Contacts of the helix formed by residues 201 - 217 (chain C) in PDB entry 6B3I
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 SER 201 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ARG* 4.4 1.3 - - - +
161C ASN* 3.1 35.2 + - - +
162C GLU* 4.7 1.3 - - - -
163C GLY 4.1 17.3 + - - -
165C ASP 4.6 5.0 + - - -
199C LYS 3.8 0.4 + - - -
200C ARG* 1.3 77.6 - - - +
202C TYR* 1.3 60.2 + - - +
203C LYS* 3.6 7.1 + - - +
204C GLN* 2.9 27.0 + - - +
205C LEU* 2.8 27.7 + - - +
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Residues in contact with TYR 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C CYS 4.5 5.5 + - - -
115C THR 4.5 0.5 - - - -
116C ARG 3.7 25.8 + - - -
117C THR* 4.9 15.1 - - + -
160C ARG* 3.7 39.8 + - - +
201C SER* 1.3 74.9 - - - +
203C LYS* 1.3 65.0 + - - +
205C LEU* 3.1 3.0 + - - +
206C ARG* 3.0 46.1 + - - +
239C LEU 5.5 1.8 - - - -
242C CYS* 4.4 24.5 - - + -
243C ALA* 3.7 33.5 - - + +
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Residues in contact with LYS 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C GLY 5.2 5.2 - - - +
164C ASP* 2.9 47.2 + - - +
165C ASP 5.5 0.7 - - - +
166C VAL* 3.7 29.3 - - + +
201C SER* 3.3 6.3 + - - +
202C TYR* 1.3 78.8 - - - +
204C GLN* 1.3 61.3 + - - +
206C ARG* 3.3 27.9 + - + +
207C ALA* 3.4 16.8 + - - +
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Residues in contact with GLN 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C ASP 4.3 3.8 - - - +
166C VAL* 3.5 11.2 - - - +
167C ASP* 2.9 48.5 + - - +
170C LEU* 3.7 18.1 - - + +
171C ALA* 3.2 26.5 - - - +
174C ASP* 4.7 0.6 + - - -
200C ARG* 4.1 23.1 - - + -
201C SER* 2.9 28.0 + - - +
203C LYS* 1.3 75.0 - - - +
205C LEU* 1.3 54.1 + - - +
207C ALA* 3.4 4.2 + - - +
208C THR* 2.6 36.4 + - - +
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Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C ARG* 3.5 27.8 - - - +
196C VAL* 3.4 39.9 - - + +
197C LEU* 3.9 20.2 - - + +
200C ARG* 3.8 8.7 - - + +
201C SER 2.8 18.6 + - - +
202C TYR* 3.1 4.9 + - + +
204C GLN* 1.3 75.5 - - - +
206C ARG* 1.3 60.8 + - - +
208C THR* 3.0 7.0 + - - +
209C PHE* 2.8 52.9 + - + -
239C LEU 5.1 3.1 - - - +
243C ALA* 3.8 21.1 - - + -
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Residues in contact with ARG 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C TYR* 3.0 30.8 + - - +
203C LYS* 3.3 43.6 - - + +
204C GLN 3.3 0.2 - - - -
205C LEU* 1.3 77.5 - - - +
207C ALA* 1.3 62.0 + - - +
209C PHE* 3.2 11.6 + - - +
210C GLN* 3.0 36.3 + - - +
243C ALA 2.9 25.4 + - - +
244C GLN* 3.8 34.7 + - - +
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Residues in contact with ALA 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C VAL* 3.8 28.3 - - + -
168C LYS* 5.8 3.4 - - + -
171C ALA* 3.8 12.2 - - + +
203C LYS 3.4 6.1 + - - +
204C GLN 3.4 9.1 + - - +
205C LEU 3.3 0.6 - - - -
206C ARG* 1.3 77.9 - - - +
208C THR* 1.3 61.1 + - - +
210C GLN* 3.9 13.1 - - - +
211C ALA* 3.0 24.3 + - - +
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Residues in contact with THR 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ALA* 3.6 31.6 - - - +
174C ASP* 3.8 22.2 + - + +
175C ALA* 3.7 10.6 - - - +
178C LEU* 4.5 7.6 - - + -
196C VAL* 4.5 11.0 - - + +
200C ARG* 5.6 0.3 - - - +
204C GLN* 2.6 26.4 + - - +
205C LEU* 3.0 15.1 + - - +
207C ALA* 1.3 78.6 - - - +
209C PHE* 1.3 62.2 + - + +
211C ALA* 3.4 2.9 + - - +
212C TYR* 3.0 26.6 + - + +
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Residues in contact with PHE 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C LEU* 5.5 2.7 - - + -
