Contacts of the helix formed by residues 176 - 199 (chain O) 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 SER 176 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174O GLY 3.5 2.2 - - - -
175O ARG* 1.3 73.3 - - - +
177O SER* 1.3 68.2 + - - +
178O LEU 3.7 1.1 - - - -
179O ASP* 3.9 5.6 - - - +
180O ASN* 3.1 25.8 + - - +
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Residues in contact with SER 177 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175O ARG* 2.8 9.0 - - - -
176O SER* 1.3 80.3 - - - +
178O LEU* 1.3 57.6 + - - -
180O ASN* 3.3 6.0 - - - +
181O ILE* 3.1 21.0 + - - +
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Residues in contact with LEU 178 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175O ARG* 2.8 21.0 + - + +
177O SER* 1.3 78.3 - - - +
179O ASP* 1.3 66.1 + - - +
181O ILE* 4.1 12.6 - - + -
182O GLU* 4.9 2.7 - - + +
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Residues in contact with ASP 179 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175O ARG 4.3 3.4 - - - +
176O SER* 3.9 8.5 - - - +
178O LEU* 1.3 77.8 - - - +
180O ASN* 1.3 55.7 + - - +
181O ILE 3.2 3.0 - - - +
182O GLU* 3.4 19.0 - - - +
183O MET* 2.6 33.3 + - - +
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Residues in contact with ASN 180 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176O SER* 3.1 19.1 + - - +
177O SER* 3.3 7.0 - - - +
179O ASP* 1.3 78.8 - - - +
181O ILE* 1.3 57.3 + - - +
183O MET* 3.2 5.9 + - - +
184O ALA* 2.8 29.4 + - - +
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Residues in contact with ILE 181 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177O SER 3.1 12.9 + - - +
178O LEU* 4.1 12.6 - - + -
179O ASP 3.2 0.2 - - - -
180O ASN* 1.3 77.7 - - - +
182O GLU* 1.3 64.7 + - - +
184O ALA* 3.1 7.9 + - - +
185O TYR* 3.0 25.3 + - - +
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Residues in contact with GLU 182 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178O LEU* 4.7 1.9 - - + +
179O ASP* 3.3 23.8 + - - +
180O ASN 3.2 0.2 - - - -
181O ILE* 1.3 79.5 - - - +
183O MET* 1.3 57.0 + - - +
185O TYR* 3.4 5.1 + - - +
186O ALA* 2.9 29.8 + - - +
487O CYS* 6.4 2.2 - - - -
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Residues in contact with MET 183 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179O ASP 2.6 21.5 + - - +
180O ASN* 3.6 6.5 - - - +
182O GLU* 1.3 72.2 - - - +
184O ALA* 1.3 59.1 + - - +
186O ALA* 3.6 7.0 - - - +
187O ARG* 2.8 31.4 + - - +
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Residues in contact with ALA 184 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180O ASN 2.8 17.5 + - - +
181O ILE* 3.1 8.0 + - - +
183O MET* 1.3 75.4 - - - +
185O TYR* 1.3 63.0 + - - +
187O ARG* 3.2 10.3 + - - +
188O GLN* 3.2 19.8 + - - +
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Residues in contact with TYR 185 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181O ILE 3.0 15.7 + - - +
182O GLU* 3.7 4.9 - - - +
184O ALA* 1.3 72.6 - - - +
186O ALA* 1.3 67.0 + - - +
188O GLN* 3.1 9.8 + - - +
189O ILE* 3.0 20.1 + - - +
487O CYS* 5.9 7.0 - - + -
491O HIS* 6.0 7.0 - - + -
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Residues in contact with ALA 186 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182O GLU 2.9 17.7 + - - +
183O MET* 3.6 8.1 - - - +
185O TYR* 1.3 76.0 - - - +
187O ARG* 1.3 63.4 + - - +
189O ILE* 3.2 7.0 + - - +
190O TYR* 2.9 24.3 + - - +
546O GLU* 4.9 17.9 - - + -
549O GLN* 5.7 1.9 - - - +
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Residues in contact with ARG 187 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183O MET 2.8 14.5 + - - +
184O ALA* 3.2 14.8 - - - +
186O ALA* 1.3 75.6 - - - +
188O GLN* 1.3 56.9 + - - +
190O TYR* 3.1 9.7 + - - +
191O ILE* 2.9 27.1 + - - +
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Residues in contact with GLN 188 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184O ALA 3.2 7.5 + - - +
