Contacts of the helix formed by residues 163 - 183 (chain J) in PDB entry 5IJO
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 163 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161J CYS* 4.8 1.6 - - + -
162J VAL* 1.3 74.2 - - - +
164J LYS* 1.3 62.6 + - - +
165J LEU 3.5 1.8 - - - -
166J GLU* 4.3 11.9 - - + +
167J LYS* 3.3 26.2 + - + +
224J TYR* 6.6 0.2 - - + -
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Residues in contact with LYS 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162J VAL* 3.5 7.4 + - + +
163J ASP* 1.3 77.2 - - - +
165J LEU* 1.4 69.3 + - - +
167J LYS* 3.4 8.8 + - - +
168J GLU* 3.4 10.2 + - - +
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Residues in contact with LEU 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J GLU* 6.1 5.4 - - + -
162J VAL 5.3 0.4 + - - -
163J ASP 3.5 0.2 - - - -
164J LYS* 1.4 77.2 - - - +
166J GLU* 1.3 60.7 + - - +
168J GLU* 2.8 31.0 + - - +
169J LEU* 3.7 2.1 + - - +
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Residues in contact with GLU 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163J ASP* 3.9 12.7 + - + +
164J LYS 3.3 0.6 - - - -
165J LEU* 1.3 80.7 - - + +
167J LYS* 1.3 63.4 + - - +
169J LEU* 3.1 22.4 + - - +
170J VAL 4.4 0.5 + - - -
221J TYR* 5.3 4.7 - - - +
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Residues in contact with LYS 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163J ASP* 3.3 21.0 + - + +
164J LYS* 3.8 4.9 - - - +
165J LEU 3.2 0.8 - - - -
166J GLU* 1.3 78.3 - - - +
168J GLU* 1.3 62.4 + - - +
169J LEU 3.1 1.2 + - - -
170J VAL* 3.1 20.4 + - - +
171J SER 4.4 0.5 + - - -
221J TYR* 5.4 4.3 - - - +
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Residues in contact with GLU 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J LYS 3.4 7.8 + - - +
165J LEU* 2.8 17.6 + - - +
167J LYS* 1.3 79.4 - - - +
169J LEU* 1.3 60.6 + - - +
170J VAL 3.1 0.7 + - - -
171J SER* 3.4 7.9 + - - -
172J LYS* 3.3 19.6 + - - +
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Residues in contact with LEU 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165J LEU 3.7 1.6 + - - -
166J GLU* 3.1 16.9 + - - +
168J GLU* 1.3 78.0 - - - +
170J VAL* 1.3 63.0 + - - +
172J LYS* 3.2 6.8 + - - +
173J TYR* 2.9 28.0 + - + +
217J ILE* 6.5 0.7 - - + -
221J TYR* 5.7 4.0 - - + -
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Residues in contact with VAL 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166J GLU 4.4 0.2 + - - -
167J LYS 3.1 13.1 + - - +
168J GLU 3.1 0.6 + - - -
169J LEU* 1.3 78.6 - - - +
171J SER* 1.3 64.9 + - - +
173J TYR* 4.1 1.2 - - - +
174J ARG* 3.0 24.4 + - - +
218J ILE* 4.7 18.8 - - + +
221J TYR* 4.3 22.0 - - + +
222J TYR 5.9 0.2 - - - +
231J ASP* 6.1 4.7 - - + -
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Residues in contact with SER 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167J LYS 4.4 0.8 + - - -
168J GLU* 3.4 8.4 + - - -
170J VAL* 1.3 79.1 - - - +
172J LYS* 1.3 63.8 + - - +
174J ARG* 3.1 9.6 - - - +
175J GLN* 3.1 21.7 + - - +
231J ASP* 6.2 5.8 - - - -
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Residues in contact with LYS 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44J LEU 4.9 12.3 - - - +
168J GLU 3.3 10.8 + - - +
169J LEU* 3.2 11.3 + - - +
171J SER* 1.3 78.5 - - - +
173J TYR* 1.3 63.5 + - - +
175J GLN* 3.1 20.4 + - - +
176J GLN* 3.6 4.2 + - - +
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Residues in contact with TYR 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169J LEU* 2.9 16.4 + - + +
170J VAL* 4.3 2.5 - - - +
172J LYS* 1.3 76.1 - - - +
174J ARG* 1.3 63.9 + - - +
176J GLN* 2.9 26.3 + - + +
