Contacts of the helix formed by residues 185 - 198 (chain B) in PDB entry 3IKM
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 LEU 185 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ALA* 5.4 0.5 - - - +
182B ARG* 4.7 10.5 - - + +
183B GLU 3.1 4.9 + - - +
184B ASN* 1.3 74.5 - - - +
186B LEU* 1.3 59.4 + - + +
187B HIS* 2.8 7.2 + - - -
188B GLY* 3.4 10.8 + - - +
189B ALA* 4.3 1.9 + - - +
210B GLN* 3.5 29.0 + - - +
212B GLY* 3.5 21.5 - - - +
214B CYS* 3.2 24.0 - - + -
236B GLU* 3.8 18.2 - - + +
237B ALA 3.9 12.6 - - - +
238B SER* 3.3 21.9 + - - -
240B VAL* 5.3 0.5 - - - +
339B ASN* 2.9 27.8 - - + +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASN* 3.5 22.9 - - - +
185B LEU* 1.3 81.4 - - + +
187B HIS* 1.3 57.0 + - - +
189B ALA* 3.9 1.7 - - - +
190B LEU* 2.8 33.5 - - + +
238B SER* 4.1 4.9 - - - -
240B VAL* 3.8 19.7 - - + +
304B TRP* 5.1 4.5 - - + -
306B LEU* 4.3 20.2 - - + -
310B GLU* 6.2 0.9 - - + -
335B VAL* 4.8 3.1 - - + -
336B LEU 3.5 19.1 - - - +
337B SER* 3.0 39.9 - - - +
339B ASN* 4.1 13.5 - - + +
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Residues in contact with HIS 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LYS* 6.1 3.6 - - - +
184B ASN* 2.5 29.9 + - + +
185B LEU 2.8 0.4 - - - -
186B LEU* 1.3 69.5 - - - +
188B GLY* 1.3 71.0 + - - +
189B ALA 2.9 2.2 - - - -
190B LEU* 2.7 29.8 + - - +
191B GLU* 3.7 26.5 + - + +
314B MET* 3.5 43.5 - - + +
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Residues in contact with GLY 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA* 3.6 26.5 - - - -
131B LEU 5.4 2.0 - - - -
185B LEU* 3.4 8.2 + - - +
187B HIS* 1.3 83.4 - - - +
189B ALA* 1.3 63.8 + - - +
191B GLU* 3.4 18.2 + - - +
192B HIS* 3.7 16.1 + - - -
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 5.0 4.0 - - - -
130B ALA* 4.4 2.2 - - - +
185B LEU 4.3 3.7 + - - +
186B LEU 3.9 2.9 + - - +
187B HIS 2.7 4.4 + - - -
188B GLY* 1.3 72.0 - - - +
190B LEU* 1.3 68.1 - - - +
192B HIS* 2.7 17.2 + - - +
193B TYR* 3.1 9.4 + - - -
208B LEU* 3.5 34.5 - - + +
210B GLN* 4.7 4.4 + - - +
240B VAL* 3.4 37.5 - - + -
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 2.8 43.1 - - + +
187B HIS* 2.7 21.9 + - - +
189B ALA* 1.3 76.1 - - + +
191B GLU* 1.3 59.6 + - - +
193B TYR* 3.2 20.3 + - - +
194B VAL* 4.5 0.7 + - - +
240B VAL* 4.8 5.8 - - + -
310B GLU* 2.9 39.9 - - + +
311B LEU* 4.0 7.4 - - + -
314B MET* 3.5 8.7 - - + -
315B TYR* 2.7 35.7 + - + +
322B LEU* 6.1 0.2 - - - +
335B VAL* 4.9 11.0 - - + -
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LYS* 5.9 2.9 - - - -
187B HIS* 3.9 25.8 + - + +
188B GLY* 3.4 13.6 + - - +
189B ALA 2.9 2.4 + - - -
190B LEU* 1.3 74.4 - - - +
192B HIS* 1.3 65.2 + - + +
194B VAL* 3.2 23.4 - - - +
195B ASN* 4.3 1.2 + - - +
314B MET* 5.7 0.4 - - + -
315B TYR* 2.6 25.5 + - + +
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Residues in contact with HIS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 4.4 22.2 - - + -
129B ASP 3.8 18.9 + - - -
130B ALA* 4.7 3.9 - - - -
188B GLY 3.7 11.8 + - - -
