Contacts of the helix formed by residues 194 - 210 (chain A) in PDB entry 1QZW
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 GLU 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A HIS* 2.8 59.3 + - + +
191A GLY 2.5 22.8 + - - +
192A TYR* 2.8 24.7 + - - +
193A GLY* 1.3 68.3 - - - +
195A GLU* 1.3 67.0 + - - +
196A THR* 2.9 4.9 - - - -
197A LYS* 2.6 32.4 + - + +
198A LEU 3.0 3.6 + - - -
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Residues in contact with GLU 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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191A GLY 2.2 20.3 + - - +
192A TYR* 4.7 1.1 - - - -
193A GLY* 2.7 26.9 - - - +
194A GLU* 1.3 72.0 - - - +
196A THR* 1.3 62.5 + - - +
197A LYS 2.5 2.8 + - - -
198A LEU* 2.4 34.0 + - + -
199A LEU* 2.7 23.8 + - + +
228A ASP* 4.1 6.5 - - - +
229A LEU* 3.3 40.0 + - + +
232A ARG* 3.0 33.9 + - - +
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Residues in contact with THR 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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193A GLY 3.1 12.8 + - - -
194A GLU* 3.9 2.8 - - - -
195A GLU* 1.3 74.3 - - - +
197A LYS* 1.3 71.6 + - + +
199A LEU* 3.3 16.0 - - + +
200A GLU* 2.8 27.7 + - - +
232A ARG* 2.5 38.0 + - - +
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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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190A HIS* 3.8 13.2 - - + +
194A GLU* 2.6 32.0 + - + +
195A GLU 2.5 4.2 + - - -
196A THR* 1.3 81.0 - - - +
198A LEU* 1.3 68.2 + - - +
200A GLU* 2.8 34.8 + - - +
201A GLU* 2.7 26.8 + - + +
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Residues in contact with LEU 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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102A VAL* 6.0 3.1 - - + -
103A GLY 3.3 22.9 - - - +
104A VAL* 3.3 43.7 - - + +
187A ALA* 4.5 1.8 - - - -
188A GLY 4.0 12.8 - - - +
190A HIS 3.3 6.8 + - - +
191A GLY* 4.0 13.7 - - - -
194A GLU 3.0 4.4 + - - -
195A GLU* 2.4 27.4 + - + +
197A LYS* 1.3 65.7 - - - +
199A LEU* 1.3 58.2 + - + +
201A GLU* 2.5 56.1 + - - +
202A MET* 3.0 3.6 + - - +
205A MET* 4.7 0.2 - - - +
216A LEU* 5.4 5.6 - - + -
229A LEU* 4.5 8.7 - - + -
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Residues in contact with LEU 199 (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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195A GLU* 2.7 43.7 - - + +
196A THR* 3.3 22.7 - - + +
198A LEU* 1.3 80.3 - - + +
200A GLU* 1.3 57.4 + - - +
202A MET* 2.6 23.4 + - + +
203A LYS* 2.6 34.9 + - - -
229A LEU 5.4 1.1 - - - +
232A ARG* 3.7 35.0 - - + +
233A PHE* 5.7 3.6 - - + -
236A ALA* 5.5 8.1 - - + -
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Residues in contact with GLU 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 THR* 2.8 19.9 + - - +
197A LYS* 2.8 47.4 + - - +
199A LEU* 1.3 79.2 - - - +
201A GLU* 1.3 58.3 + - + +
203A LYS* 2.8 35.7 - - + +
204A GLU* 4.2 3.3 + - - +
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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
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135A TYR* 3.0 14.3 + - - +
187A ALA 4.2 0.6 - - - -
188A GLY* 2.8 44.6 + - - +
189A ARG* 3.4 5.0 + - - +
190A HIS 4.0 2.8 - - - +
197A LYS* 2.7 15.4 + - + +
198A LEU* 2.5 38.7 + - - +
200A GLU* 1.3 72.1 - - + +
202A MET* 1.3 53.5 + - - +
203A LYS 2.5 15.5 + - - -
204A GLU* 3.1 14.2 + - - +
205A MET* 2.8 33.7 + - + +
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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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100A MET* 4.0 11.0 - - - -
