Contacts of the helix formed by residues 184 - 202 (chain U) in PDB entry 3SDI
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 184 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45U CYS* 5.1 1.1 - - - -
184U GLU* 1.3 82.8 - - + +
186U TRP* 1.3 62.3 + - + +
187U GLU* 3.4 17.6 + - - +
188U LYS* 3.5 34.5 + - - +
189U VAL* 3.6 15.3 + - - +
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Residues in contact with TRP 186 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45U CYS* 3.7 30.5 - - + -
184U SER* 1.3 73.0 - - + +
187U GLU* 1.3 96.1 + - + +
189U VAL* 3.2 2.5 + - - +
190U VAL* 3.0 35.4 + - + +
214U VAL* 3.8 26.9 - - + -
216U THR* 4.4 16.3 - - + +
222U PHE* 3.8 20.7 - + - -
224U LEU* 3.7 42.0 - - + -
228U ASN* 5.4 5.4 - - + -
232U ARG* 5.0 3.8 - - - -
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Residues in contact with GLU 187 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184U SER* 3.4 22.3 + - - +
186U TRP* 1.3 124.8 + - + +
188U LYS* 1.3 58.0 + - + +
190U VAL* 3.4 3.4 + - - +
191U GLU* 3.0 34.1 + - - +
232U ARG* 3.6 37.1 + - - +
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Residues in contact with LYS 188 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180U ILE* 5.2 0.4 - - - +
184U SER* 3.2 60.2 - - - +
186U TRP 3.3 0.4 - - - -
187U GLU* 1.3 76.5 - - + +
189U VAL* 1.3 57.7 + - - +
191U GLU* 3.3 30.8 + - + +
192U PHE* 2.8 29.6 + - - +
232U ARG* 5.8 0.4 - - - +
235U ALA* 5.8 1.3 - - - -
239U GLN* 6.2 2.0 - - - +
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Residues in contact with VAL 189 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40U VAL* 4.0 17.7 - - + +
42U GLY* 3.9 27.8 - - - +
45U CYS* 3.8 17.7 - - - -
47U VAL* 3.6 19.3 - - + -
180U ILE* 4.2 19.7 - - + -
184U SER* 3.6 25.3 + - + +
186U TRP 3.2 7.7 + - - +
188U LYS* 1.3 72.1 - - - +
190U VAL* 1.3 60.1 + - - +
192U PHE* 3.3 7.2 + - - +
193U ALA* 2.9 27.2 + - - +
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Residues in contact with VAL 190 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47U VAL* 3.7 26.9 - - + -
49U ILE* 4.6 1.1 - - + -
186U TRP* 3.0 27.3 + - + +
187U GLU 3.6 7.4 - - - +
189U VAL* 1.3 76.3 - - - +
191U GLU* 1.3 58.0 + - - +
193U ALA* 3.2 1.7 + - - +
194U ILE* 2.9 42.9 + - + +
212U VAL* 3.8 22.2 - - + -
214U VAL* 3.9 19.1 - - + -
224U LEU* 4.5 2.2 - - + -
232U ARG* 3.5 23.3 - - + -
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Residues in contact with GLU 191 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187U GLU 3.0 16.8 + - - +
188U LYS* 3.3 38.9 - - + +
189U VAL 3.2 0.2 - - - -
190U VAL* 1.3 73.3 - - - +
192U PHE* 1.3 67.9 + - - +
194U ILE* 3.4 2.1 + - - -
195U THR* 3.0 28.2 + - - -
232U ARG* 2.5 59.2 + - + +
235U ALA* 3.4 23.9 - - - +
236U ILE* 3.8 14.8 - - + +
239U GLN* 5.4 9.0 + - - +
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Residues in contact with PHE 192 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40U VAL* 4.3 7.4 - - + -
176U LEU* 4.3 17.7 - - + -
179U HIS* 3.3 39.5 - + + -
180U ILE* 3.5 42.6 - - + -
188U LYS 2.8 16.7 + - - +
189U VAL* 3.5 8.3 - - - +
191U GLU* 1.3 77.4 - - - +
193U ALA* 1.3 69.4 + - + +
195U THR* 3.3 6.3 + - - -
196U HIS* 3.0 60.5 + + + -
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Residues in contact with ALA 193 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U LEU* 3.7 16.7 - - + +
40U VAL* 3.9 19.3 - - + -
47U VAL* 4.1 0.7 - - + -
49U ILE* 3.3 31.1 - - + +
189U VAL 2.9 18.4 + - - +
190U VAL 3.5 1.3 - - - +
192U PHE* 1.3 83.8 - - - +
194U ILE* 1.3 61.3 + - - +
196U HIS* 3.5 1.4 + - - -
197U MET* 3.2 22.0 + - - +
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Residues in contact with ILE 194 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49U ILE* 4.2 13.7 - - + -
190U VAL* 2.9 38.0 + - + +
191U GLU* 4.0 4.7 - - - +
193U ALA* 1.3 69.5 - - - +
195U THR* 1.3 66.9 + - - +
197U MET* 2.8 17.3 + - - +
198U ILE* 2.9 33.8 + - + +
205U PHE* 4.3 4.7 - - + -
