Contacts of the helix formed by residues 190 - 209 (chain A) in PDB entry 5A6C
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 ASP 190 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A VAL* 3.3 13.0 + - + +
188A LEU* 3.0 7.0 + - + +
189A GLY* 1.3 73.0 - - - +
191A ARG* 1.3 64.5 + - - +
192A ALA* 3.6 12.8 + - - +
193A ALA* 3.6 23.9 + - + +
194A GLN* 3.2 24.0 + - - +
196A ARG* 5.1 2.6 + - - -
29B LYS* 3.6 32.2 + - + +
385B SER* 3.3 9.4 + - - -
387B ALA* 4.4 10.3 - - - +
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Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLY 4.2 2.9 - - - +
190A ASP* 1.3 73.2 + - - +
192A ALA* 1.3 60.5 + - - +
194A GLN* 3.1 31.2 + - - +
195A GLY 2.9 22.2 + - - -
198A PHE* 6.1 0.6 - - - -
223A LEU* 3.9 18.4 - - - +
224A ILE* 3.2 33.8 - - + +
227A GLU* 2.7 41.2 + - - +
228A PHE* 3.7 10.8 - - + -
92B LEU* 4.8 2.8 - - - +
132B VAL* 5.8 0.2 - - - +
136B ARG* 3.7 31.4 - - - +
382B GLU* 5.3 1.4 + - - -
383B ASP* 3.3 32.4 + - - +
385B SER* 2.8 20.6 + - - +
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ASP* 3.6 2.5 + - - +
191A ARG* 1.3 76.0 - - - +
193A ALA* 1.3 65.3 + - - +
195A GLY* 3.1 3.0 + - - +
196A ARG* 3.0 44.4 + - - +
221A ARG* 4.6 1.7 + - - -
224A ILE* 4.3 3.6 - - - -
228A PHE* 3.4 30.3 - - + -
387B ALA 4.2 19.3 - - - +
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TYR* 5.3 1.2 - - - -
181A ASN* 4.3 4.6 - - - +
185A VAL* 3.9 22.7 - - + -
190A ASP* 3.6 31.1 + - - +
192A ALA* 1.3 78.1 - - - +
194A GLN* 1.3 57.2 + - - +
196A ARG* 3.3 23.8 + - - +
197A ALA* 3.0 28.2 + - - +
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Residues in contact with GLN 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 3.9 9.8 - - + +
185A VAL* 2.8 38.4 + - + -
186A THR* 3.0 32.3 + - - +
189A GLY* 4.2 3.6 - - - -
190A ASP 3.2 17.9 + - - +
191A ARG* 3.1 43.9 + - - +
193A ALA* 1.3 76.9 - - - +
195A GLY* 1.3 65.6 + - - +
197A ALA* 3.2 3.3 + - - +
198A PHE* 2.9 32.7 + - + -
224A ILE* 3.8 7.5 - - + +
136B ARG* 5.6 1.3 + - - +
383B ASP* 5.4 1.2 + - - +
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Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ARG 2.9 12.1 + - - -
192A ALA 3.1 3.5 + - - -
194A GLN* 1.3 75.5 - - - +
196A ARG* 1.3 56.6 + - - +
198A PHE* 3.2 5.1 + - - +
199A GLY 3.0 22.9 + - - -
221A ARG* 3.1 38.3 - - - +
224A ILE* 3.5 18.2 - - - +
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Residues in contact with ARG 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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139A TYR* 3.7 28.9 + - + +
190A ASP* 5.1 2.8 + - - -
192A ALA* 3.0 30.4 + - - +
193A ALA* 3.3 32.7 - - - +
195A GLY* 1.3 74.3 - - - +
197A ALA* 1.3 65.5 + - - +
199A GLY 3.2 1.2 + - - -
200A ASN* 3.0 23.4 + - - +
221A ARG* 3.9 4.7 - - - +
377A GLU* 3.4 34.2 - - + +
378A GLU* 5.2 1.3 - - - -
387B ALA 5.4 3.6 + - - -
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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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139A TYR* 4.1 11.5 - - + -
178A TYR* 4.4 11.9 - - + +
181A ASN* 3.5 24.9 - - + +