177J PHE* 3.6 2.4 + - - +
214J LEU* 4.6 29.7 - - + +
217J ILE* 5.4 7.0 - - + -
218J ILE* 5.4 4.3 - - + -
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Residues in contact with ARG 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170J VAL 3.0 15.8 + - - +
171J SER* 3.1 18.2 - - - +
172J LYS 3.1 0.2 - - - -
173J TYR* 1.3 77.8 - - - +
175J GLN* 1.3 59.5 + - - +
177J PHE* 3.1 22.6 + - - +
178J GLU 4.4 0.3 + - - -
218J ILE* 5.6 6.7 - - + +
234J VAL* 6.3 2.5 - - + -
238J MET* 5.5 5.4 - - - +
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Residues in contact with GLN 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171J SER 3.1 11.3 + - - +
172J LYS* 3.1 12.5 + - - +
174J ARG* 1.3 74.6 - - - +
176J GLN* 1.3 63.0 + - - +
177J PHE 3.1 1.2 + - - -
178J GLU* 3.1 20.8 + - - +
179J GLU* 4.2 0.9 + - - +
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Residues in contact with GLN 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172J LYS 3.6 2.9 + - - +
173J TYR* 2.9 20.5 + - + +
175J GLN* 1.3 77.3 - - - +
177J PHE* 1.3 64.9 + - - +
179J GLU* 2.9 20.9 + - + +
180J LEU* 3.2 10.0 + - - +
214J LEU* 5.4 7.0 - - + -
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Residues in contact with PHE 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J TYR 3.6 2.6 + - - +
174J ARG* 3.1 16.2 + - - +
176J GLN* 1.3 78.8 - - - +
178J GLU* 1.3 63.9 + - - +
180J LEU* 2.9 10.6 + - - +
181J TYR* 2.8 25.8 + - + +
211J GLN* 6.0 6.7 - - + +
214J LEU* 5.8 5.6 - - + +
238J MET* 5.7 8.1 - - + -
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Residues in contact with GLU 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174J ARG 4.4 0.4 + - - -
175J GLN 3.1 12.9 + - - +
176J GLN 3.1 0.6 - - - -
177J PHE* 1.3 78.0 - - - +
179J GLU* 1.3 58.1 + - - +
181J TYR* 3.3 6.6 + - - +
182J LYS* 2.8 30.6 + - - +
238J MET* 6.2 3.0 - - + +
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Residues in contact with GLU 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175J GLN 4.2 0.6 + - - -
176J GLN* 2.9 15.1 + - + +
178J GLU* 1.3 77.6 - - - +
180J LEU* 1.3 64.4 + - - +
182J LYS* 3.0 17.9 + - - +
183J THR* 3.1 13.2 + - - -
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Residues in contact with LEU 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J GLN 3.2 7.2 + - - +
177J PHE* 2.9 13.3 + - - +
179J GLU* 1.3 79.6 - - - +
181J TYR* 1.3 62.3 + - - +
183J THR* 3.2 18.2 + - - -
207J CYS* 4.2 31.6 - - - +
210J GLU* 4.7 8.1 - - + -
211J GLN* 4.5 19.1 - - + +
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Residues in contact with TYR 181 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177J PHE* 2.8 15.4 + - + +
178J GLU* 3.7 7.2 - - - +
180J LEU* 1.3 76.1 - - - +
182J LYS* 1.3 63.1 + - - +
183J THR 3.1 1.6 + - - -
184J GLU* 3.5 13.7 + - - +
242J GLN* 4.6 21.8 - - + -
245J GLY* 6.4 1.1 - - - -
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Residues in contact with LYS 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178J GLU 2.8 14.7 + - - +
179J GLU* 3.0 15.0 + - - +
181J TYR* 1.3 72.3 - - - +
183J THR* 1.3 51.1 + - - +
184J GLU* 2.6 22.3 + - - +
185J ALA 4.0 4.2 + - - +
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Residues in contact with THR 183 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179J GLU 3.1 9.2 + - - -
180J LEU* 3.7 12.8 - - - -
181J TYR 3.1 5.0 - - - -
182J LYS* 1.3 73.7 - - - +
184J GLU* 1.3 62.3 + - - +
185J ALA 3.2 14.2 - - - +
203J TRP 5.7 1.8 - - - +
204J PHE* 5.6 3.3 - - - -
207J CYS* 4.5 17.9 - - - +
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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