Contacts of the helix formed by residues 185 - 202 (chain Q) 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 THR 185 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Q ASN* 5.4 0.7 - - - +
45Q CYS* 4.4 2.9 - - - -
183Q PRO 3.0 12.1 - - - +
184Q ALA* 1.3 81.3 - - - +
186Q VAL* 1.3 70.6 + - + +
187Q GLU* 3.5 24.2 - - + +
188Q GLU* 3.2 28.7 + - - +
189Q CYS* 3.2 16.1 + - - +
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Residues in contact with VAL 186 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Q ASN* 4.5 12.2 - - - +
45Q CYS* 3.9 16.1 - - + -
47Q VAL* 4.7 0.8 - - + +
185Q THR* 1.3 76.5 - - + +
187Q GLU* 1.3 57.2 + - - +
189Q CYS* 3.3 3.3 - - - +
190Q VAL* 3.0 36.0 + - + +
214Q VAL* 3.6 37.5 - - + -
216Q LYS* 3.9 29.2 - - + +
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Residues in contact with GLU 187 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185Q THR* 3.1 15.5 - - + +
186Q VAL* 1.3 75.9 - - - +
188Q GLU* 1.3 59.3 + - - +
189Q CYS 3.0 3.8 - - - -
190Q VAL 3.1 3.5 + - - -
191Q LYS* 2.9 24.4 + - + +
232Q TYR* 3.2 42.2 + - + +
235Q GLN* 5.4 6.4 + - - -
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Residues in contact with GLU 188 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180Q GLU* 5.0 8.5 - - - +
183Q PRO* 3.6 25.4 - - + +
184Q ALA* 3.7 11.0 + - - +
185Q THR* 3.2 34.0 + - - +
187Q GLU* 1.3 78.1 - - - +
189Q CYS* 1.3 56.5 + - - +
191Q LYS* 3.7 18.3 - - + +
192Q LEU* 3.4 21.3 + - - +
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Residues in contact with CYS 189 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40Q VAL* 3.5 30.1 - - - +
42Q GLY* 3.6 28.5 - - - -
45Q CYS* 3.8 9.0 - - - -
47Q VAL* 3.6 19.1 - - + -
183Q PRO* 3.7 11.9 - - + +
185Q THR 3.2 18.3 + - - +
186Q VAL 3.3 5.6 - - - +
187Q GLU 3.0 0.6 - - - -
188Q GLU* 1.3 77.7 - - - +
190Q VAL* 1.3 63.7 + - - +
191Q LYS 3.2 0.2 - - - -
192Q LEU* 3.6 1.0 + - - +
193Q THR* 2.9 28.0 + - - -
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Residues in contact with VAL 190 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47Q VAL* 4.2 10.5 - - + -
186Q VAL* 3.0 18.6 + - + +
187Q GLU 3.6 5.6 - - - +
189Q CYS* 1.3 75.0 - - - +
191Q LYS* 1.3 58.3 + - - +
193Q THR* 3.2 6.7 + - - -
194Q VAL* 2.8 49.0 + - + +
212Q ILE* 4.1 17.5 - - + -
214Q VAL* 4.1 25.4 - - + -
224Q LEU* 4.3 9.4 - - + -
229Q ILE* 6.2 0.4 - - - -
232Q TYR* 4.0 29.6 - - + +
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Residues in contact with LYS 191 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187Q GLU* 2.9 16.4 + - + +
188Q GLU* 3.7 17.0 - - + +
190Q VAL* 1.3 76.3 - - - +
192Q LEU* 1.3 56.7 + - - +
194Q VAL 3.2 0.7 + - - -
195Q ARG* 3.0 48.9 + - - +
232Q TYR* 4.0 17.6 - - + -
235Q GLN* 3.3 27.5 + - - +
236Q ILE* 3.7 30.5 - - + +
239Q GLU* 3.5 23.3 + - - -
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Residues in contact with LEU 192 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Q VAL* 4.4 15.3 - - + -
175Q PHE* 4.1 11.2 - - + -
176Q LEU* 4.6 7.4 - - + +
179Q ASN* 4.0 32.8 - - + +
180Q TYR* 3.9 33.2 - - + -
183Q PRO* 4.2 15.5 - - + -
188Q GLU 3.4 15.3 + - - +
189Q CYS 3.6 4.9 + - - +
190Q VAL 3.4 0.2 - - - -
191Q LYS* 1.3 78.9 - - - +
193Q THR* 1.3 58.4 + - - +
195Q ARG* 3.7 22.8 + - - +
196Q SER* 2.8 27.0 + - - -
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Residues in contact with THR 193 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Q VAL* 3.9 22.4 - - + +
40Q VAL* 3.3 24.4 - - + +
47Q VAL* 3.9 20.3 + - + +
48Q LEU 4.7 0.2 - - - -
49Q GLY* 4.3 5.2 - - - +
189Q CYS 2.9 21.2 + - - -
190Q VAL* 3.2 7.0 + - - -
192Q LEU* 1.3 75.6 - - - +
194Q VAL* 1.3 62.1 + - - +
196Q SER* 2.9 15.5 + - - -
197Q LEU* 3.3 15.5 + - - +
212Q ILE* 3.8 22.7 - - + -