182A LEU* 3.8 25.4 - - + -
193A ALA 3.0 10.3 + - - +
194A GLN 3.6 7.0 - - - +
196A ARG* 1.3 74.8 - - - +
198A PHE* 1.3 64.6 + - - +
200A ASN* 3.4 0.7 + - - +
201A LEU* 2.9 28.3 + - + +
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Residues in contact with PHE 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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182A LEU* 3.4 37.9 - - + -
186A THR* 5.8 1.1 - - - -
191A ARG* 6.1 0.4 - - - -
194A GLN* 2.9 31.2 + - + -
195A GLY* 3.5 6.7 - - - +
196A ARG 3.1 0.4 - - - -
197A ALA* 1.3 76.8 - - - +
199A GLY* 1.3 56.9 - - - +
201A LEU* 4.3 4.9 - - + -
202A GLY* 2.8 28.1 + - - -
216A ILE* 6.6 0.2 - - + -
217A ALA* 3.4 36.0 - - + +
218A HIS* 4.5 0.2 + - - -
220A GLN* 3.4 41.5 - - + -
221A ARG 3.9 5.6 - - - +
224A ILE* 3.9 19.1 - - + -
132B VAL* 5.2 7.4 - - + -
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Residues in contact with GLY 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 GLY 3.0 12.1 + - - -
196A ARG 3.2 2.9 + - - -
198A PHE* 1.3 75.9 - - - +
200A ASN* 1.3 64.7 + - - +
202A GLY 3.1 1.6 + - - -
203A ASN* 3.0 26.7 + - - +
218A HIS* 3.5 13.3 - - - -
221A ARG* 3.6 17.0 - - - +
240A ASN* 6.1 0.7 - - - -
375A TYR 5.9 0.7 - - - -
377A GLU* 4.3 11.4 - - - -
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Residues in contact with ASN 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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139A TYR* 3.1 15.5 + - - -
143A ASN* 2.9 26.9 + - - -
146A HIS* 4.0 7.4 - - + -
178A TYR* 3.4 27.3 + - + +
196A ARG 3.0 10.9 + - - +
197A ALA 4.2 0.2 - - - +
199A GLY* 1.3 76.5 - - - +
201A LEU* 1.3 57.8 + - - +
203A ASN* 4.8 3.4 - - - -
204A THR* 2.9 33.8 + - - -
376A ASN* 3.9 6.3 - - - +
377A GLU* 3.0 32.2 + - - +
378A GLU* 2.9 17.4 + - - +
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Residues in contact with LEU 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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175A VAL* 3.9 30.5 - - + +
178A TYR* 3.8 27.5 - - + +
179A GLU* 3.8 25.8 - - + +
182A LEU* 4.2 20.4 - - + -
197A ALA 2.9 19.9 + - - +
198A PHE* 3.7 8.5 - - + +
200A ASN* 1.3 77.0 - - - +
202A GLY* 1.3 65.8 + - - +
204A THR* 3.8 0.6 - - - -
205A HIS* 2.9 47.8 + - + +
217A ALA* 4.7 4.5 - - + -
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Residues in contact with GLY 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 PHE 2.8 14.6 + - - -
199A GLY 3.1 0.2 + - - -
201A LEU* 1.3 78.2 - - - +
203A ASN* 1.3 56.4 + - - +
205A HIS* 3.3 4.4 + - - +
206A TYR* 3.0 22.9 + - - +
214A ALA* 3.5 9.2 - - - +
217A ALA* 3.6 16.6 - - - +
218A HIS* 3.1 27.6 + - - -
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Residues in contact with ASN 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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146A HIS* 4.3 5.2 - - + +
150A LYS* 5.6 1.3 - - - +
199A GLY 3.0 13.8 + - - +
200A ASN 4.2 2.0 - - - +
202A GLY* 1.3 74.9 - - - +
204A THR* 1.3 59.8 + - - +
206A TYR* 3.1 12.9 + - + +
207A LEU* 2.9 33.4 + - + +
218A HIS* 3.3 15.9 + - - -
