Contacts of the helix formed by residues 185 - 201 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42R THR* 4.6 0.4 - - - -
44R GLU* 3.9 20.2 - - - +
180R SER 4.2 7.2 - - - -
184R LEU* 1.3 76.4 - - - +
186R LEU* 1.3 64.4 + - - +
187R LYS* 3.6 7.5 + - - +
188R GLU* 3.2 39.3 + - - +
189R ALA* 3.0 20.8 + - - +
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Residues in contact with LEU 186 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R THR* 4.5 4.9 - - + +
44R GLU* 3.2 27.8 + - + +
45R GLY* 3.9 29.2 - - - +
46R VAL 4.3 1.3 - - - +
47R VAL* 3.6 26.7 - - + -
184R LEU 3.9 0.8 + - - -
185R THR* 1.3 72.4 - - - +
187R LYS* 1.3 59.0 + - + +
189R ALA* 3.2 7.2 + - - +
190R GLU* 3.0 46.2 + - + +
214R CYS* 4.5 9.6 - - + -
216R THR* 4.3 18.4 - - + -
224R TYR* 4.5 5.8 - - - +
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Residues in contact with LYS 187 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44R GLU* 5.0 0.2 + - - -
185R THR* 3.3 7.4 + - - +
186R LEU* 1.3 77.3 - - + +
188R GLU* 1.3 65.8 + - + +
190R GLU* 3.4 23.2 + - - +
191R LEU* 3.3 30.7 + - + +
232R LEU* 5.3 7.0 - - + +
236R GLU* 4.3 23.8 + - - +
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Residues in contact with GLU 188 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180R HIS* 3.8 12.5 - - - -
184R LEU* 3.5 25.4 - - + +
185R THR* 3.2 42.3 + - - +
187R LYS* 1.3 77.6 - - - +
189R ALA* 1.3 62.3 + - - +
191R LEU* 3.2 16.1 + - + +
192R LEU* 3.1 25.7 + - + +
240R LYS* 6.4 0.4 - - - +
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Residues in contact with ALA 189 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R ILE* 3.5 17.0 - - + +
42R THR* 3.7 24.2 - - + -
47R VAL* 4.3 11.0 - - + -
184R LEU* 3.9 10.5 - - + +
185R THR 3.0 12.7 + - - +
186R LEU 3.2 8.5 + - - +
188R GLU* 1.3 72.6 - - - +
190R GLU* 1.3 64.7 + - - +
192R LEU* 3.4 7.1 + - - +
193R VAL* 3.1 27.6 + - - +
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Residues in contact with GLU 190 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47R VAL* 4.3 22.2 - - + +
186R LEU* 3.0 30.5 + - + +
187R LYS* 3.6 24.9 - - - +
188R GLU 3.3 0.2 - - - -
189R ALA* 1.3 74.9 - - - +
191R LEU* 1.3 63.5 + - - +
193R VAL* 3.1 13.2 + - - +
194R LEU* 3.1 20.4 + - - +
212R LEU* 4.1 10.5 - - + +
224R TYR* 2.4 42.4 + - + +
228R LYS* 5.1 2.3 + - - -
232R LEU* 3.4 26.1 - - + +
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Residues in contact with LEU 191 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187R LYS* 3.3 21.7 + - + +
188R GLU* 3.2 12.3 + - + +
190R GLU* 1.3 78.7 - - - +
192R LEU* 1.3 54.2 + - + +
194R LEU* 3.2 7.8 + - + +
195R LYS* 2.8 35.9 + - - +
232R LEU* 3.9 45.5 - - + +
236R GLU* 4.1 23.1 - - + +
237R LEU* 4.0 23.1 - - + +
240R LYS* 4.5 22.9 - - + +
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Residues in contact with LEU 192 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R ILE* 3.8 18.2 - - + -
176R LEU* 5.3 3.1 - - + -
179R GLU* 3.5 49.8 - - + +
180R TRP* 4.8 1.3 - - + +
184R LEU* 4.1 27.1 - - + -
188R GLU* 3.1 16.1 + - + +
189R ALA 3.4 10.8 - - - +
190R GLU 3.3 0.2 - - - -
191R LEU* 1.3 79.0 - - + +
193R VAL* 1.3 58.5 + - - +
195R LYS* 4.1 11.2 - - + -
196R ILE* 3.0 43.3 + - + +
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Residues in contact with VAL 193 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R ILE* 4.2 22.3 - - + +
40R ILE* 3.4 22.7 - - + -
47R VAL* 3.9 19.1 - - + +
49R GLY* 3.7 18.6 - - - +
189R ALA 3.1 15.1 + - - +
190R GLU 3.1 8.3 + - - +
192R LEU* 1.3 73.7 - - - +
194R LEU* 1.3 67.8 + - - +
196R ILE 3.9 0.3 - - - -
197R LEU* 2.9 36.3 + - + +