189B ALA 2.7 13.4 + - - +
191B GLU* 1.3 77.0 - - + +
193B TYR* 1.3 54.8 - - - +
194B VAL 3.1 2.9 - - - -
195B ASN* 2.6 28.3 + - + +
196B CYS* 2.6 38.9 + - + +
208B LEU* 4.5 2.9 - - + -
80C SER* 3.1 33.0 - - - -
97C PRO* 3.6 26.5 + - + +
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Residues in contact with TYR 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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189B ALA 3.1 9.2 + - - +
190B LEU* 3.2 16.9 + - - +
192B HIS* 1.3 73.1 - - - +
194B VAL* 1.3 52.0 + - - +
196B CYS* 3.5 8.4 - - - -
197B LEU* 2.5 58.3 + - + +
206B TYR* 4.9 1.8 - - - -
208B LEU* 4.6 3.5 - - + +
242B PHE* 3.8 49.1 - + + -
311B LEU* 6.1 0.9 - - + -
315B TYR* 6.4 0.4 - + - -
322B LEU* 3.2 44.9 - - + -
323B HIS 3.1 29.2 + - - -
325B ARG* 3.4 11.0 + - - -
333B PRO* 3.6 13.3 - - + +
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU 5.1 0.9 - - - +
191B GLU 3.2 21.1 - - - +
193B TYR* 1.3 81.9 - - - +
195B ASN* 1.3 74.9 + - + +
197B LEU* 3.2 23.7 + - + +
198B ASP* 3.7 6.1 + - - +
315B TYR* 5.5 8.5 - - + -
321B LYS* 5.8 7.6 - - - +
322B LEU* 4.8 12.5 - - + +
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Residues in contact with ASN 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 GLU 4.5 2.0 - - - +
192B HIS* 2.6 49.9 + - - +
194B VAL* 1.3 82.7 - - + +
196B CYS* 1.3 60.6 + - - +
198B ASP* 4.1 11.6 - - - +
199B LEU 4.7 0.5 + - - -
77C HIS* 4.8 8.3 + - - -
80C SER* 2.5 43.1 + - - +
100C GLY* 5.6 2.2 - - - -
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Residues in contact with CYS 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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128B VAL* 6.5 0.2 - - + -
192B HIS* 2.6 20.0 + - + +
193B TYR* 3.5 20.6 - - - -
195B ASN* 1.3 73.8 - - + +
197B LEU* 1.3 54.6 + - - +
198B ASP 3.1 2.5 - - - -
199B LEU* 2.4 47.8 + - + +
206B TYR* 3.2 34.2 + - + +
208B LEU* 4.4 15.7 - - - -
242B PHE* 5.1 0.7 - - - -
77C HIS* 5.5 3.6 - - + -
101C PRO* 5.6 8.5 - - + -
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Residues in contact with LEU 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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193B TYR* 2.5 43.9 + - + +
194B VAL* 3.2 14.8 + - + +
196B CYS* 1.3 71.6 - - - +
198B ASP* 1.3 55.5 + - - +
199B LEU 2.6 12.3 + - - -
200B VAL* 3.3 16.2 + - + +
201B ASN 3.6 6.3 - - - +
202B LYS* 2.9 40.6 - - + +
203B ARG 4.9 2.0 - - - +
206B TYR* 4.0 9.6 - - + +
242B PHE* 6.2 0.2 - - + -
321B LYS 4.0 13.2 - - - +
322B LEU* 4.3 10.8 - - - +
323B HIS 4.3 0.9 - - - +
325B ARG* 3.5 34.3 - - - +
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Residues in contact with ASP 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 VAL 3.7 4.9 + - - +
195B ASN 4.1 12.3 - - - +
197B LEU* 1.3 80.0 - - - +
199B LEU* 1.3 65.2 + - - +
200B VAL 3.6 0.2 - - - -
201B ASN* 3.7 16.4 + - - +
202B LYS* 5.3 8.2 + - - +
77C HIS* 4.1 14.3 + - + -
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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