Contacts of the helix formed by residues 188 - 207 (chain A) in PDB entry 4II9
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 188 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ASN* 1.3 77.6 - - - +
189A ALA* 1.3 63.8 + - - +
190A THR* 3.2 17.3 + - - -
191A GLU* 2.4 27.3 + - - -
192A LEU 3.1 14.0 + - - -
220A GLN* 3.1 16.4 - - - +
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Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A SER* 1.3 74.5 - - - +
190A THR* 1.4 57.8 - - - +
192A LEU* 3.8 4.1 - - - +
193A ASP* 2.9 39.2 + - - +
220A GLN* 3.7 12.7 - - - +
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Residues in contact with THR 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A HIS* 6.0 0.4 - - - +
188A SER* 3.1 12.2 + - - -
189A ALA* 1.4 78.6 - - - +
191A GLU* 1.3 67.5 + - + +
193A ASP* 3.3 8.8 + - - +
194A GLU* 3.2 36.9 + - + +
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A HIS* 4.2 16.5 - - + -
185A SER 3.6 6.8 - - - +
186A GLY* 3.5 33.6 - - - +
188A SER* 2.4 43.2 + - - +
190A THR* 1.3 75.9 - - + +
192A LEU* 1.3 60.7 + - - +
194A GLU* 3.3 18.2 + - - +
195A PHE* 2.9 29.1 + - - +
230A ILE* 3.7 26.6 - - + +
232A VAL* 4.2 6.4 - - + +
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A SER 3.1 17.1 + - - +
189A ALA* 3.8 6.3 - - - +
190A THR 3.3 0.2 - - - -
191A GLU* 1.3 77.4 - - - +
193A ASP* 1.4 57.5 + - - +
195A PHE* 3.3 16.6 + - + -
196A PHE* 2.8 26.9 + - - +
213A ILE* 4.4 15.5 - - + -
216A PHE* 3.5 26.2 - - + +
217A GLN* 3.6 44.9 - - + +
220A GLN* 3.9 20.0 - - - +
228A MET* 5.5 0.7 - - + -
230A ILE* 3.8 14.7 - - + +
244A ILE* 5.0 1.3 - - + -
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Residues in contact with ASP 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA* 2.9 27.2 + - - +
190A THR* 3.3 6.9 + - - +
192A LEU* 1.4 77.1 - - - +
194A GLU* 1.3 62.1 + - + +
196A PHE* 3.2 5.1 + - - +
197A LYS* 3.1 23.2 + - - +
213A ILE* 3.8 19.8 - - - +
217A GLN* 5.9 0.3 + - - -
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Residues in contact with GLU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A HIS* 3.0 26.1 + - - -
190A THR* 3.2 22.6 + - + +
191A GLU* 3.3 21.4 + - - +
193A ASP* 1.3 72.6 - - + +
195A PHE* 1.4 68.4 + - - +
196A PHE 3.3 0.2 + - - -
197A LYS* 3.4 2.7 + - - -
198A THR* 3.2 24.8 + - - +
232A VAL* 3.6 20.5 - - + +
234A GLU* 3.6 16.3 - - - +
239A LEU* 3.8 20.5 - - + +
242A THR* 4.0 2.7 - - - -
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Residues in contact with PHE 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLU 2.9 15.2 + - - +
192A LEU* 3.6 20.9 - - + +
194A GLU* 1.4 76.2 - - - +
196A PHE* 1.4 62.6 + - + +
198A THR* 2.8 5.7 + - - -
199A TYR* 2.8 65.8 + + + +
216A PHE* 3.7 28.5 - + - -
230A ILE* 3.8 14.1 - - + -
242A THR* 3.4 27.8 - - - +
243A GLY 4.9 0.9 - - - -
244A ILE* 3.7 36.6 - - + -
256A TYR* 3.8 20.0 - - + -
257A ALA* 4.0 14.1 - - - -
258A GLY 4.6 0.2 - - - -
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Residues in contact with PHE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 2.8 20.6 + - + +
193A ASP* 3.2 4.4 + - - +
195A PHE* 1.4 78.5 - + + +
197A LYS* 1.4 57.2 + - - +
199A TYR* 3.9 14.6 - + - -
200A THR* 2.9 61.5 + - + +
210A HIS* 5.5 2.2 - + - -
211A ARG 3.5 18.2 - - - -
212A PRO* 4.0 2.7 - - + -
213A ILE* 3.5 65.3 - - + -
216A PHE* 4.4 7.4 - + - -
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Residues in contact with LYS 197 (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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193A ASP 3.1 15.3 + - - +
194A GLU* 3.8 4.9 - - - +
195A PHE 3.3 0.2 - - - -
196A PHE* 1.4 77.6 - - - +
198A THR* 1.4 55.9 + - - +
200A THR* 3.4 6.2 + - - -
201A THR* 2.7 35.8 + - - +
239A LEU* 4.5 14.4 - - + -
260A MET* 4.1 26.2 - - + -
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Residues in contact with THR 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLU 3.2 12.5 + - - +
195A PHE 2.8 11.7 + - - -
197A LYS* 1.4 76.7 - - - +
