Contacts of the helix formed by residues 189 - 205 (chain A) in PDB entry 5V89
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 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A SER 4.0 3.5 + - - +
186A PHE* 3.8 10.3 - - - +
187A LEU 3.2 0.4 - - - -
188A ASN* 1.3 79.6 - - - +
190A SER* 1.3 61.1 + - - +
191A THR* 3.2 12.1 + - - -
192A ASN* 2.8 41.6 + - + +
193A PHE* 2.8 33.5 + - - +
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Residues in contact with SER 190 (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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188A ASN 4.1 2.0 + - - -
189A ASP* 1.3 74.1 + - - +
191A THR* 1.3 64.8 + - - +
193A PHE* 4.5 0.9 - - - -
194A LYS* 3.1 12.1 + - - +
260A ARG* 2.9 44.7 + - - +
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Residues in contact with THR 191 (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 ASP* 3.2 10.2 + - - -
190A SER* 1.3 78.2 - - - +
192A ASN* 1.3 66.8 + - - +
194A LYS* 3.3 7.2 + - - +
195A LEU* 3.1 33.5 + - + +
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Residues in contact with ASN 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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146A TRP* 4.0 8.5 - - + -
186A PHE* 3.5 47.7 - - + +
189A ASP* 2.8 28.4 + - - +
191A THR* 1.3 74.3 - - - +
193A PHE* 1.3 66.5 + - - +
195A LEU* 3.2 23.1 + - - +
196A ILE* 2.9 28.1 + - - +
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Residues in contact with PHE 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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186A PHE 3.7 4.6 + - - -
187A LEU* 3.5 47.1 - - + +
189A ASP 2.8 19.6 + - - +
190A SER* 3.8 4.0 - - - +
192A ASN* 1.3 77.1 - - - +
194A LYS* 1.3 58.5 + - - +
196A ILE* 3.2 6.2 + - - +
197A TYR* 2.8 38.0 + + - +
224A LEU* 3.4 43.1 - - + -
225A LEU* 3.9 9.9 - - + -
228A ILE* 3.8 18.6 - - + -
256A LEU* 3.7 25.8 - - + -
260A ARG* 3.8 15.9 - - - +
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Residues in contact with LYS 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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190A SER 3.1 14.6 + - - +
191A THR* 3.6 6.3 - - - +
192A ASN 3.2 0.2 - - - -
193A PHE* 1.3 79.6 - - - +
195A LEU* 1.3 63.7 + - + +
197A TYR* 3.7 0.3 - - - +
198A ARG* 2.9 60.8 + - - +
256A LEU* 3.8 18.6 - - + -
257A GLU* 3.2 26.5 + - - +
260A ARG* 3.9 19.9 - - - +
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Residues in contact with LEU 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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146A TRP* 4.0 24.2 + - + +
191A THR* 3.1 25.5 + - + +
192A ASN* 3.2 28.2 + - - +
194A LYS* 1.3 77.9 - - + +
196A ILE* 1.3 56.2 + - - +
198A ARG* 4.0 6.1 - - - +
199A TYR* 2.9 30.8 + - - +
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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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142A LEU* 4.7 16.4 - - + +
143A VAL* 4.1 15.3 - - + -
146A TRP* 3.5 36.3 - - + -
186A PHE* 3.7 30.1 - - + -
187A LEU* 4.1 20.9 - - + -
192A ASN 2.9 22.2 + - - +
193A PHE* 3.6 3.6 - - - +
195A LEU* 1.3 74.3 - - - +
197A TYR* 1.3 58.4 + - - +
199A TYR* 3.3 8.2 + - + +
200A ALA* 2.9 28.9 + - - +
224A LEU* 4.2 17.7 - - + -
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Residues in contact with TYR 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 PHE* 2.8 38.2 + + + +
194A LYS* 3.7 6.7 - - - +
195A LEU 3.3 0.2 - - - -
196A ILE* 1.3 77.9 - - - +
198A ARG* 1.3 65.2 + - + +
200A ALA* 3.4 12.0 + - - +
221A LEU* 3.3 31.4 - - + +
224A LEU* 3.8 28.5 - - + +
225A LEU* 4.1 14.6 - - + -
252A TRP* 2.7 70.8 + + - -
253A CYS* 4.4 2.7 - - - -
255A VAL* 3.6 11.6 - - - +
256A LEU* 3.6 30.2 + - + -
