Contacts of the helix formed by residues 188 - 206 (chain A) in PDB entry 3N9Z
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 188 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLN* 4.6 11.4 + - - +
181A GLY 5.1 1.4 + - - -
182A MET* 4.1 7.9 - - - -
186A VAL 4.3 0.4 + - - -
187A VAL* 1.3 78.9 - - - +
189A PRO* 1.4 69.1 - - - +
190A GLU* 3.0 24.1 + - - +
191A ALA* 3.2 23.0 + - + +
192A GLN 3.1 17.7 + - - -
241A TYR* 5.5 2.4 + - - -
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Residues in contact with PRO 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A VAL* 3.1 14.5 - - + +
188A ASN* 1.4 87.4 - - - +
190A GLU* 1.3 70.3 + - + +
191A ALA 3.4 0.2 - - - -
192A GLN* 3.5 9.3 + - + +
193A ARG* 3.0 28.1 + - - +
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Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ASN* 3.0 12.0 + - - +
189A PRO* 1.3 85.1 - - + +
191A ALA* 1.3 64.5 + - - +
193A ARG* 3.2 25.2 + - - -
194A PHE 3.3 15.1 + - - -
237A LYS* 2.7 47.6 + - - +
241A TYR* 5.2 1.3 - - - -
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Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 3.9 18.1 - - + -
180A GLN* 5.4 2.5 - - + -
182A MET* 3.5 30.3 - - + -
188A ASN* 3.2 16.0 + - + +
190A GLU* 1.3 76.2 - - - +
192A GLN* 1.3 63.8 + - - +
194A PHE* 3.1 9.3 + - - +
195A ILE* 3.1 24.1 + - - +
241A TYR* 3.9 16.7 + - - +
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Residues in contact with GLN 192 (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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161A ASP* 5.6 1.4 + - - +
164A PHE* 5.9 0.4 - - - +
165A ARG* 2.9 41.5 + - - +
182A MET* 3.6 8.4 - - + +
187A VAL* 4.2 8.8 - - + +
188A ASN 3.1 13.6 + - - +
189A PRO* 3.6 12.6 - - + +
190A GLU 3.3 0.2 - - - -
191A ALA* 1.3 76.6 - - - +
193A ARG* 1.3 55.8 + - - +
195A ILE* 3.3 21.4 + - - +
196A ASP* 3.0 63.5 + - - +
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Residues in contact with ARG 193 (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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189A PRO 3.0 13.8 + - - +
190A GLU* 3.2 34.2 + - - +
192A GLN* 1.3 73.6 - - - +
194A PHE* 1.3 64.1 + - - +
196A ASP* 3.6 9.2 + - + +
197A ALA* 3.1 24.1 + - - +
233A VAL* 3.8 29.8 - - - +
236A SER* 6.4 0.4 - - - -
237A LYS* 3.8 20.1 - - - +
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Residues in contact with PHE 194 (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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168A PHE* 3.4 33.4 - + + -
190A GLU 3.3 3.9 + - - +
191A ALA* 3.1 12.8 + - - +
193A ARG* 1.3 76.1 - - - +
195A ILE* 1.3 64.8 + - - +
197A ALA* 3.3 3.6 + - - +
198A ILE* 3.0 49.4 + - + +
233A VAL* 4.3 3.8 - - - -
234A ILE* 3.4 43.7 - - + -
237A LYS* 3.7 36.0 - - + +
238A ALA* 4.4 9.0 - - + -
241A TYR* 5.3 4.7 - + - +
282A THR 5.2 0.2 - - - -
285A LEU* 3.9 32.3 - - + -
286A ALA 4.5 0.2 - - - -
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Residues in contact with ILE 195 (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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164A PHE* 3.7 28.9 - - + -
165A ARG* 4.0 28.9 - - + -
168A PHE* 3.7 40.4 - - + -
182A MET* 4.0 11.4 - - + -
191A ALA 3.1 13.6 + - - +
192A GLN* 3.3 20.4 + - - +
194A PHE* 1.3 74.8 - - - +
196A ASP* 1.3 64.5 + - - +
198A ILE* 3.3 19.8 + - - +
199A TYR* 3.4 11.8 + - + +
289A VAL* 4.1 10.8 - - + +
290A ASP* 4.8 1.0 - - - +
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Residues in contact with ASP 196 (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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192A GLN* 3.0 44.2 + - - +
193A ARG* 4.0 9.3 - - + +
194A PHE 3.4 0.4 - - - -
195A ILE* 1.3 76.3 - - - +
197A ALA* 1.3 56.7 + - - +
199A TYR* 3.4 9.3 + - - +
200A GLN* 3.0 33.2 + - + +
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Residues in contact with ALA 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 ARG 3.1 18.6 + - - +
194A PHE 3.3 5.8 + - - +
196A ASP* 1.3 73.1 - - - +
198A ILE* 1.3 55.3 + - - +
200A GLN* 3.2 6.4 + - - -
201A MET* 2.7 36.2 + - - +
230A ALA* 3.5 22.8 - - - +
233A VAL* 3.6 24.5 - - + -
234A ILE* 4.3 5.8 - - + -