199A TYR* 1.4 57.2 + - - +
202A MET* 3.0 22.9 + - - +
239A LEU* 3.8 26.2 - - + -
241A SER* 4.4 7.2 - - - -
242A THR* 2.7 34.4 + - + -
258A GLY* 3.4 18.4 - - - -
259A SER* 3.3 14.6 + - - +
260A MET* 3.9 19.1 - - + -
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Residues in contact with TYR 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A PHE* 2.8 39.9 + + + +
196A PHE* 3.5 23.8 - + - +
198A THR* 1.4 73.5 + - - +
200A THR* 1.3 67.6 + - + +
202A MET* 3.4 29.0 + - + +
203A ALA* 3.0 23.9 + - - +
209A THR 4.8 1.1 + - - -
210A HIS* 3.5 14.7 - - + -
211A ARG* 2.9 53.3 + - - +
216A PHE* 3.6 16.9 - + - -
256A TYR* 4.0 22.0 - + - -
257A ALA 3.7 6.7 - - - -
258A GLY* 4.0 7.4 - - - -
102B MUB 5.0 1.0 - - - +
10C A9Z 6.1 0.2 - - - -
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Residues in contact with THR 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 2.9 61.2 + - + +
197A LYS* 3.4 8.8 + - - +
199A TYR* 1.3 80.4 - - + +
201A THR* 1.3 64.7 + - - +
203A ALA* 3.9 6.2 - - - +
204A GLU* 3.2 23.6 + - - +
210A HIS* 4.6 15.6 - - + +
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Residues in contact with THR 201 (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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197A LYS* 2.7 27.2 + - - +
198A THR 3.8 4.0 - - - -
199A TYR 3.2 0.2 - - - -
200A THR* 1.3 80.1 + - - +
202A MET* 1.3 64.0 + - - +
204A GLU* 3.4 7.6 + - - +
205A ARG* 3.0 27.7 + - - +
259A SER 4.0 2.2 - - - +
260A MET* 3.6 24.6 - - + +
261A ASP* 3.5 37.8 - - - +
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Residues in contact with MET 202 (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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198A THR 3.0 18.4 + - - +
199A TYR* 3.7 34.3 - - + +
201A THR* 1.3 77.4 - - - +
203A ALA* 1.3 63.2 + - + +
205A ARG* 3.1 23.9 + - - +
206A HIS* 2.9 43.5 + - + -
208A ILE* 3.8 15.0 - - + -
209A THR 5.8 0.9 - - - +
257A ALA 3.7 14.6 - - - +
258A GLY* 4.0 3.4 - - - -
259A SER 3.7 5.6 + - - +
10C A9Z 3.3 53.2 - - - +
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Residues in contact with ALA 203 (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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199A TYR 3.0 18.2 + - - +
200A THR 3.9 4.3 - - - +
201A THR 3.2 0.6 - - - -
202A MET* 1.3 86.4 - - + +
204A GLU* 1.3 58.8 + - - +
207A GLY* 2.9 24.3 + - - -
208A ILE* 3.0 36.1 + - + +
209A THR 4.5 0.2 - - - +
210A HIS* 3.7 31.0 - - + +
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Residues in contact with GLU 204 (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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200A THR 3.2 15.9 + - - +
201A THR* 3.7 6.6 - - - +
203A ALA* 1.3 79.9 - - - +
205A ARG* 1.3 62.9 + - - +
207A GLY* 3.3 11.1 + - - -
210A HIS* 5.5 1.3 + - - -
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Residues in contact with ARG 205 (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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201A THR* 3.0 18.5 + - - +
202A MET* 3.6 16.4 - - - +
204A GLU* 1.3 78.7 - - - +
206A HIS* 1.3 73.2 + - - +
207A GLY 3.5 0.5 + - - -
259A SER* 2.8 47.4 + - - -
260A MET 3.4 11.6 + - - -
261A ASP* 2.9 35.8 + - - +
262A GLY 5.5 1.6 - - - +
9C C 5.3 9.4 + - - -
10C A9Z 3.1 17.8 + - - -
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Residues in contact with HIS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A MET* 2.9 40.1 + - + +
205A ARG* 1.3 91.9 + - + +
207A GLY* 1.3 63.1 + - - +
208A ILE* 3.4 24.6 + - + +
9C C 3.1 41.3 + + - -
10C A9Z 2.6 46.5 + + + +
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Residues in contact with GLY 207 (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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203A ALA 2.9 7.6 + - - -
204A GLU* 3.3 8.3 + - - -
205A ARG 3.3 4.4 + - - -
206A HIS* 1.3 79.4 - - - +
208A ILE* 1.3 61.8 + - - +
4B FGA 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