185O TYR* 3.1 11.7 + - - +
187O ARG* 1.3 77.2 - - - +
189O ILE* 1.3 66.7 + - - +
191O ILE* 3.3 7.6 + - - +
192O TYR* 3.0 21.5 + - - +
207O ASP* 5.0 16.4 - - + -
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Residues in contact with ILE 189 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185O TYR 3.0 12.4 + - - +
186O ALA* 3.2 8.3 + - - +
188O GLN* 1.3 76.6 - - - +
190O TYR* 1.3 52.6 + - - +
192O TYR* 2.9 11.1 + - - +
193O ASN* 2.7 34.8 + - - +
549O GLN* 5.2 16.4 - - + +
550O TYR* 5.9 2.7 - - + +
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Residues in contact with TYR 190 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186O ALA 2.9 13.6 + - - +
187O ARG* 3.1 13.9 - - - +
189O ILE* 1.3 76.6 - - - +
191O ILE* 1.3 60.9 + - - +
193O ASN* 3.2 9.6 + - - +
194O GLU* 2.9 21.0 + - - +
549O GLN* 5.1 10.3 - - + +
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Residues in contact with ILE 191 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187O ARG 2.9 12.4 + - - +
188O GLN* 3.9 8.5 - - - +
189O ILE 3.2 0.2 - - - -
190O TYR* 1.3 75.0 - - - +
192O TYR* 1.3 62.7 + - - +
194O GLU* 3.0 10.3 + - - +
195O LYS* 2.9 21.7 + - - +
202O GLN* 5.2 5.0 - - + +
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Residues in contact with TYR 192 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188O GLN 3.0 13.2 + - - +
189O ILE* 2.9 15.4 + - - +
191O ILE* 1.3 76.5 - - - +
193O ASN* 1.4 54.4 + - - +
195O LYS* 3.1 9.4 + - - +
196O ILE* 2.9 27.5 + - - +
202O GLN* 5.2 7.0 - - + +
204O ASN* 5.6 12.1 - - + -
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Residues in contact with ASN 193 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189O ILE 2.7 15.3 + - - +
190O TYR* 3.6 10.5 - - - +
192O TYR* 1.4 68.6 - - - +
194O GLU* 1.3 65.8 + - - +
196O ILE* 3.9 6.4 - - - +
197O VAL* 3.1 23.6 + - - +
549O GLN* 5.4 13.0 - - + +
552O TYR* 5.7 6.7 - - + -
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Residues in contact with GLU 194 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190O TYR 2.9 14.1 + - - +
191O ILE* 3.0 12.7 + - - +
193O ASN* 1.3 77.2 - - - +
195O LYS* 1.4 51.1 + - - +
197O VAL* 3.2 7.3 + - - +
198O ASN* 2.7 37.8 + - + +
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Residues in contact with LYS 195 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191O ILE 2.9 12.0 + - - +
192O TYR* 3.4 9.0 - - - +
194O GLU* 1.4 73.4 - - - +
196O ILE* 1.3 56.4 + - - +
198O ASN* 2.9 1.1 + - - +
199O GLY 2.6 33.1 + - - -
200O HIS* 2.8 40.0 + - + +
202O GLN* 3.9 22.2 - - + +
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Residues in contact with ILE 196 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192O TYR 2.9 15.0 + - - +
193O ASN* 3.9 7.4 - - - +
194O GLU 3.3 0.4 - - - -
195O LYS* 1.3 76.3 - - - +
197O VAL* 1.3 63.2 + - - +
199O GLY* 3.4 8.5 + - - +
200O HIS 5.9 0.2 - - - -
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Residues in contact with VAL 197 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193O ASN 3.1 13.9 + - - +
194O GLU* 3.4 10.1 - - - +
196O ILE* 1.3 80.1 - - - +
198O ASN* 1.4 57.9 + - + +
199O GLY 3.5 0.5 + - - -
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Residues in contact with ASN 198 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194O GLU* 2.7 22.4 + - + +
195O LYS* 2.9 4.0 + - - +
197O VAL* 1.4 72.6 - - + +
199O GLY* 1.3 66.4 + - - +
200O HIS* 4.2 5.6 - - + +
899W GLU* 5.7 1.2 - - - +
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Residues in contact with GLY 199 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195O LYS 2.6 10.9 + - - -
196O ILE* 3.4 7.7 + - - -
197O VAL 3.3 4.9 + - - -
198O ASN* 1.3 75.5 - - - +
200O HIS* 1.4 59.4 + - - -
899W GLU* 4.6 22.3 - - - +
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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