Contacts of the helix formed by residues 185 - 199 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C ASN* 4.8 5.4 - - - +
45C CYS* 4.6 3.8 - - - -
183C PRO 2.9 3.9 + - - +
184C ALA* 1.3 81.8 + - - +
186C VAL* 1.3 69.8 + - + +
187C GLU* 4.1 14.4 - - + +
188C GLU* 3.6 23.0 + - - +
189C CYS* 3.0 31.6 + - - +
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Residues in contact with VAL 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ASN* 4.5 12.0 - - - +
45C CYS* 4.1 20.1 - - + -
185C THR* 1.3 75.6 - - + +
187C GLU* 1.3 67.6 + - - +
189C CYS* 3.2 2.4 + - - +
190C VAL* 2.9 30.9 + - + +
214C VAL* 3.8 30.7 - - + -
216C LYS* 4.0 32.8 - - + +
232C TYR* 5.8 1.1 - - - +
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Residues in contact with GLU 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C THR* 3.4 10.5 - - + +
186C VAL* 1.3 78.7 - - - +
188C GLU* 1.3 60.4 + - + +
190C VAL 3.3 0.3 + - - -
191C LYS* 3.0 26.9 + - + +
232C TYR* 3.3 36.4 + - + +
235C GLN* 4.8 13.7 + - - +
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Residues in contact with GLU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C GLU* 5.6 1.7 - - - +
183C PRO* 3.8 16.7 - - - +
184C ALA* 3.6 20.1 + - - +
185C THR* 3.6 33.8 + - - +
187C GLU* 1.3 78.2 - - + +
189C CYS* 1.3 61.3 + - - +
190C VAL 3.4 0.2 - - - -
191C LYS* 4.0 9.8 - - + +
192C LEU* 3.5 20.6 + - - +
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Residues in contact with CYS 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 3.5 27.2 - - - +
41C LYS 4.0 0.9 - - - -
42C GLY* 3.5 28.7 - - - -
45C CYS* 3.9 10.5 - - - -
47C VAL* 3.7 13.9 - - + -
183C PRO* 3.6 15.5 - - + +
185C THR 3.0 19.8 + - - +
186C VAL 3.2 3.8 + - - +
188C GLU* 1.3 74.6 - - - +
190C VAL* 1.3 64.2 + - - +
192C LEU* 3.6 2.0 + - - +
193C THR* 2.9 27.4 + - - -
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Residues in contact with VAL 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL* 3.9 14.8 - - + -
186C VAL* 2.9 24.1 + - + +
187C GLU 3.7 4.0 - - - +
189C CYS* 1.3 74.6 - - - +
191C LYS* 1.3 61.2 + - - +
193C THR* 3.0 6.8 + - - -
194C VAL* 2.9 38.6 + - + +
212C ILE* 4.4 7.2 - - + -
214C VAL* 3.7 29.6 - - + -
224C LEU* 4.3 13.9 - - + -
232C TYR* 3.6 33.0 - - + +
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Residues in contact with LYS 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C GLU* 3.0 19.1 + - + +
188C GLU* 4.1 9.6 - - + +
189C CYS 3.4 0.2 - - - -
190C VAL* 1.3 77.5 - - - +
192C LEU* 1.3 57.5 + - - +
194C VAL* 3.2 5.7 + - - +
195C ARG* 2.8 44.1 + - - +
232C TYR* 4.0 18.4 - - + +
235C GLN* 4.0 16.3 + - + +
236C ILE* 4.0 28.0 - - + +
239C GLU* 2.9 39.6 + - - -
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Residues in contact with LEU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 4.7 8.5 - - + -
175C PHE* 4.1 11.9 - - + -
176C LEU* 4.7 12.6 - - + -
179C ASN* 4.0 35.9 - - + +
180C TYR* 4.2 19.1 - - + -
183C PRO* 3.9 25.6 - - + -
188C GLU 3.5 14.9 + - - +
189C CYS 3.9 3.6 - - - +
190C VAL 3.3 0.4 - - - -
191C LYS* 1.3 78.2 - - - +
193C THR* 1.3 62.0 + - - +
195C ARG* 3.2 21.3 + - - +
196C SER* 3.1 23.1 + - - -