197C LEU* 4.2 16.6 - - + -
205C LEU* 2.8 48.6 + - + +
206C ARG* 3.2 4.9 + - - +
208C THR* 1.3 80.9 - - + +
210C GLN* 1.3 66.3 + - + +
212C TYR* 3.1 8.2 + - + +
213C GLN* 3.0 22.7 + - - +
219C ASP* 5.6 3.9 - - - +
220C ILE* 3.7 36.1 + - + +
240C VAL* 3.8 45.8 - - + -
243C ALA* 4.3 5.8 - - + -
244C GLN* 3.5 24.5 - - + +
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Residues in contact with GLN 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ARG* 3.0 26.8 + - - +
207C ALA* 3.9 12.3 - - - +
208C THR 3.4 0.2 - - - -
209C PHE* 1.3 75.9 - - + +
211C ALA* 1.3 62.6 + - - +
213C GLN* 3.4 6.9 + - - +
214C ILE* 3.2 34.2 + - + +
244C GLN* 5.5 8.2 - - - +
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Residues in contact with ALA 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ALA* 4.1 10.1 - - + +
172C GLY* 4.2 11.4 - - - -
175C ALA* 4.1 13.2 - - + -
207C ALA 3.0 18.5 + - - +
208C THR 3.7 4.7 - - - +
209C PHE 3.2 0.2 - - - -
210C GLN* 1.3 76.5 - - - +
212C TYR* 1.3 57.9 + - - +
214C ILE* 3.4 7.8 + - - +
215C LEU* 2.9 37.0 + - + +
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Residues in contact with TYR 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ALA* 3.6 33.8 - - + +
178C LEU* 4.3 7.2 + - + -
179C TYR* 3.9 29.7 - - + -
193C PHE* 5.8 1.0 - + - -
208C THR 3.0 15.3 + - - +
209C PHE* 3.1 12.5 + - + +
211C ALA* 1.3 77.5 - - - +
213C GLN* 1.3 56.5 + - - +
215C LEU* 4.7 0.2 - - - -
216C ILE* 2.9 62.2 + - + +
218C LYS* 3.4 21.0 - - + +
219C ASP 4.1 4.7 - - - -
220C ILE* 4.0 31.9 - - + +
223C ALA* 3.2 32.2 - - + +
227C GLU* 4.6 3.6 + - - -
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Residues in contact with GLN 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C PHE 3.0 11.3 + - - +
210C GLN* 3.8 9.9 - - - +
211C ALA 3.4 0.2 - - - -
212C TYR* 1.3 75.8 - - - +
214C ILE* 1.3 63.1 + - + +
217C GLY* 2.9 52.2 + - - -
218C LYS 3.3 8.4 + - - +
219C ASP* 3.3 35.5 + - - +
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Residues in contact with ILE 214 (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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210C GLN* 3.2 24.2 + - + +
211C ALA* 3.9 6.3 - - - +
213C GLN* 1.3 81.3 - - + +
215C LEU* 1.3 68.0 + - + +
216C ILE 4.9 0.2 - - - -
217C GLY* 4.5 1.6 + - - -
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Residues in contact with LEU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TRP* 4.6 18.6 - - + -
172C GLY* 3.8 12.6 - - - +
175C ALA* 4.1 11.4 - - + -
176C LYS* 3.8 40.4 - - + +
211C ALA* 2.9 27.9 + - + +
212C TYR* 4.1 0.9 - - - +
214C ILE* 1.3 84.0 - - + +
216C ILE* 1.3 73.6 + - + +
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Residues in contact with ILE 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TRP* 4.3 11.4 - - + -
175C ALA 5.0 2.0 - - - +
176C LYS* 5.8 0.4 - - - -
179C TYR* 3.5 53.2 - - + -
212C TYR* 2.9 49.6 + - + +
215C LEU* 1.3 93.5 - - + +
217C GLY* 1.3 58.9 + - - +
218C LYS* 3.3 18.9 + - + +
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Residues in contact with GLY 217 (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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213C GLN* 2.9 35.5 + - - -
214C ILE 4.5 1.2 + - - -
215C LEU 3.8 0.4 - - - -
216C ILE* 1.3 77.7 - - - +
218C LYS* 1.3 60.1 + - - +
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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