Contacts of the helix formed by residues 195 - 213 (chain C) in PDB entry 4HYY
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 195 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C ALA 3.7 0.4 - - - -
194C TYR* 1.3 86.0 - - + +
196C SER* 1.3 53.8 + - - +
197C GLU* 3.4 9.7 + - - +
198C HIS* 2.8 32.1 + - + +
199C GLN* 2.7 35.3 + - - +
228C LEU* 3.5 13.2 - - - +
232C ASP* 3.7 16.6 - - - +
251D SER* 4.0 17.0 - - - +
255D LYS* 5.6 4.3 - - - +
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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
----------------------------------------------------------
195C THR* 1.3 66.9 - - - +
197C GLU* 1.3 67.6 + - - +
199C GLN* 3.1 5.1 + - - +
200C MET* 3.0 23.0 + - - +
228C LEU* 3.1 35.4 + - - +
229C PHE* 3.5 36.5 - - - -
232C ASP* 3.0 22.7 + - - +
233C PHE* 4.1 6.6 - - - -
245C LYS* 6.1 0.4 - - - -
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Residues in contact with GLU 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C THR* 3.4 10.4 + - - +
196C SER* 1.3 78.3 - - - +
198C HIS* 1.3 63.4 + - - +
200C MET* 3.0 10.9 + - - +
201C GLU* 3.0 36.4 + - + +
232C ASP* 4.1 1.3 + - - +
245C LYS* 5.9 7.5 - - - -
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Residues in contact with HIS 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C ARG 3.4 13.5 + - - -
193C ALA* 3.5 6.7 - - - -
194C TYR* 3.0 42.9 - + + -
195C THR* 2.8 27.5 + - + +
197C GLU* 1.3 75.2 - - - +
199C GLN* 1.3 62.2 + - - +
201C GLU* 3.0 28.8 + - + +
202C LEU* 3.1 35.5 + - + +
84D GLY* 6.4 1.1 - - - -
255D LYS* 6.0 1.3 - - - -
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Residues in contact with GLN 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C ILE* 4.8 8.5 - - + +
161C THR* 3.6 25.9 - - + +
193C ALA* 4.0 17.0 - - + +
195C THR 2.7 18.6 + - - +
196C SER 3.1 5.6 + - - +
198C HIS* 1.3 73.0 - - - +
200C MET* 1.3 62.3 + - - +
202C LEU* 3.2 14.2 + - - +
203C LEU* 3.2 24.2 + - + +
222C ILE* 4.2 11.6 - - + +
224C SER 4.4 1.6 + - - -
225C ILE* 2.8 27.5 + - - +
228C LEU* 3.6 20.6 - - - +
229C PHE* 3.9 12.0 - - + -
249C MET* 3.4 18.3 - - - +
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Residues in contact with MET 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C SER 3.0 12.0 + - - +
197C GLU* 3.0 10.5 + - - +
199C GLN* 1.3 75.7 - - - +
201C GLU* 1.3 62.9 + - + +
203C LEU* 3.0 28.2 + - - +
204C ASP* 3.5 14.6 + - - +
229C PHE* 5.6 3.4 - - + -
245C LYS* 5.2 6.7 - - + +
248C GLN* 3.7 19.1 - - + +
249C MET* 3.7 39.8 - - + +
252C ARG* 3.6 29.8 - - + -
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Residues in contact with GLU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C GLU* 3.0 30.3 + - + +
198C HIS* 3.0 25.1 + - - +
200C MET* 1.3 77.8 - - + +
202C LEU* 1.3 63.2 + - + +
204C ASP* 3.3 22.5 + - - +
205C TYR* 3.4 10.7 + - - +
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Residues in contact with LEU 202 (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 ILE* 4.2 17.7 - - + -
191C ALA* 3.9 17.9 - - + -
192C ARG 3.8 23.1 - - - +
193C ALA* 4.1 18.6 - - + -
198C HIS* 3.1 31.1 + - + +
199C GLN* 3.7 5.6 - - - +
200C MET 3.1 0.6 - - - -
201C GLU* 1.3 77.4 - - + +
203C LEU* 1.3 61.8 + - - +
205C TYR* 3.2 7.8 + - + +
206C VAL* 2.8 32.4 + - - +
84D GLY* 4.8 10.8 - - - -
85D PHE* 3.8 26.6 - - + -
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Residues in contact with LEU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C ILE* 4.4 17.0 - - + -
199C GLN* 3.2 35.5 + - + +
200C MET* 3.0 16.4 + - - +
202C LEU* 1.3 79.7 - - - +
204C ASP* 1.3 53.0 + - - +
206C VAL* 3.1 5.8 + - + +
207C ALA* 2.7 36.3 + - - +
220C LEU* 4.0 26.5 - - + -
222C ILE* 4.7 9.4 - - + -
249C MET* 4.3 22.0 - - + -
252C ARG* 5.3 8.3 - - + +
253C LEU* 4.2 16.2 - - + -
256C ILE* 4.1 15.4 - - + +
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Residues in contact with ASP 204 (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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200C MET* 3.5 19.6 + - - +
201C GLU* 3.3 15.3 + - - +
202C LEU 3.1 0.2 - - - -
203C LEU* 1.3 79.9 - - - +
205C TYR* 1.3 64.2 + - - +
207C ALA* 3.4 6.3 + - - +
