Contacts of the helix formed by residues 188 - 201 (chain B) in PDB entry 3SWD
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 GLU 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B VAL* 3.5 36.6 - - + +
186B ALA* 3.4 7.9 + - - +
187B ARG* 1.3 84.2 + - - +
189B PRO* 1.3 70.4 - - + +
190B GLU* 3.6 11.0 - - + +
191B ILE* 2.8 26.5 + - + +
192B VAL* 3.4 5.0 + - - +
232B ARG* 3.6 23.6 + - - +
298B PRO* 3.8 9.5 - - - +
299B HIS* 2.8 33.9 + - + +
501B EPZ 4.6 7.4 + - - +
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Residues in contact with PRO 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ARG 3.5 1.5 - - - +
188B GLU* 1.3 86.3 - - + +
190B GLU* 1.3 62.8 + - - +
192B VAL* 3.0 27.1 + - + +
193B ASP* 3.1 12.8 + - - +
229B LEU* 4.0 19.3 - - + +
232B ARG* 3.7 25.4 - - - +
255B GLN* 5.8 0.4 - - - +
258B THR* 3.9 24.5 - - + +
299B HIS* 3.7 33.4 - - + +
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 4.5 11.8 - - + +
23B ASN* 3.3 46.1 - - + +
24B ALA* 3.8 10.7 - - + +
27B PRO* 5.4 1.1 - - + -
163B VAL* 6.0 4.7 - - + +
167B VAL* 5.9 0.4 - - - -
188B GLU* 3.6 11.1 - - + +
189B PRO* 1.3 80.5 - - - +
191B ILE* 1.3 57.6 + - + +
193B ASP* 3.5 9.0 + - - +
194B THR* 2.9 31.2 + - - -
229B LEU* 4.7 3.9 - - + +
230B PRO 5.4 0.7 - - - +
232B ARG* 2.7 51.8 + - - +
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Residues in contact with ILE 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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163B VAL* 4.1 20.0 - - + +
166B THR* 3.7 24.0 - - + -
167B VAL* 3.9 15.7 - - + -
170B MET* 3.8 16.3 - - + +
186B ALA* 3.3 48.7 - - + +
187B ARG 5.0 0.2 - - - -
188B GLU* 2.8 15.6 + - + +
190B GLU* 1.3 74.8 - - + +
192B VAL* 1.3 66.9 + - + +
194B THR* 3.3 6.7 + - - -
195B ALA* 3.0 22.2 + - - +
208B GLN* 5.0 4.7 - - + -
209B GLY 5.3 3.1 - - - +
213B ILE* 4.3 9.9 - - + -
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ARG 4.7 1.3 - - - +
188B GLU 3.4 6.9 + - - +
189B PRO* 3.0 14.9 + - + +
191B ILE* 1.3 78.2 - - - +
193B ASP* 1.3 57.8 + - - +
195B ALA* 3.2 2.9 + - - +
196B ASN* 2.9 46.8 + - - +
208B GLN* 3.8 18.8 - - + +
209B GLY* 3.6 35.0 - - - +
229B LEU* 6.6 0.2 - - + -
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Residues in contact with ASP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA* 4.1 8.6 - - + +
28B ILE* 4.1 4.3 - - + +
189B PRO 3.1 11.3 + - - +
190B GLU* 3.8 8.5 - - - +
192B VAL* 1.3 80.0 - - - +
194B THR* 1.3 56.9 + - - +
196B ASN* 4.7 1.7 + - - -
197B PHE* 3.1 23.2 + - - +
226B TYR* 2.9 40.9 + - - -
227B ARG 4.6 1.2 - - - +
228B VAL* 3.5 10.6 - - - -
229B LEU* 3.0 53.4 + - + +
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Residues in contact with THR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA 4.5 0.9 + - - -
27B PRO* 3.4 39.6 - - + +
28B ILE* 4.1 14.7 - - + +
31B ALA* 4.6 4.9 - - + -
167B VAL* 4.7 5.4 - - + +
170B MET* 4.2 14.1 - - + -
171B CYS* 4.2 19.3 - - - -
190B GLU 2.9 18.4 + - - -
191B ILE* 3.8 6.9 - - - -
192B VAL 3.3 0.2 - - - -
193B ASP* 1.3 72.9 - - - +
195B ALA* 1.3 64.8 - - - +
197B PHE* 3.3 2.6 + - + +
198B LEU* 3.0 24.7 + - + +
