Contacts of the helix formed by residues 206 - 225 (chain C) in PDB entry 4S10
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 ASN 206 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167C GLY 2.7 23.3 + - - -
168C ARG* 3.2 33.0 - - - +
204C ASN 3.8 1.5 + - - +
205C SER* 1.3 74.9 - - - +
207C ARG* 1.3 64.8 + - - +
208C TYR* 3.0 15.6 + - + +
209C GLU* 2.8 48.8 + - - +
210C ARG* 2.9 18.9 + - - +
259C ASP* 2.9 22.8 + - - -
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Residues in contact with ARG 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C SER 4.2 0.2 + - - -
206C ASN* 1.3 74.7 - - - +
208C TYR* 1.3 115.4 + - + +
210C ARG* 3.5 12.7 + - - +
211C LEU* 3.2 45.0 + - + +
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Residues in contact with TYR 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C GLY 4.3 0.7 - - - +
168C ARG* 3.8 31.4 - - + -
169C ARG* 3.5 52.6 + - + +
171C VAL* 4.0 18.8 - - + +
206C ASN* 3.0 14.6 + - + +
207C ARG* 1.3 114.5 + - + +
209C GLU* 1.3 67.6 + - - +
211C LEU* 3.1 9.3 + - + +
212C LYS* 3.0 23.9 + - - +
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Residues in contact with GLU 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C VAL* 3.6 29.8 - - - +
166C LYS* 3.4 1.3 - - - -
167C GLY 2.6 38.6 + - - +
171C VAL* 4.3 3.6 - - + -
186C GLY 3.3 6.4 - - - +
187C ASP* 3.3 5.9 - - - +
188C CYS* 4.1 4.9 - - - -
205C SER* 3.4 9.1 + - - +
206C ASN* 2.8 41.8 + - - +
208C TYR* 1.3 72.2 - - - +
210C ARG* 1.3 52.7 + - - +
212C LYS 3.2 1.0 + - - -
213C ALA* 2.7 36.2 + - - +
259C ASP* 3.3 1.2 - - - +
301C CA 2.6 29.8 - - - -
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Residues in contact with ARG 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C CYS* 3.8 11.6 - - - -
199C GLN* 4.3 2.3 + - - -
201C CYS* 3.5 18.2 - - - +
202C GLY 3.1 24.2 + - - -
203C SER* 3.7 11.3 + - - +
205C SER* 3.6 29.3 + - - +
206C ASN 2.9 19.3 - - - +
207C ARG* 3.8 10.1 - - - +
208C TYR 3.3 0.2 - - - -
209C GLU* 1.3 75.4 - - - +
211C LEU* 1.3 58.4 + - + +
213C ALA* 3.8 2.8 - - - +
214C THR* 2.7 32.4 + - - -
233C VAL* 6.3 0.2 - - - +
235C GLU* 3.4 30.1 + - - -
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Residues in contact with LEU 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C ARG* 3.2 41.9 + - + +
208C TYR* 3.1 12.9 + - + +
210C ARG* 1.3 80.1 - - + +
212C LYS* 1.3 64.1 + - - +
214C THR* 3.6 8.4 - - - +
215C GLN* 3.4 23.3 + - - +
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Residues in contact with LYS 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C VAL* 3.9 7.0 - - + -
171C VAL* 3.7 45.3 - - + -
173C ALA* 5.1 7.9 - - + +
208C TYR 3.0 16.4 + - - +
209C GLU 3.7 2.7 - - - +
211C LEU* 1.3 74.7 - - - +
213C ALA* 1.3 54.1 + - - +
214C THR 3.1 1.3 - - - -
215C GLN* 2.8 17.9 + - + +
216C VAL* 2.8 47.9 + - + +
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Residues in contact with ALA 213 (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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165C VAL* 3.9 6.9 - - + +
188C CYS* 3.9 23.6 - - + -
190C ILE* 3.0 37.1 - - + +
199C GLN* 3.5 15.7 - - + +
201C CYS* 4.6 0.9 - - - -
209C GLU 2.7 21.9 + - - +
210C ARG* 3.8 6.5 - - - +
212C LYS* 1.3 71.8 - - - +
214C THR* 1.3 63.5 + - - +
217C SER* 3.1 11.4 + - - -
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Residues in contact with THR 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C GLN* 3.4 19.1 + - - +
210C ARG 2.7 21.5 + - - -
211C LEU* 3.6 11.7 - - - +
212C LYS 3.1 0.2 - - - -
213C ALA* 1.3 78.9 - - - +
215C GLN* 1.3 65.4 + - - +
217C SER* 3.5 2.1 + - - -
218C LYS* 3.1 61.8 + - - +
233C VAL* 6.2 0.4 - - + -
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Residues in contact with GLN 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C LEU 3.4 14.3 + - - +
212C LYS* 2.8 23.8 + - + +
214C THR* 1.3 83.6 - - - +
216C VAL* 1.3 66.2 + - - +
218C LYS* 3.3 17.1 + - - +
219C GLY* 3.2 18.4 + - - -