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Residues in contact with THR 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C VAL* 4.1 23.8 - - + +
40C VAL* 3.0 23.9 - - + +
47C VAL* 3.6 20.7 - - + +
49C GLY* 4.2 6.7 - - - +
189C CYS 2.9 14.1 + - - -
190C VAL 3.0 9.5 + - - -
192C LEU* 1.3 79.0 - - - +
194C VAL* 1.3 60.7 + - - +
196C SER* 2.7 20.0 + - - +
197C LEU* 3.3 13.4 + - + +
212C ILE* 3.9 22.0 - - + -
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Residues in contact with VAL 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C VAL* 2.9 34.2 + - + +
191C LYS* 3.6 5.8 - - - +
193C THR* 1.3 73.0 - - - +
195C ARG* 1.3 66.5 + - - +
197C LEU* 3.3 8.9 + - - +
198C LEU* 2.9 28.3 + - + +
210C ILE* 4.2 20.2 - - + -
212C ILE* 4.3 17.9 - - + -
229C ILE* 5.3 4.7 - - + +
232C TYR* 4.3 13.0 - - + -
233C VAL* 4.3 15.9 - - + -
236C ILE* 3.8 18.6 - - + -
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Residues in contact with ARG 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C PHE* 3.6 26.5 - - + -
179C ASN* 2.9 29.5 + - - +
191C LYS* 2.8 31.1 + - - +
192C LEU* 3.2 24.2 + - - +
194C VAL* 1.3 76.5 - - - +
196C SER* 1.3 59.4 + - - +
198C LEU* 3.3 17.0 + - - +
199C GLU* 3.5 18.2 + - - +
236C ILE* 3.8 28.0 - - + +
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Residues in contact with SER 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C VAL* 4.4 8.3 - - - +
172C VAL* 3.6 29.0 - - - +
175C PHE* 3.4 29.4 - - - -
176C LEU* 3.7 17.9 - - - +
192C LEU 3.1 10.0 + - - -
193C THR* 2.7 24.9 + - - -
195C ARG* 1.3 74.7 - - - +
197C LEU* 1.3 59.5 + - - +
199C GLU* 3.5 19.1 - - - +
200C VAL* 4.2 1.7 + - - +
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Residues in contact with LEU 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C CYS* 4.7 17.9 - - + +
38C VAL* 3.8 26.0 - - + -
49C GLY* 4.1 16.6 - - - +
50C CYS* 4.3 18.6 - - - +
51C GLU* 4.5 3.8 - - + +
172C VAL* 5.7 1.3 - - + -
193C THR 3.3 16.3 + - - +
194C VAL* 3.3 4.1 + - - +
196C SER* 1.3 74.2 - - - +
198C LEU* 1.3 56.9 + - - +
199C GLU 3.1 4.9 - - - -
200C VAL* 2.9 7.6 + - + +
201C VAL* 2.8 42.1 + - + +
210C ILE* 3.8 42.0 - - + -
212C ILE* 4.2 4.7 - - + -
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Residues in contact with LEU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C VAL* 2.9 19.4 + - + +
195C ARG* 3.3 9.6 + - - +
197C LEU* 1.3 75.5 - - - +
199C GLU* 1.3 63.2 + - - +
200C VAL 3.2 0.4 + - - -
201C VAL* 4.4 2.7 - - + +
202C GLN* 4.1 16.1 + - - +
203C THR* 4.6 19.7 + - - +
206C GLY 5.2 1.8 - - - +
210C ILE* 4.2 15.9 - - + -
233C VAL* 4.3 25.1 - - + +
236C ILE* 3.8 45.3 - - + -
237C GLU* 5.2 9.0 - - + +
240C LYS* 6.2 3.6 - - - -
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Residues in contact with GLU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C THR* 4.2 23.8 - - + +
172C VAL* 5.3 0.7 - - - -
175C PHE* 3.6 42.9 - - + +
195C ARG 3.6 14.8 - - - +
196C SER 3.5 12.8 - - - +
197C LEU 3.1 0.6 - - - -
198C LEU* 1.3 80.2 - - - +
200C VAL* 1.3 60.9 + - + +
202C GLN* 3.5 16.8 + - - -
240C LYS* 5.3 7.6 + - - -
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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