Contacts of the helix formed by residues 192 - 209 (chain A) in PDB entry 2ADU
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 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A GLY 3.9 1.8 + - - +
191A MET* 1.3 77.0 - - - +
193A MET* 1.3 64.1 + - - +
194A ILE* 3.6 8.3 + - - +
195A GLU* 2.9 44.5 + - - +
196A ILE* 3.3 20.4 + - - +
238A ASP 5.3 3.6 - - - +
239A THR* 5.0 6.1 - - - +
240A THR 3.3 10.8 - - - +
241A VAL* 4.1 17.9 - - + +
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Residues in contact with MET 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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192A THR* 1.3 73.4 - - - +
194A ILE* 1.3 60.7 + - - +
196A ILE* 3.5 15.0 + - + +
197A CYS* 3.1 28.6 + - - -
223A CYS* 3.6 42.2 - - + +
225A LEU* 3.6 23.1 - - + -
232A TYR* 4.1 17.3 - - + +
234A PRO* 3.8 10.5 - - + -
238A ASP* 5.6 0.9 + - - +
240A THR* 3.0 39.4 + - + +
242A LEU* 3.9 29.8 - - + -
248A CYS* 3.9 7.9 - - - -
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Residues in contact with ILE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A THR* 3.2 6.8 + - - +
193A MET* 1.3 76.2 - - + +
195A GLU* 1.3 63.1 + - + +
197A CYS* 3.3 1.7 + - - +
198A GLU* 2.9 57.0 + - + +
234A PRO* 3.5 26.0 - - + -
235A ASN 3.5 19.5 - - - +
236A ALA* 4.7 1.6 - - - -
237A GLY* 4.2 8.1 - - - +
238A ASP 3.3 29.6 + - - +
418A ARG* 4.7 8.1 - - - +
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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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190A GLY 4.9 0.9 - - - +
191A MET* 3.8 22.2 - - + +
192A THR* 2.9 49.1 + - + +
193A MET 3.4 0.2 - - - -
194A ILE* 1.3 79.6 - - + +
196A ILE* 1.3 62.3 + - - +
198A GLU* 4.0 4.6 - - - +
199A LYS* 3.0 28.3 + - - +
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Residues in contact with ILE 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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183A VAL* 5.2 2.9 - - + -
186A TRP* 3.5 22.6 - - + -
187A ILE* 4.0 20.0 - - + -
191A MET* 4.0 22.2 - - + -
192A THR 3.3 15.6 + - - +
193A MET* 3.7 20.0 - - + +
194A ILE 3.3 0.4 - - - -
195A GLU* 1.3 77.7 - - - +
197A CYS* 1.3 61.9 + - - +
200A LEU* 3.0 31.1 + - + +
221A THR* 5.9 0.2 - - + -
223A CYS* 5.6 1.8 - - + -
242A LEU* 3.7 38.1 - - + -
248A CYS* 5.7 0.2 - - - -
250A ILE* 4.5 14.8 - - + -
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Residues in contact with CYS 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 MET 3.1 18.3 + - - +
194A ILE 3.9 2.9 - - - +
196A ILE* 1.3 81.9 - - - +
198A GLU* 1.3 60.3 + - - +
200A LEU* 3.8 3.9 - - - +
201A GLU* 2.9 39.0 + - - +
221A THR* 3.7 28.5 - - - -
223A CYS* 3.6 27.6 - - - -
233A THR* 3.8 1.6 - - - -
234A PRO* 3.8 9.9 - - + -
418A ARG* 3.5 21.1 - - - +
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Residues in contact with GLU 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 ILE* 2.9 40.4 + - + +
195A GLU* 4.2 4.8 - - - +
197A CYS* 1.3 76.2 - - - +
199A LYS* 1.3 58.3 + - - +
201A GLU* 4.1 5.2 - - - +
202A ASP* 2.9 41.5 + - - +
418A ARG* 4.2 21.3 + - - +
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Residues in contact with LYS 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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182A TYR* 3.4 23.4 + - + +
186A TRP* 3.3 59.9 - - + +
191A MET* 4.3 9.4 - - + -
195A GLU 3.0 17.2 + - - +
198A GLU* 1.3 74.0 - - - +
200A LEU* 1.3 64.9 - - - +
202A ASP* 3.6 7.1 + - - +
203A CYS* 3.3 22.0 + - - +
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Residues in contact with LEU 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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179A VAL* 3.8 16.4 - - + +
182A TYR* 5.7 0.2 - - - -
183A VAL* 3.5 33.7 - - + -
186A TRP* 4.1 6.9 - - + -
196A ILE* 3.0 19.7 + - + +
197A CYS* 3.8 3.4 - - - +
199A LYS* 1.3 78.6 - - - +
201A GLU* 1.3 61.4 + - + +
203A CYS* 3.3 6.7 + - - +
204A SER* 2.9 27.1 + - - -
221A THR* 3.7 33.4 - - + +
250A ILE* 3.9 24.5 - - + -
252A PHE* 4.0 19.7 - - + -
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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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197A CYS 2.9 17.4 + - - +