212R LEU* 3.5 24.5 - - + -
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Residues in contact with LEU 194 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190R GLU 3.1 17.8 + - - +
191R LEU* 3.5 9.2 - - - +
193R VAL* 1.3 79.2 - - - +
195R LYS* 1.3 51.9 + - - +
197R LEU* 3.2 4.6 + - + -
198R LYS* 2.7 36.9 + - - +
207R LEU* 3.4 29.1 - - + +
210R ALA* 4.9 6.7 - - + -
211R GLN 6.2 0.4 - - - +
212R LEU* 3.3 40.4 - - + -
229R THR* 4.5 9.9 - - + +
232R LEU* 4.0 21.3 - - + -
233R ILE* 4.2 26.0 - - + +
237R LEU* 4.5 11.7 - - + -
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Residues in contact with LYS 195 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175R GLU* 4.3 12.0 + - - -
179R GLU* 3.0 30.2 + - + +
191R LEU 2.8 20.3 + - - +
192R LEU* 3.7 13.0 - - + +
193R VAL 3.3 0.2 - - - -
194R LEU* 1.3 72.0 - - - +
196R ILE* 1.3 68.7 + - + +
198R LYS* 3.0 19.4 + - + +
199R GLN* 3.0 36.6 + - + +
237R LEU* 4.1 18.6 - - + +
241R GLU* 3.6 28.9 + - - +
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Residues in contact with ILE 196 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38R ILE* 3.8 14.8 - - + -
172R ALA* 3.6 36.1 - - + +
175R GLU* 4.0 31.0 - - + +
176R LEU* 3.8 35.2 - - + +
179R GLU* 5.3 1.8 - - + -
192R LEU* 3.0 29.2 + - + +
195R LYS* 1.3 82.2 - - + +
197R LEU* 1.3 61.9 + - - +
199R GLN* 3.5 8.8 + - + +
200R VAL* 3.2 25.3 + - + +
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Residues in contact with LEU 197 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R THR* 4.3 21.5 - - + +
38R ILE* 3.7 22.9 - - + +
49R GLY* 4.1 1.3 - - - +
50R VAL* 3.8 30.7 - - - +
51R GLU* 4.3 16.8 - - + +
193R VAL* 2.9 33.8 + - + +
194R LEU* 3.5 7.9 - - + +
196R ILE* 1.3 74.3 - - - +
198R LYS* 1.3 66.1 + - - +
200R VAL* 4.0 2.0 - - + -
201R MET* 3.0 36.9 + - + +
207R LEU* 3.8 9.4 - - + -
210R ALA* 4.4 12.8 - - + -
211R GLN 5.2 0.9 - - - +
212R LEU* 5.5 0.7 - - + -
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Residues in contact with LYS 198 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194R LEU 2.7 16.7 + - - +
195R LYS* 3.0 11.2 + - + +
197R LEU* 1.3 74.1 - - - +
199R GLN* 1.3 63.8 + - + +
201R MET* 4.0 11.4 + - - +
205R GLU 4.7 4.0 - - - +
206R LYS* 4.3 28.5 - - - +
207R LEU* 3.8 33.9 + - + +
237R LEU* 4.4 20.2 - - + -
238R LYS* 6.5 1.1 - - - -
241R GLU* 5.1 7.2 - - - +
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Residues in contact with GLN 199 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175R GLU* 3.5 40.6 + - - +
195R LYS* 3.0 36.7 + - + +
196R ILE* 3.7 10.6 - - - +
197R LEU 3.2 0.2 - - - -
198R LYS* 1.3 79.8 - - + +
200R VAL* 1.3 66.1 + - + +
201R MET 4.2 2.9 - - - +
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Residues in contact with VAL 200 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R THR* 4.1 31.5 + - + +
38R ILE* 5.1 0.2 - - + -
51R GLU* 5.5 0.2 - - - +
168R GLY* 3.8 30.3 - - - +
171R GLY* 4.8 4.9 - - - -
172R ALA* 4.2 16.2 - - + +
196R ILE* 3.2 19.9 + - + +
197R LEU* 3.7 9.4 - - + +
199R GLN* 1.3 82.7 - - + +
201R MET* 1.3 68.1 + - + +
202R GLU* 3.7 4.7 + - - +
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Residues in contact with MET 201 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51R GLU* 3.7 40.2 - - + +
53R ARG* 5.6 1.1 - - - +
197R LEU* 3.0 36.7 + - + +
198R LYS 4.1 7.9 - - - +
199R GLN 3.5 3.3 - - - +
200R VAL* 1.3 80.8 - - + +
202R GLU* 1.3 66.1 + - - +
205R GLU* 3.6 26.1 - - + +
207R LEU* 4.3 21.3 - - - -
209R ASN* 3.5 45.5 - - + +
210R ALA* 4.5 3.8 - - - -
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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