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Residues in contact with ILE 198 (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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194A PHE* 3.0 47.2 + - + +
195A ILE* 3.5 6.5 - - - +
196A ASP 3.3 0.2 - - - -
197A ALA* 1.3 77.6 - - - +
199A TYR* 1.3 63.4 + - - +
201A MET* 3.3 4.1 + - + +
202A PHE* 3.3 32.0 + - + -
234A ILE* 4.2 18.4 - - + -
286A ALA* 3.8 31.4 - - + +
289A VAL* 3.5 26.2 - - + -
290A ASP* 3.8 22.2 - - - +
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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
----------------------------------------------------------
164A PHE* 4.4 21.1 - + + -
195A ILE* 3.4 8.2 + - + +
196A ASP* 3.4 10.9 + - - +
197A ALA 3.3 0.4 - - - -
198A ILE* 1.3 77.6 - - - +
200A GLN* 1.3 77.2 + - - +
202A PHE* 3.4 4.3 + - - +
203A HIS* 3.0 46.2 + + + +
290A ASP* 3.3 17.7 + - - +
459A ASN* 4.1 14.3 + - + -
463A MET* 3.4 36.1 - - + +
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Residues in contact with GLN 200 (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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196A ASP* 3.0 21.2 + - + +
197A ALA* 3.2 9.4 + - - +
199A TYR* 1.3 94.3 - - - +
201A MET* 1.3 54.6 + - - +
203A HIS* 4.4 11.9 - - - +
204A THR* 2.7 58.4 + - + +
226A ASP* 5.4 2.3 - - - +
230A ALA* 4.0 11.9 - - + -
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Residues in contact with MET 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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87A TRP* 3.2 43.3 - - + -
197A ALA 2.7 20.3 + - - +
198A ILE* 3.3 5.6 + - + +
200A GLN* 1.3 74.7 - - - +
202A PHE* 1.3 74.0 + - + +
204A THR* 3.8 4.0 - - - -
205A SER* 2.6 27.7 + - - -
227A HIS* 3.3 10.8 - - + -
230A ALA* 3.6 9.1 - - + +
231A TRP* 3.4 53.6 - - + +
234A ILE* 3.8 14.4 - - + -
286A ALA* 5.4 2.7 - - + -
602A HC9 4.0 13.0 - - + -
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Residues in contact with PHE 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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87A TRP* 3.6 34.5 - + - -
198A ILE* 3.3 34.7 + - + -
199A TYR 3.7 5.8 - - - +
201A MET* 1.3 81.0 - - + +
203A HIS* 1.3 66.3 + - - +
205A SER* 3.1 19.9 + - - -
206A VAL* 3.9 2.3 + - - +
286A ALA 4.6 3.6 - - - -
290A ASP* 3.7 23.8 - - + +
291A THR* 5.6 2.7 - - + -
459A ASN* 3.6 14.8 - - + +
460A LEU* 3.5 27.8 - - + +
461A ILE* 4.1 24.9 - - + -
463A MET* 5.8 2.2 - - + -
602A HC9 3.6 33.7 - - + -
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Residues in contact with HIS 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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33A HIS* 4.8 11.4 - + - -
199A TYR* 3.0 38.4 + + + +
200A GLN* 4.0 16.2 - - - +
202A PHE* 1.3 75.5 - - - +
204A THR* 1.3 67.7 + - + +
205A SER 3.2 0.9 + - - -
206A VAL* 3.4 16.1 + - - +
207A PRO* 3.7 7.4 - - - +
459A ASN* 3.3 41.0 + - + +
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Residues in contact with THR 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 GLN* 2.7 45.2 + - + +
203A HIS* 1.3 76.6 - - + +
205A SER* 1.3 62.6 + - - +
206A VAL 3.3 0.2 - - - -
207A PRO* 3.5 3.3 - - - +
208A MET* 4.1 5.2 - - - +
223A THR* 3.1 32.6 - - + +
226A ASP* 3.9 27.8 - - + +
227A HIS* 2.9 40.7 + - - +
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Residues in contact with SER 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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84A ILE* 4.8 0.4 - - - -
86A PRO* 4.2 12.3 - - - +
87A TRP* 2.9 23.1 + - - -
201A MET 2.6 21.5 + - - -
202A PHE 3.1 5.2 + - - -
204A THR* 1.3 79.4 - - - +
206A VAL* 1.3 64.3 + - - +
208A MET* 3.2 14.2 + - - +
209A LEU* 3.4 13.5 + - - +
227A HIS* 3.2 8.4 - - - -
460A LEU* 3.0 31.1 - - - +
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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
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32A THR* 3.8 28.1 - - + +
33A HIS* 3.7 28.0 - - + +
202A PHE 3.9 2.0 - - - +
203A HIS 3.7 10.3 - - - +
204A THR 3.3 0.2 - - - -
205A SER* 1.3 75.8 - - - +
207A PRO* 1.3 70.4 - - + +
208A MET 2.9 2.1 + - - -
209A LEU* 3.1 22.2 + - - +
458A PHE* 3.9 18.2 - - + +
459A ASN* 3.6 14.6 - - - -
460A LEU* 3.3 31.4 - - - +
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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