198A GLU* 4.1 4.8 - - - +
200A LEU* 1.3 76.7 - - + +
202A ASP* 1.3 58.1 + - - +
204A SER* 3.2 7.3 + - - -
205A ARG* 2.8 51.2 + - - +
217A LEU* 3.8 16.2 - - + -
221A THR* 2.9 34.4 + - - +
418A ARG* 3.1 34.1 + - - -
419A TRP* 2.8 30.7 + - + -
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Residues in contact with ASP 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 GLU* 2.9 31.8 + - - +
199A LYS* 3.8 7.9 - - - +
200A LEU 3.3 0.2 - - - -
201A GLU* 1.3 76.1 - - - +
203A CYS* 1.3 63.2 + - - +
205A ARG* 3.3 17.1 + - - +
206A LYS* 3.0 42.1 + - + +
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Residues in contact with CYS 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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116A PRO* 3.4 37.7 - - - +
179A VAL* 4.0 20.0 - - + -
182A TYR* 3.6 29.6 - - + -
199A LYS 3.3 10.5 + - - +
200A LEU* 3.6 8.3 - - - +
201A GLU 3.3 0.4 - - - -
202A ASP* 1.3 79.4 - - - +
204A SER* 1.3 63.4 + - - +
206A LYS* 3.1 9.3 + - - +
207A LEU* 2.9 24.4 + - - +
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Residues in contact with SER 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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175A ALA* 5.4 0.3 - - - +
179A VAL* 3.6 21.2 - - - +
200A LEU* 2.9 23.1 + - - -
201A GLU* 3.5 8.3 - - - -
203A CYS* 1.3 77.7 - - - +
205A ARG* 1.3 62.1 + - - +
207A LEU* 4.4 0.2 - - - +
208A ILE* 3.0 28.8 + - - +
217A LEU* 3.0 22.0 - - - +
252A PHE* 4.7 5.0 - - - -
253A GLY 4.8 0.2 + - - -
254A THR* 3.5 19.6 - - - +
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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 GLU* 2.8 43.1 + - - +
202A ASP* 3.7 19.4 + - - +
204A SER* 1.3 72.7 - - - +
206A LYS* 1.3 60.6 + - + +
208A ILE* 3.8 6.7 - - - -
209A LYS* 3.0 22.7 + - - -
210A GLU* 2.8 47.7 + - + +
217A LEU* 3.8 23.8 - - + +
419A TRP* 3.6 27.9 - - - +
422A ARG* 3.3 51.9 - - - +
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Residues in contact with LYS 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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116A PRO 5.0 5.8 + - - +
117A SER* 4.6 21.8 - - - +
119A PRO* 3.5 16.0 - - - +
202A ASP* 3.0 32.3 + - - +
203A CYS* 3.1 12.1 + - - +
205A ARG* 1.3 82.2 - - + +
207A LEU* 1.3 70.3 + - + +
209A LYS* 3.1 14.1 + - - +
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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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112A GLN* 3.6 7.6 - - - +
116A PRO* 3.7 18.4 - - + -
117A SER* 3.6 20.4 - - - +
118A VAL 3.6 23.6 - - - +
119A PRO* 3.5 5.6 - - - +
120A ILE* 3.0 41.9 + - + +
121A CYS 4.8 0.2 + - - -
171A GLU* 5.7 0.5 - - - +
175A ALA* 4.3 8.3 - - + +
178A GLN* 3.6 38.6 - - + +
179A VAL* 4.1 15.0 - - + +
203A CYS* 2.9 22.2 + - - +
204A SER 4.4 1.6 - - - +
206A LYS* 1.3 76.3 - - + +
208A ILE* 1.3 60.0 + - - +
209A LYS 3.3 0.5 + - - -
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Residues in contact with ILE 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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120A ILE* 5.4 0.2 - - - -
171A GLU* 4.7 6.0 - - + +
172A ALA* 4.0 10.5 - - - -
175A ALA* 3.8 16.0 - - + +
204A SER 3.0 25.6 + - - +
205A ARG* 3.3 11.9 - - - +
207A LEU* 1.3 73.5 - - - +
209A LYS* 1.3 72.5 + - - +
210A GLU 3.4 8.5 - - - +
215A ALA* 3.6 10.2 - - - +
216A GLY* 3.7 34.3 - - - +
217A LEU* 4.8 0.4 - - + -
254A THR* 3.7 26.0 - - + -
255A HIS 3.7 11.9 - - - +
256A ILE* 3.7 25.0 - - + +
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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
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119A PRO* 3.9 22.7 - - + -
121A CYS* 3.4 27.9 - - - -
122A ASP* 3.5 24.3 + - - -
171A GLU* 6.1 0.2 - - - +
205A ARG 3.0 8.4 + - - -
206A LYS* 3.1 6.5 + - - +
207A LEU 3.0 2.8 - - - +
208A ILE* 1.3 82.5 - - - +
210A GLU* 1.3 69.5 + - - +
211A ASN* 3.3 9.2 + - + +
215A ALA* 3.9 3.6 - - - +
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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
------------------------------------------------------------
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