210U LEU* 3.7 31.4 - - + -
212U VAL* 4.8 5.4 - - + -
229U ILE* 5.0 2.7 - - + -
232U ARG* 4.2 13.2 - - + -
233U LEU* 3.7 28.0 - - + +
236U ILE* 5.1 5.6 - - + -
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Residues in contact with THR 195 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191U GLU 3.0 20.2 + - - -
192U PHE* 3.4 6.9 - - - -
194U ILE* 1.3 76.2 - - - +
196U HIS* 1.3 71.4 + - + +
198U ILE* 3.3 11.8 + - - +
199U ASP* 2.9 49.2 + - - +
236U ILE* 3.6 18.8 - - - +
239U GLN* 4.8 8.0 + - - +
240U ASP* 3.6 24.6 + - - +
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Residues in contact with HIS 196 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38U LEU* 4.9 4.7 - - + +
172U ILE* 5.2 2.6 - - - +
175U ASN* 2.9 31.8 + - - +
176U LEU* 4.7 9.7 - - + +
179U HIS* 3.9 24.5 - + + +
192U PHE* 3.0 64.0 + + + +
193U ALA* 4.2 3.4 - - - +
194U ILE 3.2 0.2 - - - -
195U THR* 1.3 89.8 - - + +
197U MET* 1.3 59.6 + - - +
199U ASP* 4.0 11.3 + - - -
200U ALA* 3.5 22.2 + - - +
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Residues in contact with MET 197 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36U ASN* 3.5 46.4 - - + +
37U SER* 4.0 10.1 - - - +
38U LEU* 3.9 15.0 - - + +
49U ILE* 3.7 26.2 - - + -
51U GLN* 4.5 4.9 - - + -
172U ILE* 3.9 16.4 - - + -
193U ALA 3.2 11.3 + - - +
194U ILE* 2.8 11.2 + - - +
196U HIS* 1.3 78.4 - - - +
198U ILE* 1.3 63.9 + - - +
200U ALA* 3.9 1.7 - - - -
201U LEU* 3.1 39.0 + - + +
205U PHE* 4.2 19.3 - - + -
210U LEU* 5.0 0.4 - - - -
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Residues in contact with ILE 198 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194U ILE* 2.9 36.1 + - + +
195U THR* 3.5 9.6 - - - +
197U MET* 1.3 72.1 - - - +
199U ASP* 1.3 66.2 + - - +
200U ALA 2.9 10.6 + - - -
201U LEU* 3.3 0.4 + - - -
202U GLY* 3.1 21.5 + - - -
203U THR 3.1 28.8 + - - +
204U GLU* 4.0 20.2 - - + +
205U PHE* 3.6 24.0 - - + +
233U LEU* 5.6 1.3 - - + -
236U ILE* 4.2 22.7 - - + -
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Residues in contact with ASP 199 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175U ASN* 4.0 17.5 + - - +
195U THR* 2.9 38.5 + - - +
196U HIS* 4.2 11.6 + - - +
197U MET 3.4 0.4 - - - -
198U ILE* 1.3 80.8 - - - +
200U ALA* 1.3 57.1 + - - +
202U GLY* 4.6 2.8 + - - -
240U ASP* 4.9 9.8 - - - +
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Residues in contact with ALA 200 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168U LYS* 4.7 2.4 - - - +
171U GLU* 3.9 21.1 - - + +
172U ILE* 4.3 19.3 - - + -
175U ASN* 3.7 23.8 - - + +
196U HIS 3.5 16.6 + - - +
197U MET 3.5 2.6 + - - +
198U ILE 3.0 0.8 - - - -
199U ASP* 1.3 80.2 - - - +
201U LEU* 1.3 66.6 + - - +
202U GLY 3.5 1.6 - - - -
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Residues in contact with LEU 201 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36U ASN* 4.2 3.4 - - - +
51U GLN* 3.5 36.1 - - - +
168U LYS* 3.7 51.7 + - + +
172U ILE* 3.9 22.2 - - + -
197U MET* 3.1 35.8 + - + +
198U ILE* 5.2 0.2 - - - -
200U ALA* 1.3 84.8 - - - +
202U GLY* 1.3 59.6 + - - +
203U THR* 3.0 24.0 + - - +
205U PHE* 4.3 7.6 - - + -
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Residues in contact with GLY 202 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198U ILE* 3.1 9.1 + - - -
199U ASP 4.6 2.4 + - - -
200U ALA 3.5 2.6 - - - +
201U LEU* 1.3 78.1 - - - +
203U THR* 1.3 58.0 + - - +
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Residues in contact with THR 203 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51U GLN* 6.2 0.9 - - - +
168U LYS* 5.0 3.1 + - - -
198U ILE* 3.1 35.3 + - - +
201U LEU* 3.0 27.6 + - - +
202U GLY* 1.3 78.8 + - - +
204U GLU* 1.3 75.6 + - - +
205U PHE* 4.5 16.4 - - + -
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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
------------------------------------------------------------
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