102A VAL* 3.2 37.2 - - + -
198A LEU 3.0 2.9 + - - +
199A LEU* 2.6 26.3 + - + +
201A GLU* 1.3 71.8 - - - +
203A LYS* 1.3 80.5 + - - +
205A MET* 2.7 20.0 - - - -
206A TYR* 2.4 39.2 + - + -
214A VAL* 5.4 3.4 - - - -
233A PHE* 5.2 11.4 - - - -
236A ALA* 5.0 19.1 - - + -
237A SER* 5.9 2.7 - - - -
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Residues in contact with LYS 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 LEU 2.6 9.2 + - - +
200A GLU* 2.8 32.1 - - + +
201A GLU 2.5 3.6 + - - -
202A MET* 1.3 91.3 - - - +
204A GLU* 1.3 74.5 + - + +
206A TYR* 2.7 4.9 + - - +
207A ASP* 2.8 18.3 + - + +
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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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164A ILE* 4.2 23.5 - - + +
200A GLU 5.0 2.5 - - - +
201A GLU* 3.1 6.4 + - - +
203A LYS* 1.3 88.6 - - + +
205A MET* 1.3 70.4 + - + +
206A TYR 2.6 0.7 + - - -
207A ASP* 2.8 11.6 + - - -
208A VAL* 2.6 34.9 - - + +
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Residues in contact with MET 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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100A MET* 2.9 22.7 - - + +
135A TYR* 4.5 6.3 - - + +
163A PRO* 4.9 20.4 - - + -
164A ILE* 5.6 6.5 - - + +
186A THR* 3.6 24.7 - - + +
187A ALA* 3.2 29.8 - - - +
198A LEU 4.7 0.4 - - - +
201A GLU* 2.8 34.3 - - + +
202A MET* 2.7 38.6 - - + +
204A GLU* 1.3 80.0 - - + +
206A TYR* 1.3 60.2 + - - +
208A VAL* 2.6 23.5 - - - +
209A LEU* 3.5 5.0 - - - +
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Residues in contact with TYR 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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100A MET* 3.2 17.2 - - - +
202A MET* 2.4 48.2 + - + +
203A LYS 3.3 1.8 - - - +
204A GLU 2.6 4.8 + - - -
205A MET* 1.3 62.6 - - - +
207A ASP* 1.3 80.6 + - + +
208A VAL 2.6 15.6 + - - -
209A LEU 2.8 13.2 + - - -
210A LYS* 3.0 19.4 + - + -
211A PRO* 3.3 40.7 + - + +
214A VAL* 3.8 19.7 - - + -
237A SER* 3.9 20.8 + - - -
239A ILE* 4.2 14.2 - - + +
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Residues in contact with ASP 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 LYS* 2.8 12.4 + - + +
204A GLU* 2.8 11.1 + - - +
206A TYR* 1.3 86.2 - - + +
208A VAL* 1.3 70.0 + - - +
210A LYS* 2.7 33.5 + - - +
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Residues in contact with VAL 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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164A ILE* 5.2 21.5 - - + -
168A LYS* 5.4 8.1 + - - +
204A GLU* 2.6 46.0 - - + +
205A MET* 2.6 25.8 - - - +
206A TYR 2.6 0.8 + - - -
207A ASP* 1.3 83.0 - - - +
209A LEU* 1.3 72.4 + - + +
210A LYS* 2.7 18.4 - - - +
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Residues in contact with LEU 209 (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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98A ILE* 3.3 40.6 - - + -
100A MET* 3.6 18.2 - - + -
167A ALA* 6.3 3.6 - - + -
168A LYS* 5.9 6.7 - - + -
171A VAL* 5.4 17.7 - - + -
205A MET 3.5 11.7 - - - +
206A TYR 2.8 1.4 + - - +
208A VAL* 1.3 81.3 - - + +
210A LYS* 1.3 86.2 + - - +
211A PRO* 3.3 16.8 - - + -
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Residues in contact with LYS 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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98A ILE* 2.8 22.5 - - - +
206A TYR* 3.0 8.2 + - + +
207A ASP* 2.7 35.4 + - - +
208A VAL* 2.7 33.8 - - - +
209A LEU* 1.3 83.7 - - - +
211A PRO* 1.3 67.1 - - - +
212A ASP* 3.7 3.1 - - - +
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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