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Residues in contact with ALA 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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170B MET* 3.9 12.9 - - + +
191B ILE 3.0 14.3 + - - +
192B VAL 3.5 8.1 - - - +
194B THR* 1.3 75.8 - - - +
196B ASN* 1.3 57.9 + - - +
198B LEU* 3.0 4.5 + - - +
199B ILE* 2.9 32.1 + - - +
205B ILE* 4.0 20.0 - - + +
208B GLN* 3.6 32.1 - - + +
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Residues in contact with ASN 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 VAL* 2.9 35.0 + - - +
193B ASP* 4.9 1.6 + - - +
195B ALA* 1.3 76.5 - - - +
197B PHE* 1.3 57.8 + - - +
199B ILE* 3.6 12.1 + - - +
200B THR* 3.0 27.5 + - - -
208B GLN* 3.2 21.9 + - - -
226B TYR* 3.2 27.6 + - + +
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Residues in contact with PHE 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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28B ILE* 3.8 48.9 - - + -
31B ALA* 3.9 19.3 - - + -
32B ALA* 4.1 11.9 - - + -
39B VAL* 3.6 29.8 - - + -
41B ILE* 4.1 7.0 - - + -
193B ASP 3.1 16.7 + - - +
194B THR 3.7 5.4 - - - +
195B ALA 3.2 0.2 - - - -
196B ASN* 1.3 75.8 - - - +
198B LEU* 1.3 66.5 + - + +
200B THR* 3.2 19.0 + - + -
201B LEU* 3.3 38.5 + - + +
224B GLY 6.0 0.4 - - - -
226B TYR* 3.7 38.1 - - + -
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Residues in contact with LEU 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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31B ALA* 3.9 20.9 - - + +
34B LEU* 3.9 25.8 - - + -
170B MET* 4.4 9.9 - - + -
171B CYS* 3.9 24.7 - - - -
174B THR* 4.0 13.7 - - + -
194B THR* 3.0 18.8 + - + +
195B ALA 3.0 6.5 + - - +
197B PHE* 1.3 78.8 - - + +
199B ILE* 1.3 65.5 + - - +
201B LEU* 2.9 20.3 + - + +
202B GLY 3.3 0.7 + - - -
203B ALA* 3.1 22.1 + - + +
205B ILE* 3.8 24.0 - - + -
221B LEU* 4.3 7.1 - - + +
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Residues in contact with ILE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ALA 2.9 14.5 + - - +
196B ASN* 3.9 14.6 - - - +
198B LEU* 1.3 73.9 - - - +
200B THR* 1.3 56.7 - - - +
202B GLY* 2.8 24.8 + - - -
203B ALA 3.3 20.7 + - - +
205B ILE* 3.4 36.1 - - + +
208B GLN* 3.6 20.6 - - - +
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Residues in contact with THR 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 ASN 3.0 13.0 + - - -
197B PHE* 3.2 15.9 - - + +
198B LEU 3.2 0.2 - - - -
199B ILE* 1.3 80.2 - - - +
201B LEU* 1.3 64.9 + - + +
202B GLY 3.5 0.7 + - - -
223B GLY 3.9 9.4 - - - +
224B GLY* 4.8 1.1 - - - -
225B VAL 4.1 28.5 - - - +
226B TYR* 3.8 15.1 - - + -
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Residues in contact with LEU 201 (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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31B ALA 5.0 2.2 - - - +
35B ALA* 3.9 24.7 - - + +
39B VAL* 4.2 10.1 - - + -
197B PHE* 3.5 44.4 - - + +
198B LEU* 2.9 18.2 + - + +
200B THR* 1.3 79.4 - - + +
202B GLY* 1.3 57.7 + - - +
203B ALA 3.6 0.2 - - - -
220B ARG 4.7 0.2 - - - +
221B LEU* 3.4 15.8 - - + +
222B GLY* 2.9 33.2 + - - +
223B GLY* 3.2 41.1 - - - +
224B GLY* 3.9 3.1 - - - +
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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