Contacts of the helix formed by residues 182 - 194 (chain F) in PDB entry 3J8B
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 HIS 182 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F ASP 4.2 19.1 - - - +
146F VAL* 5.4 9.9 - - + -
180F THR* 3.3 5.3 - - - -
181F GLU* 1.3 77.7 - - - +
183F SER* 1.3 58.8 + - - +
184F VAL 3.3 1.1 - - - -
185F LEU* 3.1 12.3 + - + +
186F ILE* 2.9 29.7 + - + +
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Residues in contact with SER 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F ILE* 5.3 4.7 - - - -
180F THR* 3.0 29.4 + - - -
181F GLU 3.2 0.8 - - - -
182F HIS* 1.3 77.6 - - - +
184F VAL* 1.3 58.0 + - - +
186F ILE* 3.8 7.2 - - - +
187F HIS* 2.9 31.5 + - - +
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Residues in contact with VAL 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180F THR 4.9 0.2 + - - -
181F GLU 4.4 4.2 + - - +
182F HIS 3.3 0.8 - - - -
183F SER* 1.3 77.2 - - - +
185F LEU* 1.3 61.3 + - - +
187F HIS* 3.4 8.5 - - - +
188F GLU* 3.2 19.9 + - - +
230F VAL* 5.7 11.2 - - + +
231F MET* 6.3 1.6 - - - -
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Residues in contact with LEU 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F GLU 5.3 0.6 + - - -
182F HIS* 3.1 14.5 + - + +
184F VAL* 1.3 76.0 - - - +
186F ILE* 1.3 66.2 + - - +
188F GLU* 3.2 16.8 + - - +
189F TYR* 3.4 9.0 + - - +
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Residues in contact with ILE 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146F VAL* 6.4 2.2 - - + -
182F HIS* 2.9 19.7 + - + +
183F SER* 3.8 7.2 - - - +
185F LEU* 1.3 75.0 - - - +
187F HIS* 1.3 64.0 + - - +
189F TYR* 2.9 25.0 + - - +
190F TYR* 3.3 6.5 + - - +
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Residues in contact with HIS 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F SER 2.9 18.5 + - - +
184F VAL* 3.4 9.6 - - - +
186F ILE* 1.3 77.9 - - - +
188F GLU* 1.3 61.6 + - - +
190F TYR* 3.1 8.0 + - - +
191F SER* 3.1 17.8 + - - -
197F PRO* 3.7 22.3 - - + +
199F HIS* 5.9 7.2 - - + -
218F SER* 5.4 11.2 - - - -
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Residues in contact with GLU 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F VAL 3.2 12.9 + - - +
185F LEU* 3.4 12.6 - - - +
186F ILE 3.1 0.6 - - - -
187F HIS* 1.3 75.2 - - - +
189F TYR* 1.3 63.7 + - - +
191F SER* 3.2 20.8 - - - -
192F ARG* 3.9 2.9 + - - +
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Residues in contact with TYR 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F VAL* 6.1 5.2 - - + -
185F LEU 3.4 5.0 + - - +
186F ILE* 2.9 15.6 + - - +
188F GLU* 1.3 78.6 - - - +
190F TYR* 1.3 61.6 + - - +
192F ARG* 3.0 23.0 + - - +
193F GLU 4.2 0.7 + - - -
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Residues in contact with TYR 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F GLY* 5.2 9.6 - - - +
172F TRP* 4.9 18.4 - - + -
186F ILE 3.3 5.6 + - - +
187F HIS* 3.1 12.0 + - - +
189F TYR* 1.3 79.5 - - - +
191F SER* 1.3 62.5 + - - +
193F GLU* 3.1 19.4 + - + +
194F ALA* 3.1 11.9 + - - +
197F PRO* 4.7 8.7 - - + -
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Residues in contact with SER 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F HIS 3.1 11.1 + - - -
188F GLU* 3.2 20.2 - - - -
189F TYR 3.0 0.2 - - - -
190F TYR* 1.3 78.3 - - - +
192F ARG* 1.3 61.4 + - - +
194F ALA 2.8 26.4 - - - +
195F PRO* 4.0 10.7 - - - +
197F PRO* 4.4 9.2 - - - +
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Residues in contact with ARG 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F GLU 3.9 2.7 + - - +
189F TYR* 3.0 15.2 + - - +
190F TYR 3.0 0.8 - - - -
191F SER* 1.3 81.1 - - - +
193F GLU* 1.3 61.1 + - - +
194F ALA* 4.5 0.2 - - - -
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Residues in contact with GLU 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F ALA* 6.3 3.4 - - + -
169F ILE* 5.2 13.0 - - + +
189F TYR 4.2 0.6 + - - -
190F TYR* 3.1 13.0 + - + +
192F ARG* 1.3 82.2 - - - +
194F ALA* 1.3 61.9 + - + +
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Residues in contact with ALA 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F ILE* 3.3 26.9 - - + +
170F LEU* 4.9 7.6 - - - -
190F TYR 3.1 4.6 + - - +
191F SER* 2.8 27.2 + - - +
193F GLU* 1.3 83.8 - - + +
195F PRO* 1.3 63.8 - - - +
196F ASN 4.6 2.2 - - - +
197F PRO* 4.1 6.5 - - - +
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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