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Residues in contact with VAL 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C PHE* 5.0 10.5 - - + -
165C VAL* 4.7 1.8 - - + -
173C ALA* 3.7 31.6 - - + -
190C ILE* 3.4 31.0 - - + -
212C LYS* 2.8 43.1 + - + +
213C ALA* 4.5 0.4 - - - -
215C GLN* 1.3 70.6 - - - +
217C SER* 1.3 63.5 + - - +
219C GLY* 3.2 11.0 + - - -
220C ILE* 3.3 20.5 + - + +
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Residues in contact with SER 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C ILE* 3.9 7.2 - - - +
197C ILE* 3.4 25.0 - - - +
199C GLN* 3.0 34.8 - - - +
213C ALA 3.1 9.8 + - - -
214C THR 3.6 9.0 - - - -
215C GLN 3.2 0.2 - - - -
216C VAL* 1.3 74.0 - - - +
218C LYS* 1.3 68.0 + - - +
220C ILE* 3.2 13.7 + - - +
221C ARG* 3.2 13.3 + - - +
231C VAL* 3.6 16.0 - - - +
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Residues in contact with LYS 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C GLN* 4.4 6.3 + - - -
214C THR* 3.1 45.0 + - - +
215C GLN* 3.3 24.7 + - - +
217C SER* 1.3 80.3 - - - +
219C GLY* 1.3 59.9 + - - +
221C ARG* 3.2 35.9 + - - +
222C ASP* 2.8 42.5 + - - +
231C VAL* 5.1 7.6 - - + +
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Residues in contact with GLY 219 (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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215C GLN 3.2 6.2 + - - -
216C VAL 3.2 7.8 + - - -
217C SER 3.2 0.8 - - - -
218C LYS* 1.3 79.5 - - - +
220C ILE* 1.3 54.7 + - - +
223C ASN* 2.7 54.2 + - - +
224C GLU* 3.3 3.8 + - - +
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Residues in contact with ILE 220 (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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161C ARG* 3.8 13.2 - - - +
163C PHE* 4.1 17.7 - - + -
190C ILE* 4.1 18.8 - - + -
192C ASP* 4.0 13.5 - - + +
197C ILE* 4.1 16.2 - - + -
216C VAL* 3.3 16.0 + - + +
217C SER 3.2 6.9 + - - +
219C GLY* 1.3 74.1 - - - +
221C ARG* 1.3 53.4 + - - +
224C GLU* 2.9 26.9 + - - +
225C ARG* 2.7 69.6 + - + +
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Residues in contact with ARG 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ILE* 3.8 19.4 - - + +
217C SER 3.2 6.0 + - - +
218C LYS* 3.2 45.8 + - - +
220C ILE* 1.3 77.4 - - - +
222C ASP* 1.3 85.1 + - - +
225C ARG* 3.2 1.4 - - - -
226C ASP 3.0 9.7 + - - -
227C GLY* 2.7 43.9 + - - +
229C ALA* 3.0 35.6 + - + +
231C VAL* 3.9 20.0 - - + +
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Residues in contact with ASP 222 (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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218C LYS* 2.8 30.3 + - - +
221C ARG* 1.3 105.1 + - - +
223C ASN* 1.3 72.3 + - - +
226C ASP* 3.6 16.8 - - - +
227C GLY* 3.9 7.2 + - - +
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Residues in contact with ASN 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C GLY* 2.7 34.0 + - - +
222C ASP* 1.3 88.4 - - - +
224C GLU* 1.3 63.6 + - + +
225C ARG 3.7 0.4 - - - -
226C ASP* 4.3 2.5 + - - -
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Residues in contact with GLU 224 (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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161C ARG* 2.7 38.2 + - - -
219C GLY 4.1 3.1 - - - +
220C ILE* 2.9 30.5 + - - +
223C ASN* 1.3 82.3 - - + +
225C ARG* 1.3 81.9 + - - +
226C ASP* 3.5 1.3 - - - +
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Residues in contact with ARG 225 (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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159C VAL* 5.0 9.0 - - - +
161C ARG* 3.6 3.2 - - - +
192C ASP* 2.5 44.5 + - - -
194C GLY* 2.9 45.6 + - - +
197C ILE* 5.1 0.6 - - - +
220C ILE* 2.7 28.2 + - + +
221C ARG 3.6 4.5 - - - +
224C GLU* 1.3 104.0 + - - +
226C ASP* 1.3 60.9 + - - +
227C GLY 3.1 1.1 - - - -
228C ASP* 2.8 46.1 + - + +
229C ALA* 3.9 11.0 - - + -
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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