Contacts of the helix formed by residues 195 - 213 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ALA 3.7 0.4 - - - -
194A TYR* 1.3 87.1 + - + +
196A SER* 1.3 58.2 + - - +
197A GLU* 3.3 7.4 + - - +
198A HIS* 2.9 26.3 + - + +
199A GLN 2.9 24.1 + - - -
228A LEU* 3.3 19.5 - - - +
232A ASP* 3.8 15.7 - - - +
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Residues in contact with SER 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A THR* 1.3 70.6 - - - +
197A GLU* 1.3 72.6 + - - +
199A GLN* 3.1 15.0 + - - +
200A MET* 3.3 13.0 + - - +
228A LEU* 3.1 30.2 + - - +
229A PHE* 3.4 37.4 - - - -
232A ASP* 3.0 20.6 + - - -
233A PHE* 4.1 8.3 - - - -
245A LYS* 6.3 0.9 - - - -
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Residues in contact with GLU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A THR* 3.3 6.8 + - - +
196A SER* 1.3 81.9 - - - +
198A HIS* 1.3 67.1 + - - +
200A MET* 2.9 17.6 + - - +
201A GLU* 2.9 25.8 + - - +
232A ASP* 5.3 2.2 - - - +
233A PHE* 6.4 1.6 - - + -
245A LYS* 3.9 25.7 + - + +
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Residues in contact with HIS 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ARG 3.4 15.3 + - - -
193A ALA* 3.4 8.3 - - + -
194A TYR* 3.0 41.9 - + + -
195A THR* 2.9 26.6 + - + +
197A GLU* 1.3 76.0 - - - +
199A GLN* 1.3 63.1 + - - +
201A GLU* 3.1 24.0 + - + +
202A LEU* 3.0 45.7 + - + +
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Residues in contact with GLN 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 5.0 7.4 - - + -
161A THR* 3.7 12.5 - - + +
193A ALA* 3.9 18.6 - - + -
195A THR 2.9 12.0 + - - +
196A SER 3.1 9.8 + - - +
198A HIS* 1.3 76.5 - - - +
200A MET* 1.3 62.1 + - - +
202A LEU* 3.3 13.5 + - - +
203A LEU* 3.4 18.2 + - + +
222A ILE* 4.1 12.8 - - + +
224A SER 4.4 0.2 + - - -
225A ILE 2.7 30.2 + - - +
228A LEU* 3.4 31.5 - - - +
229A PHE* 3.7 10.0 - - - -
249A MET* 3.2 20.6 - - - +
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Residues in contact with MET 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A SER 3.3 9.3 + - - +
197A GLU* 2.9 10.4 + - - +
199A GLN* 1.3 79.8 - - - +
201A GLU* 1.3 61.2 + - - +
203A LEU* 3.2 28.9 + - - +
204A ASP* 3.4 17.0 + - - +
229A PHE* 5.5 2.5 - - + -
245A LYS* 5.8 4.9 - - + +
248A GLN* 4.0 13.7 - - + -
249A MET* 3.6 42.8 - - + +
252A ARG* 3.4 33.0 - - + +
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Residues in contact with GLU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLU* 2.9 24.7 + - + +
198A HIS* 3.5 26.4 + - - +
200A MET* 1.3 77.0 - - - +
202A LEU* 1.3 61.6 + - + +
204A ASP* 3.4 11.7 + - - +
205A TYR* 3.4 19.2 + - - +
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 3.8 26.7 - - + -
191A ALA* 4.0 20.6 - - + -
192A ARG 3.8 12.1 - - - +
193A ALA* 3.7 30.1 - - + -
198A HIS* 3.0 34.6 + - + +
199A GLN* 3.4 8.5 - - - +
200A MET 3.2 0.2 - - - -
201A GLU* 1.3 76.4 - - + +
203A LEU* 1.3 61.4 + - - +
205A TYR* 3.4 11.2 + - + +
206A VAL* 2.9 32.6 + - + +
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 3.6 27.6 - - + -
199A GLN* 3.4 14.1 + - + +
200A MET* 3.2 17.3 + - - +
202A LEU* 1.3 75.5 - - - +
204A ASP* 1.3 58.2 + - - +
206A VAL* 3.1 6.2 + - + +
207A ALA* 2.7 36.8 + - - +
220A LEU* 4.7 8.5 - - + -
222A ILE* 4.6 12.3 - - + -
249A MET* 3.5 37.2 - - + +
252A ARG* 5.3 4.7 - - + +
253A LEU* 4.4 15.5 - - + -
256A ILE* 4.0 18.2 - - + +
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Residues in contact with ASP 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A MET* 3.4 21.7 + - - +
201A GLU* 3.4 12.8 + - - +
202A LEU 3.2 0.4 - - - -
203A LEU* 1.3 79.5 - - - +
205A TYR* 1.3 65.2 + - - +
