1.3 83.2 - - + +
170B GLU* 1.3 57.7 + - - +
171B ARG 3.2 0.2 - - - -
172B ILE* 3.1 44.7 - - - +
173B LYS* 3.7 8.6 - - - +
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Residues in contact with GLU 170 (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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166B GLN* 4.8 14.6 - - + +
167B ASN* 2.5 37.9 + - + +
169B ASN* 1.3 72.4 - - - +
171B ARG* 1.3 57.1 + - - -
172B ILE 3.5 0.2 - - - -
173B LYS* 3.1 30.9 - - - +
174B LEU* 3.1 23.8 - - + +
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Residues in contact with ARG 171 (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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87B LEU* 3.9 44.3 + - + +
159B ILE* 5.6 0.2 - - - +
160B VAL* 3.6 19.6 + - - +
163B THR* 2.7 59.6 + - - -
164B HIS* 3.6 19.3 + - - +
166B GLN* 3.7 23.1 + - + -
167B ASN 3.0 16.4 + - - +
168B ILE* 3.0 16.9 + - - +
170B GLU* 1.3 76.5 - - - +
172B ILE* 1.3 58.8 + - - +
173B LYS 2.7 10.8 + - - -
174B LEU* 3.0 17.5 + - - +
175B MET* 3.1 14.7 + - - +
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Residues in contact with ILE 172 (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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84B GLU* 3.0 37.9 - - + +
87B LEU* 4.3 17.5 - - + +
88B THR* 4.8 4.7 - - + -
168B ILE* 2.8 28.4 + - + +
169B ASN* 3.1 36.8 - - - +
170B GLU 3.5 0.2 - - - -
171B ARG* 1.3 74.0 - - - +
173B LYS* 1.3 75.7 + - + +
175B MET* 4.4 3.1 - - - -
176B ASN* 2.7 43.8 + - - +
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Residues in contact with LYS 173 (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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169B ASN* 3.7 6.5 - - - +
170B GLU* 3.1 30.9 + - - +
171B ARG 2.7 2.2 - - - -
172B ILE* 1.3 101.9 + - + +
174B LEU* 1.3 64.1 + - + +
176B ASN* 3.2 34.8 + - - +
177B LYS* 3.0 21.0 + - - +
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Residues in contact with LEU 174 (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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159B ILE* 4.9 10.3 - - + -
163B THR* 6.2 3.8 - - + -
166B GLN* 5.7 9.2 - - + +
170B GLU* 3.1 31.4 - - + +
171B ARG* 3.0 9.9 + - - +
173B LYS* 1.3 74.2 - - + +
175B MET* 1.3 68.0 + - - +
177B LYS* 2.7 15.0 + - - -
178B PHE 2.8 10.6 + - - -
147D ALA* 3.8 27.8 - - + +
150D LYS* 4.8 16.2 - - + -
151D ILE* 3.1 38.1 - - + +
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Residues in contact with MET 175 (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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83B ASN* 3.2 44.9 - - + +
84B GLU* 4.5 2.7 - - - +
86B SER* 4.0 3.8 - - - +
87B LEU* 4.1 12.3 - - + -
156B VAL* 3.0 43.1 - - + +
159B ILE* 3.8 32.6 - - - +
160B VAL* 4.0 5.4 - - + -
171B ARG 3.1 12.8 + - - +
172B ILE* 4.3 5.8 - - - +
174B LEU* 1.3 78.3 - - - +
176B ASN* 1.3 61.3 + - - +
178B PHE* 3.0 9.5 - - - +
179B SER* 2.8 31.5 + - - +
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Residues in contact with ASN 176 (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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80B TYR* 3.5 46.1 + - + +
84B GLU* 4.2 12.1 - - - +
172B ILE* 2.7 33.3 + - - +
173B LYS* 3.2 22.1 + - - +
174B LEU 3.1 0.6 - - - -
175B MET* 1.3 81.0 - - - +
177B LYS* 1.3 69.7 + - - +
179B SER* 3.3 3.4 + - - -
180B GLN* 3.1 16.6 + - - +
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Residues in contact with LYS 177 (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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173B LYS 3.0 12.0 + - - +
174B LEU* 2.7 14.5 + - + +
176B ASN* 1.3 69.9 - - - +
178B PHE* 1.3 64.4 + - - +
180B GLN* 2.9 52.4 + - - +
181B ILE* 3.0 34.8 + - + +
143D ASN* 5.2 9.1 + - - -
144D ASP* 6.1 4.9 - - + -
147D ALA* 5.1 12.3 - - + -
148D VAL* 4.5 14.4 - - + -
151D ILE* 3.8 10.8 - - + -