208C ALA* 3.2 22.7 + - - +
252C ARG* 4.6 17.0 + - - +
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Residues in contact with TYR 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 3.8 35.1 + + - -
208A ALA* 3.5 37.6 + - + -
209A LYS* 4.0 8.7 - - - +
212A GLU* 3.2 40.1 + - + +
157C ILE* 6.3 1.1 - - + -
189C LEU* 5.9 0.9 - - + -
201C GLU 3.4 8.0 + - - +
202C LEU* 3.2 11.6 + - + +
204C ASP* 1.3 82.8 - - - +
206C VAL* 1.3 56.4 + - - +
208C ALA* 3.5 3.8 + - - +
209C LYS* 2.9 43.1 + - + +
84D GLY 4.9 3.1 - - - -
85D PHE* 3.5 34.5 - + + -
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Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C ILE* 3.8 19.1 - - + -
159C ILE* 4.3 10.1 - - + -
202C LEU 2.8 23.0 + - - +
203C LEU* 3.1 12.5 + - + +
205C TYR* 1.3 72.5 - - - +
207C ALA* 1.3 64.3 + - - +
209C LYS* 3.2 7.2 + - - +
210C PHE* 3.0 53.6 + - + -
220C LEU* 4.0 20.0 - - + -
256C ILE* 4.6 2.9 - - + -
85D PHE* 3.7 22.7 - - + -
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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
----------------------------------------------------------
203C LEU 2.7 20.1 + - - +
204C ASP* 3.8 4.9 - - - +
205C TYR 3.3 0.2 - - - -
206C VAL* 1.3 71.5 - - - +
208C ALA* 1.3 63.1 + - - +
210C PHE* 2.9 18.5 + - - +
211C HIS* 3.0 10.1 + - - -
252C ARG* 3.8 25.1 - - - +
256C ILE* 4.1 18.1 - - + +
260C TYR* 3.9 17.5 + - + +
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Residues in contact with ALA 208 (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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205A TYR* 3.3 34.5 - - + -
204C ASP 3.2 10.0 + - - +
205C TYR 3.7 5.2 - - - +
207C ALA* 1.3 75.2 - - - +
209C LYS* 1.3 69.1 + - - +
211C HIS* 2.8 22.1 + - - +
212C GLU* 3.0 16.8 + - - +
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Residues in contact with LYS 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 4.9 2.7 - - - -
209A LYS* 4.6 3.4 - - - +
212A GLU* 3.3 35.6 + - - -
157C ILE* 3.9 18.2 - - + -
189C LEU* 3.9 9.9 - - - +
205C TYR* 2.9 33.0 + - + +
206C VAL* 3.2 6.9 + - - +
208C ALA* 1.3 77.7 - - - +
210C PHE* 1.3 63.0 + - + +
212C GLU* 3.3 34.4 + - + +
213C GLU 4.0 3.6 + - - +
216C ILE* 5.0 1.5 - - + +
217C PHE* 3.4 35.9 - - + -
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Residues in contact with PHE 210 (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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157C ILE* 3.9 18.8 - - + -
206C VAL* 3.0 31.4 + - + -
207C ALA 2.9 7.7 + - - +
208C ALA 2.9 0.8 - - - -
209C LYS* 1.3 77.0 - - + +
211C HIS* 1.3 66.4 + - - +
213C GLU 2.9 23.6 - - - +
214C ALA* 4.1 2.1 + - - -
217C PHE* 3.4 41.5 - + + -
219C LEU 5.0 2.0 - - - -
220C LEU* 4.5 9.2 - - + -
256C ILE* 3.5 33.2 - - + -
260C TYR* 3.6 36.0 - + + -
262C VAL* 3.7 22.2 - - + -
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Residues in contact with HIS 211 (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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207C ALA 3.0 7.6 + - - +
208C ALA* 2.8 14.8 + - - +
210C PHE* 1.3 77.2 - - - +
212C GLU* 1.3 64.8 + - + +
213C GLU* 3.0 4.5 + - - -
214C ALA* 4.5 0.7 + - - +
259C GLU* 4.9 6.5 - - - -
260C TYR* 2.9 30.5 + + - +
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Residues in contact with GLU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 3.9 20.8 - - - +
205A TYR* 2.8 31.8 + - + +
209A LYS* 2.7 34.2 + - - -
208C ALA* 3.0 15.0 + - + +
209C LYS* 3.5 23.4 + - + +
210C PHE 3.1 0.8 - - - -
211C HIS* 1.3 76.3 - - + +
213C GLU* 1.3 63.6 + - + +
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Residues in contact with GLU 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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209C LYS 4.0 1.8 + - - -
210C PHE* 2.9 16.4 + - - +
211C HIS 3.8 1.8 - - - -
212C GLU* 1.3 82.8 - - + +
214C ALA* 1.3 64.8 + - - +
215C GLY 3.7 1.2 + - - -
216C ILE* 2.8 56.8 - - + +
217C PHE 5.1 0.2 + - - -
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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
------------------------------------------------------------
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