240A ASN* 3.1 20.4 + - - +
243A ASN* 5.7 0.2 + - - -
374A ALA* 4.4 11.3 - - + +
375A TYR 2.8 35.2 + - - +
376A ASN* 3.1 25.0 + - - +
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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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146A HIS* 3.1 24.7 + - - +
171A LEU* 3.3 25.8 - - + +
174A ALA* 4.4 2.9 - - + -
175A VAL* 3.3 31.2 - - + +
178A TYR* 3.8 7.4 - - - -
200A ASN 2.9 20.9 + - - -
201A LEU* 3.8 4.5 - - - -
203A ASN* 1.3 75.8 - - - +
205A HIS* 1.3 57.0 + - - +
207A LEU* 3.4 7.7 + - - +
208A LEU* 3.0 30.4 + - + +
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Residues in contact with HIS 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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175A VAL* 4.2 23.9 - - + +
179A GLU* 4.2 14.3 + - - -
201A LEU* 2.9 37.0 + - + +
202A GLY* 3.4 8.1 - - - +
204A THR* 1.3 75.7 - - - +
206A TYR* 1.3 57.2 + - - +
208A LEU* 3.1 3.2 + - - +
209A GLY 2.8 25.3 + - - -
210A ASN* 2.8 41.8 + - - +
213A ASP* 3.4 41.6 - - + +
214A ALA 3.8 3.6 - - - +
217A ALA* 4.8 1.6 - - + -
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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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157A PRO* 3.3 44.3 - - + +
202A GLY 3.0 12.4 + - - +
203A ASN* 3.1 20.6 + - + +
205A HIS* 1.3 76.7 - - - +
207A LEU* 1.3 78.4 + - + +
209A GLY 3.2 8.3 + - - -
211A PHE* 3.4 24.5 - + - -
214A ALA* 4.0 12.5 - - + +
218A HIS* 5.1 1.8 - - + +
240A ASN 5.2 1.6 - - - -
243A ASN* 3.5 34.9 - - + +
244A ALA* 4.2 11.4 - - + -
247A PHE* 3.7 20.5 - + - -
372A PHE* 3.7 20.8 + - - +
374A ALA* 4.5 15.5 - - + -
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Residues in contact with LEU 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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146A HIS* 4.0 26.9 - - + -
150A LYS* 4.1 26.2 - - + +
155A PRO* 6.1 0.2 - - + -
156A GLY 4.2 24.5 - - - +
157A PRO* 3.6 3.5 - - + +
158A GLN* 3.4 19.9 + - - +
171A LEU* 3.6 29.1 - - + +
203A ASN* 2.9 17.4 + - + +
204A THR* 3.8 4.9 - - - +
206A TYR* 1.3 96.4 - - + +
208A LEU* 1.3 62.6 + - - +
209A GLY 3.1 1.4 + - - -
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Residues in contact with LEU 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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158A GLN 3.4 12.2 - - - +
168A ARG* 3.8 57.3 + - + +
171A LEU* 3.7 42.4 - - + +
172A GLN* 3.8 18.8 - - - +
175A VAL* 3.9 14.4 - - + -
204A THR 3.0 19.8 + - - +
205A HIS* 3.6 4.7 - - - +
207A LEU* 1.3 77.2 - - - +
209A GLY* 1.3 58.7 + - - +
210A ASN* 3.6 17.6 + - - +
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Residues in contact with GLY 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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158A GLN 4.2 11.4 - - - -
205A HIS 2.8 2.8 + - - -
206A TYR 3.2 7.8 + - - -
207A LEU 3.1 5.3 - - - -
208A LEU* 1.3 79.4 - - - +
210A ASN* 1.3 63.9 + - - +
211A PHE* 3.4 32.1 + - - -
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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