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Residues in contact with ARG 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 LYS* 2.9 57.8 + - + +
195A LEU* 4.0 7.2 - - - +
197A TYR* 1.3 79.4 - - + +
199A TYR* 1.3 67.8 + - - +
201A PHE* 3.2 15.2 + - - +
202A ASP* 3.5 17.2 + - - +
249A LYS* 3.9 11.8 + - - +
252A TRP* 4.4 4.3 - - - +
253A CYS* 3.5 43.4 + - + +
256A LEU* 5.4 1.2 - - - +
257A GLU* 4.5 7.5 + - - +
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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
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142A LEU* 4.0 8.3 - - + -
145A ALA* 3.2 17.7 + - + +
146A TRP* 3.5 48.9 - + + -
149A ASP* 4.4 15.3 - - - -
150A ALA 2.7 30.3 + - - -
151A GLN* 5.8 0.7 - - - -
195A LEU 2.9 20.1 + - - +
196A ILE* 3.4 6.7 - - + +
198A ARG* 1.3 77.4 - - - +
200A ALA* 1.3 61.1 + - + +
202A ASP* 3.0 15.2 + - + +
203A PHE* 2.8 65.0 + + + +
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Residues in contact with ALA 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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142A LEU* 4.6 9.0 - - + -
196A ILE 2.9 13.5 + - - +
197A TYR 3.5 11.7 - - - +
198A ARG 3.2 0.6 - - - -
199A TYR* 1.3 83.5 - - + +
201A PHE* 1.3 60.6 + - - +
203A PHE* 3.8 7.0 - - + +
204A ALA* 3.2 26.0 + - - +
220A MET* 3.7 21.7 - - + +
224A LEU* 3.9 19.7 - - + -
252A TRP* 4.2 3.4 - - + -
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Residues in contact with PHE 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 TYR 3.8 2.0 + - - -
198A ARG 3.2 7.2 + - - +
199A TYR 3.2 0.8 - - - -
200A ALA* 1.3 78.9 - - - +
202A ASP* 1.3 75.5 + - - +
204A ALA 3.3 1.2 + - - -
205A ARG* 3.0 46.9 + - + +
210A ARG 3.8 15.7 - - - -
211A SER* 4.0 7.9 - - - -
212A LEU* 3.7 30.0 - - + +
247A ILE 3.5 21.3 - - - -
248A ASN 3.7 8.7 - - - -
249A LYS* 3.5 39.0 - - + +
252A TRP* 3.6 39.6 - + + +
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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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151A GLN 4.3 5.1 - - - +
198A ARG* 3.5 15.0 - - - +
199A TYR* 3.0 15.6 + - + +
201A PHE* 1.3 80.5 - - - +
203A PHE* 1.3 61.3 + - - +
204A ALA 3.6 0.2 + - - -
205A ARG* 3.7 29.7 + - - +
249A LYS* 3.0 32.2 + - - +
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Residues in contact with PHE 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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141A MET 5.2 1.3 - - - -
142A LEU* 3.8 23.8 - - + -
145A ALA* 3.4 23.3 - - + -
150A ALA* 3.6 12.8 - - + -
151A GLN 3.6 9.2 - - - +
152A ASN* 3.6 13.8 + - - -
153A MET* 3.0 70.3 + - + -
154A GLY 4.6 1.8 - - - -
155A TYR 5.4 0.7 - - - -
156A PHE* 5.6 1.3 - + - -
199A TYR* 2.8 54.7 + + + +
200A ALA* 4.0 12.6 - - - -
202A ASP* 1.3 77.8 - - - +
204A ALA* 1.3 59.1 + - - +
205A ARG 4.0 3.8 - - - +
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Residues in contact with ALA 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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153A MET* 3.7 35.4 - - + +
200A ALA 3.2 18.5 + - - +
203A PHE* 1.3 74.4 - - - +
205A ARG* 1.3 65.1 - - - +
206A GLU* 3.6 6.2 + - - +
212A LEU* 3.7 21.2 - - + +
216A THR* 4.6 5.0 - - + +
220A MET* 3.9 11.0 - - + -
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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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152A ASN* 4.5 9.9 + - - -
201A PHE* 3.0 38.0 + - + +
202A ASP* 3.7 23.2 + - - +
203A PHE 3.4 6.3 - - - +
204A ALA* 1.3 80.1 - - - +
206A GLU* 1.3 76.5 + - - +
207A LYS* 4.0 2.6 + - - +
208A ASP 4.0 5.9 - - - +
209A GLN* 2.9 36.6 + - + +
210A ARG* 3.7 19.1 - - - +
211A SER 4.5 6.5 - - - +
212A LEU* 3.5 11.8 - - + +
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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