Contacts of the helix formed by residues 187 - 200 (chain B) in PDB entry 3H60
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 THR 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B GLU* 2.5 44.9 + - + +
185B LYS* 3.5 30.6 + - + +
186B VAL* 1.3 80.2 - - - +
188B ILE* 1.3 65.6 + - - +
189B SER* 3.5 4.1 + - - -
190B PHE* 3.2 13.6 + - - +
191B MET* 3.1 25.3 + - - +
292B LEU* 3.8 10.1 - - - -
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Residues in contact with ILE 188 (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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187B THR* 1.3 74.9 - - - +
189B SER* 1.3 67.3 + - - +
191B MET* 3.3 4.7 + - + +
192B LYS* 3.0 59.9 + - + +
259B LEU* 5.2 5.8 - - + -
289B PHE* 5.8 3.1 - - + -
292B LEU* 3.8 21.9 - - + +
293B TYR* 4.1 16.6 - - - +
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Residues in contact with SER 189 (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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182B GLU* 2.8 25.0 + - - -
187B THR* 3.3 2.2 + - - -
188B ILE* 1.3 87.3 - - - +
190B PHE* 1.3 55.7 + - - +
192B LYS* 3.3 8.8 + - - +
193B GLU* 3.0 35.4 + - - +
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Residues in contact with PHE 190 (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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179B PRO* 3.7 22.7 - - + -
180B LYS* 3.4 37.0 - - - +
181B LEU* 3.7 29.8 - - + -
182B GLU* 3.9 5.4 + - + +
186B VAL* 4.3 7.4 - - + -
187B THR* 3.2 25.8 + - - +
189B SER* 1.3 76.4 + - - +
191B MET* 1.3 65.4 + - - +
193B GLU* 3.1 6.2 + - - +
194B LEU* 2.6 56.6 + - + +
204B LEU* 3.9 21.3 - - + -
208B CYS* 4.9 2.0 - - + -
212B ILE* 4.0 18.2 - - + -
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Residues in contact with MET 191 (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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186B VAL* 3.8 15.3 - - + -
187B THR 3.1 18.1 + - - +
188B ILE* 3.3 10.3 + - + +
190B PHE* 1.3 88.4 - - - +
192B LYS* 1.3 63.7 + - + +
194B LEU* 3.7 11.4 - - + +
195B MET* 3.0 32.7 + - + +
285B THR* 3.3 40.2 - - + +
288B GLY* 3.6 21.5 - - - -
289B PHE* 3.9 34.8 - - + +
292B LEU* 4.0 12.8 - - + -
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Residues in contact with LYS 192 (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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188B ILE* 3.0 46.5 + - + +
189B SER* 3.7 8.3 - - - +
191B MET* 1.3 76.4 - - + +
193B GLU* 1.3 64.5 + - + +
195B MET* 3.4 17.2 + - + +
196B GLN* 3.3 21.7 + - - +
259B LEU* 3.8 20.0 - - + -
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Residues in contact with GLU 193 (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 SER 5.6 0.9 - - - +
178B GLY 5.2 1.6 - - - +
179B PRO* 3.6 25.6 - - + +
189B SER* 3.0 22.9 + - - +
190B PHE* 3.7 4.7 - - - +
192B LYS* 1.3 76.5 - - + +
194B LEU* 1.3 64.5 + - - +
196B GLN* 4.0 4.7 - - + +
197B TRP* 3.1 24.8 + - - +
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Residues in contact with LEU 194 (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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179B PRO* 4.0 10.0 - - + +
190B PHE* 2.6 42.0 + - + +
191B MET* 3.3 24.9 + - + +
193B GLU* 1.3 73.2 - - - +
195B MET* 1.3 63.3 + - - +
197B TRP* 3.2 4.1 + - + +
198B TYR* 3.0 69.8 + - + +
204B LEU* 3.8 30.7 - - + -
212B ILE* 5.0 1.3 - - + -
284B LEU 4.2 14.8 - - - +
285B THR* 4.3 4.9 - - - +
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Residues in contact with MET 195 (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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191B MET* 3.0 30.6 + - + +
192B LYS* 3.4 17.7 + - + +
193B GLU 3.3 0.2 - - - -
194B LEU* 1.3 76.1 - - + +
196B GLN* 1.4 58.3 + - - +
198B TYR* 3.7 2.4 - - - +
199B LYS* 2.8 30.0 + - - +
247B PHE* 3.8 10.5 - - + -
251B LEU* 4.0 30.4 - - + +
254B PHE* 4.2 7.0 - - - -
259B LEU* 3.6 28.9 - - + -
285B THR* 4.1 19.3 - - + +
289B PHE* 4.0 24.0 - - + -
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Residues in contact with GLN 196 (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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192B LYS 3.3 15.1 + - - +
193B GLU* 4.0 5.8 - - + +
195B MET* 1.4 75.7 - - - +
197B TRP* 1.3 59.8 + - - +
199B LYS* 3.2 27.8 + - - +
200B ASP* 2.9 64.3 + - - +
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Residues in contact with TRP 197 (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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176B TYR* 4.2 8.1 - + - -
177B SER* 3.7 20.0 - - - -
178B GLY* 3.3 35.9 - - - -
179B PRO* 3.5 21.8 - - + +
193B GLU 3.1 19.1 + - - +
194B LEU* 3.4 4.9 - - + +
196B GLN* 1.3 76.5 - - - +
198B TYR* 1.3 64.6 + + - +
200B ASP* 3.2 11.8 + - - +
201B GLN 3.4 0.3 + - - -
202B LYS* 3.1 89.9 + - + +
203B LYS 2.9 27.5 + - - -
204B LEU* 4.1 3.4 - - + -
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Residues in contact with TYR 198 (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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194B LEU* 3.0 45.3 + - + +
195B MET 3.7 0.2 - - - +
197B TRP* 1.3 74.9 - + - +
199B LYS* 1.3 69.3 + - - +
200B ASP 3.0 1.3 - - - -
201B GLN* 2.8 13.9 + - - -
202B LYS 3.3 22.4 - - - +
203B LYS* 4.8 0.7 - - - -
204B LEU* 3.4 25.5 - - - +
247B PHE* 3.4 22.0 - + + -
248B TYR* 3.2 9.0 + - - -
280B VAL* 4.5 4.3 + - + +
281B GLU* 3.5 51.0 - - + +
284B LEU* 3.4 30.2 - - + +
285B THR* 3.6 18.8 - - - -
323B TYR* 4.7 0.4 + - - -
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Residues in contact with LYS 199 (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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195B MET 2.8 19.5 + - - +
196B GLN* 3.3 30.8 + - - +
198B TYR* 1.3 76.4 - - - +
200B ASP* 1.3 61.9 + - - +
201B GLN* 3.2 3.3 + - - +
247B PHE* 3.7 2.2 - - - -
248B TYR* 2.8 39.7 + - + -
251B LEU* 4.0 19.1 - - + -
255B GLU* 5.3 6.9 + - - -
482B PRO* 5.0 1.2 - - - +
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Residues in contact with ASP 200 (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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196B GLN* 2.9 46.1 + - - +
197B TRP* 3.5 6.5 - - - +
198B TYR 3.0 0.8 - - - -
199B LYS* 1.3 82.2 - - - +
201B GLN* 1.3 67.1 + - - +
202B LYS* 3.4 32.8 + - - +
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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