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Residues in contact with PHE 178 (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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79B PHE* 4.6 6.5 - + - -
152B ALA* 5.2 1.1 - - - -
155B ALA* 3.9 17.5 - - + -
156B VAL* 3.8 23.6 - - + -
159B ILE* 3.4 31.9 - - + -
174B LEU 2.8 10.3 + - - +
175B MET* 3.0 12.8 - - - +
177B LYS* 1.3 76.1 - - - +
179B SER* 1.3 74.0 + - - +
181B ILE* 2.9 10.4 + - - +
182B PHE* 2.9 60.7 + + + -
151D ILE* 3.5 21.9 - - + +
155D ALA* 4.2 16.4 - - + -
178D PHE* 4.3 5.6 - + - -
182D PHE* 4.4 8.7 - + - -
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Residues in contact with SER 179 (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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79B PHE* 3.9 18.8 - - - -
80B TYR* 3.6 31.2 - - - -
83B ASN* 3.2 27.0 + - - +
175B MET* 2.8 19.7 + - - +
176B ASN* 3.3 3.8 + - - -
178B PHE* 1.3 81.3 - - - +
180B GLN* 1.3 56.8 + - - +
182B PHE* 4.0 0.4 - - - +
183B LEU* 2.9 35.7 + - - +
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Residues in contact with GLN 180 (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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76B ARG* 5.0 4.4 + - - +
80B TYR* 3.2 22.6 + - + +
176B ASN 3.1 9.2 + - - +
177B LYS* 2.9 51.6 + - - +
179B SER* 1.3 73.0 - - - +
181B ILE* 1.3 74.8 + - - +
183B LEU* 4.0 1.8 - - - +
184B ASN* 2.9 30.8 + - + +
185D GLY 5.0 4.0 + - - -
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Residues in contact with ILE 181 (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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177B LYS* 3.0 44.1 + - + +
178B PHE* 2.9 8.9 + - - +
180B GLN* 1.3 78.0 - - - +
182B PHE* 1.3 56.4 + - - +
184B ASN* 2.8 5.0 + - - +
185B GLY* 2.7 33.3 + - - -
148D VAL* 4.4 10.1 - - + -
151D ILE* 5.8 1.6 - - + -
182D PHE* 3.6 53.2 - - + +
185D GLY* 3.8 16.5 - - - +
186D LEU* 3.8 21.1 - - + -
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Residues in contact with PHE 182 (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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79B PHE* 4.0 18.6 - + + -
131B PHE* 4.3 3.1 - + - -
148B VAL* 3.7 26.0 - - + -
151B ILE* 3.6 32.8 - - + -
152B ALA* 4.1 17.3 - - + -
155B ALA* 5.2 0.2 - - + -
178B PHE* 2.9 45.4 + + + +
179B SER 4.0 3.1 - - - +
181B ILE* 1.3 81.2 - - - +
183B LEU* 1.3 62.6 + - - +
185B GLY 3.3 0.5 + - - -
186B LEU* 3.2 33.0 + - + +
178D PHE* 4.0 13.9 - + - -
181D ILE* 3.5 35.6 - - + +
182D PHE* 5.6 2.5 - + - -
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Residues in contact with LEU 183 (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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76B ARG* 3.8 33.4 + - + +
79B PHE* 3.4 32.5 - - + -
80B TYR* 3.6 30.5 - - + -
131B PHE* 4.9 0.9 - - + -
140B TRP* 3.3 40.0 - - + +
179B SER 2.9 18.2 + - - +
180B GLN* 4.0 2.2 - - - +
182B PHE* 1.3 72.8 - - - +
184B ASN* 1.3 63.3 + - - +
186B LEU* 3.1 32.4 - - + +
187B SER* 4.1 2.6 + - - -
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Residues in contact with ASN 184 (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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76B ARG* 5.2 3.1 - - - +
180B GLN* 2.9 24.1 + - + +
181B ILE 2.8 4.1 + - - +
183B LEU* 1.3 72.9 - - - +
185B GLY* 1.3 52.6 + - - +
186B LEU 2.7 15.6 + - - -
187B SER* 3.0 25.2 + - - -
189B HIS* 3.4 24.7 + - - -
184D ASN 3.6 4.5 - - - +
185D GLY* 3.0 33.2 - - - +
186D LEU 5.2 1.2 - - - -
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Residues in contact with GLY 185 (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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181B ILE 2.7 15.9 + - - -
182B PHE 3.3 4.7 + - - -
184B ASN* 1.3 71.2 - - - +
186B LEU* 1.3 56.9 + - - +
187B SER 3.3 1.4 + - - +
180D GLN* 5.7 1.2 + - - -
181D ILE* 3.4 35.1 - - - +
184D ASN* 3.6 24.3 + - - +
185D GLY* 3.4 13.3 - - - -
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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