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Residues in contact with VAL 194 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190Q VAL* 2.8 35.6 + - + +
191Q LYS 3.8 3.4 - - - +
193Q THR* 1.3 74.8 - - - +
195Q ARG* 1.3 66.8 + - - +
197Q LEU* 3.1 7.1 + - - +
198Q LEU* 2.9 36.1 + - + +
210Q ILE* 4.5 12.6 - - + -
212Q ILE* 4.4 16.2 - - + -
229Q ILE* 4.6 8.1 - - + -
232Q TYR* 4.2 15.7 - - + -
233Q VAL* 4.6 12.8 - - + +
236Q ILE* 3.8 18.4 - - + -
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Residues in contact with ARG 195 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175Q PHE* 3.6 22.8 - - + -
179Q ASN* 2.9 27.6 + - - +
191Q LYS* 3.0 40.8 + - - +
192Q LEU* 3.8 19.9 - - - +
194Q VAL* 1.3 78.1 - - - +
196Q SER* 1.3 61.5 + - - +
198Q LEU* 3.2 21.7 + - - +
199Q GLU* 3.5 15.2 - - - +
236Q ILE* 3.7 30.7 - - + +
240Q LYS* 6.4 2.2 - - + -
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Residues in contact with SER 196 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Q VAL* 4.5 7.4 - - - +
172Q VAL* 3.7 30.6 - - - +
175Q PHE* 3.7 25.1 - - - -
176Q LEU* 3.8 15.5 - - - +
192Q LEU 2.8 17.5 + - - -
193Q THR* 2.9 17.8 + - - -
195Q ARG* 1.3 79.2 - - - +
197Q LEU* 1.3 60.5 + - - +
199Q GLU* 3.7 15.5 + - - +
200Q VAL* 4.6 1.4 + - - +
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Residues in contact with LEU 197 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Q CYS* 4.5 20.6 - - + -
38Q VAL* 3.8 23.8 - - + -
49Q GLY* 3.8 21.5 - - - +
50Q CYS* 4.0 3.1 - - - +
51Q GLU* 4.0 23.3 - - + +
172Q VAL* 5.6 2.0 - - + -
193Q THR 3.7 14.1 - - - +
194Q VAL 3.1 5.5 + - - +
196Q SER* 1.3 79.1 + - - +
198Q LEU* 1.3 64.9 + - - +
200Q VAL* 3.1 8.6 + - + +
201Q VAL* 3.1 39.9 + - + +
210Q ILE* 3.9 31.9 - - + -
212Q ILE* 4.4 2.2 - - + -
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Residues in contact with LEU 198 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194Q VAL* 2.9 37.0 + - + +
195Q ARG* 3.2 9.8 + - - +
197Q LEU* 1.3 76.8 - - - +
199Q GLU* 1.3 64.1 + - - +
200Q VAL 3.0 2.0 + - - -
201Q VAL* 3.6 10.1 + - + +
202Q GLN* 3.9 10.2 + - - -
203Q THR* 4.9 19.6 + - - +
206Q GLY 5.4 1.1 - - - +
210Q ILE* 4.1 16.1 - - + +
233Q VAL* 5.0 18.4 - - + -
236Q ILE* 3.8 29.2 - - + -
237Q GLU* 5.0 15.3 - - + +
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Residues in contact with GLU 199 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171Q THR* 4.7 16.4 - - + +
172Q VAL* 5.7 1.3 - - + -
175Q PHE* 4.2 33.2 - - + +
195Q ARG* 3.5 19.8 - - - +
196Q SER 3.7 12.6 - - - +
197Q LEU 3.2 0.4 - - - -
198Q LEU* 1.3 78.1 - - - +
200Q VAL* 1.3 65.2 + - + +
202Q GLN* 3.9 11.2 + - - -
240Q LYS* 4.3 20.5 + - - -
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Residues in contact with VAL 200 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q CYS* 5.1 5.8 - - + -
51Q GLU* 4.2 16.5 - - - +
167Q ARG* 4.1 7.9 - - - +
168Q ASN* 3.4 55.0 - - + +
171Q THR* 4.1 13.5 - - + -
172Q VAL* 4.2 12.3 - - + -
196Q SER 4.8 0.9 - - - +
197Q LEU* 3.1 8.1 + - + +
198Q LEU 3.1 0.4 - - - -
199Q GLU* 1.3 84.9 - - + +
201Q VAL* 1.3 66.1 + - + +
202Q GLN* 3.5 15.0 + - - +
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Residues in contact with VAL 201 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Q GLU* 3.7 34.3 - - + +
197Q LEU* 3.1 25.3 + - + +
198Q LEU* 3.6 3.7 + - + +
200Q VAL* 1.3 78.7 - - + +
202Q GLN* 1.3 68.8 + - - +
203Q THR* 4.1 10.1 - - - +
206Q GLY 4.2 5.6 - - - +
209Q ASN* 3.3 40.3 - - + +
210Q ILE* 3.9 26.2 - - + -
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Residues in contact with GLN 202 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198Q LEU 3.9 7.2 + - - -
199Q GLU 3.9 17.4 + - - -
200Q VAL* 3.5 16.3 + - - +
201Q VAL* 1.3 83.2 - - - +
203Q THR* 1.3 72.8 + - - +
209Q ASN* 4.8 0.9 - - - +
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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