207A ALA* 3.3 7.0 + - - +
208A ALA* 3.1 23.2 + - - +
252A ARG* 3.9 23.6 + - - +
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Residues in contact with TYR 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 6.1 2.0 - - + -
189A LEU* 6.4 0.7 - - + -
201A GLU 3.4 10.2 + - - +
202A LEU* 3.5 14.8 - - + +
203A LEU 3.2 0.2 - - - -
204A ASP* 1.3 79.7 - - - +
206A VAL* 1.3 68.3 + - + +
208A ALA* 3.2 4.8 + - - +
209A LYS* 2.9 35.8 + - + +
205C TYR* 3.8 30.6 + + - -
208C ALA* 3.3 34.5 + - + +
209C LYS* 4.9 2.5 - - - -
212C GLU* 2.8 45.1 + - + +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 3.8 28.9 - - + -
159A ILE* 4.4 12.8 - - + -
202A LEU* 2.9 22.8 + - + +
203A LEU* 3.4 10.3 - - + +
205A TYR* 1.3 74.8 - - + +
207A ALA* 1.3 69.0 + - - +
209A LYS* 3.0 9.6 + - - +
210A PHE* 2.9 55.5 + - + -
220A LEU* 4.4 15.3 - - + -
256A ILE* 4.7 5.8 - - + -
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU 2.7 19.2 + - - +
204A ASP 3.5 5.8 - - - +
205A TYR 3.3 0.2 - - - -
206A VAL* 1.3 76.2 - - - +
208A ALA* 1.3 63.0 + - - +
210A PHE* 3.1 6.6 + - - +
211A HIS* 3.1 19.8 + - - +
252A ARG* 3.6 24.7 - - - +
256A ILE* 4.0 15.9 - - + -
260A TYR* 3.8 17.1 + - + +
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ASP 3.1 15.9 + - - +
205A TYR 3.9 0.2 - - - +
207A ALA* 1.3 73.6 - - - +
209A LYS* 1.3 67.0 + - - +
211A HIS* 3.1 9.7 + - - +
212A GLU* 3.1 25.1 + - - +
205C TYR* 3.5 30.7 - - + -
84D GLY 4.1 15.2 + - - +
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Residues in contact with LYS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 4.0 16.8 - - + -
189A LEU* 5.2 6.7 - - - +
205A TYR* 2.9 31.8 + - + +
206A VAL* 3.0 10.5 + - - +
208A ALA* 1.3 78.0 - - - +
210A PHE* 1.3 61.8 + - - +
212A GLU* 3.1 24.3 + - + +
213A GLU 3.8 4.9 + - - +
216A ILE* 5.1 3.4 - - + +
217A PHE* 3.7 35.8 - - + -
205C TYR* 4.0 11.8 + - - +
209C LYS* 4.6 9.7 - - - +
212C GLU* 2.7 37.8 + - - -
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Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ILE* 3.6 22.2 - - + -
206A VAL* 2.9 34.9 + - + -
207A ALA* 3.5 7.4 - - - +
209A LYS* 1.3 77.9 - - - +
211A HIS* 1.3 61.4 + - - +
213A GLU 3.1 23.3 - - - +
214A ALA* 3.8 6.4 + - - +
217A PHE* 3.3 38.8 - + + -
219A LEU 4.6 5.2 - - - -
220A LEU* 4.5 14.6 - - + -
256A ILE* 3.8 23.6 - - + -
260A TYR* 3.7 27.0 - + + -
262A VAL* 3.6 32.5 - - + -
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Residues in contact with HIS 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ALA 3.1 7.4 + - - +
208A ALA* 3.6 10.8 - - - +
209A LYS 3.1 0.6 - - - -
210A PHE* 1.3 78.1 - - - +
212A GLU* 1.3 64.2 + - - +
213A GLU* 4.3 1.4 - - - -
214A ALA* 5.0 1.7 + - - +
260A TYR* 3.3 32.6 + - - +
84D GLY* 4.0 30.5 + - - -
85D PHE 4.1 15.1 + - - +
86D LEU* 5.9 2.2 - - - +
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA 3.1 7.9 + - - +
209A LYS* 3.1 19.4 + - + +
211A HIS* 1.3 79.4 - - - +
213A GLU* 1.3 64.1 + - + +
216A ILE* 6.1 0.9 - - + -
189C LEU* 3.8 21.2 - - - +
205C TYR* 3.2 34.1 + - + +
209C LYS* 3.3 30.4 + - - -
84D GLY 5.3 0.9 - - - +
85D PHE* 4.1 24.5 - - + +
86D LEU* 5.9 0.5 - - - -
90D GLU* 4.6 15.9 - - - +
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Residues in contact with GLU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LYS 3.8 2.1 + - - +
210A PHE* 3.1 13.3 + - - +
211A HIS 4.3 0.2 - - - -
212A GLU* 1.3 85.2 - - - +
214A ALA* 1.3 71.7 + - - +
215A GLY 3.8 0.5 + - - -
216A ILE* 3.0 52.7 - - + +
217A PHE 4.9 0.7 + - - -
90D GLU* 5.9 2.2 - - - +
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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