Contacts of the helix formed by residues 206 - 224 (chain A) in PDB entry 5ZUN
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 LYS 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A GLU* 3.5 20.1 + - - +
87A ARG 4.4 8.5 - - - +
88A MET* 4.7 4.4 + - + +
89A VAL* 3.4 26.2 - - + -
174A LEU 5.9 0.2 - - - -
204A GLY 3.3 8.9 + - - +
205A LEU* 1.3 80.1 - - - +
207A VAL* 1.3 66.9 + - - +
208A CYS* 4.1 15.7 - - - -
209A PHE* 3.0 8.2 + - + +
210A GLY 3.0 18.5 + - - -
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 3.5 11.9 - - + -
162A LEU* 3.7 29.6 - - + -
163A ALA* 3.9 10.5 - - + -
166A VAL* 3.9 24.0 - - + -
167A LEU* 3.4 39.9 - - + -
174A LEU 4.1 10.0 + - - +
175A SER* 5.5 0.2 - - - -
205A LEU 3.8 2.2 + - - +
206A LYS* 1.3 72.8 - - - +
208A CYS* 1.3 65.8 + - - +
210A GLY 3.2 1.2 + - - -
211A ILE* 3.0 26.8 + - + +
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Residues in contact with CYS 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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89A VAL* 3.8 29.4 - - - -
90A VAL 5.7 4.3 - - - +
167A LEU* 6.1 0.6 - - - +
206A LYS* 4.1 11.0 - - - -
207A VAL* 1.3 79.5 - - - +
209A PHE* 1.3 63.5 + - - +
211A ILE* 3.4 12.2 + - - +
212A GLN* 3.3 25.7 + - - +
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Residues in contact with PHE 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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51A ALA* 4.1 10.1 - - + -
80A HIS* 4.4 4.9 - + - -
88A MET* 3.1 52.0 - - + +
89A VAL* 3.7 13.7 - - - +
90A VAL* 3.9 26.9 - - + +
96A PHE* 3.9 14.4 - + - -
123A MET* 3.8 22.9 - - - -
205A LEU* 3.8 19.3 - - + -
206A LYS* 3.0 12.7 + - + +
208A CYS* 1.3 78.7 - - - +
210A GLY* 1.3 66.9 + - - +
212A GLN* 3.0 8.8 + - + +
213A LEU* 2.9 40.4 + - + +
401A 9JX 4.3 0.9 - - + -
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Residues in contact with GLY 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 3.4 27.9 - - - -
205A LEU* 3.8 14.4 - - - +
206A LYS 3.0 11.3 + - - -
207A VAL 3.2 0.4 + - - -
209A PHE* 1.3 77.0 - - - +
211A ILE* 1.3 54.5 + - - +
213A LEU* 3.1 10.3 + - - +
214A LEU* 2.9 30.8 + - - +
402A PG4 4.5 2.4 - - - +
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Residues in contact with ILE 211 (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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159A PHE* 4.3 10.3 - - + -
163A ALA* 4.7 3.8 - - + -
167A LEU* 3.6 35.7 - - + -
207A VAL* 3.0 23.4 + - + +
208A CYS* 3.6 11.7 - - - +
209A PHE 3.1 0.2 - - - -
210A GLY* 1.3 75.6 - - - +
212A GLN* 1.3 64.1 + - - +
214A LEU* 3.2 14.8 + - + +
215A ASN* 2.9 41.0 + - - +
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Residues in contact with GLN 212 (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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90A VAL* 3.7 34.3 - - + +
91A SER 3.7 13.5 + - - -
92A ASP* 3.4 10.8 + - - +
93A PHE* 2.9 39.6 + - + +
208A CYS 3.3 13.4 + - - +
209A PHE* 3.0 11.5 + - + +
211A ILE* 1.3 85.8 - - - +
213A LEU* 1.3 56.6 + - - +
215A ASN* 3.0 29.6 + - - +
216A ALA* 2.8 26.7 + - - +
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Residues in contact with LEU 213 (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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51A ALA* 5.0 0.7 - - + -
93A PHE* 4.2 6.3 - - + -
123A MET* 3.7 38.6 - - + -
148A LEU* 4.3 14.2 - - + +
205A LEU* 4.5 3.8 - - + -
209A PHE* 2.9 38.3 + - + +
210A GLY* 3.1 13.7 + - - +
212A GLN* 1.3 72.9 - - - +
214A LEU* 1.3 66.2 + - - +
216A ALA* 3.2 5.6 + - - +
217A VAL* 3.1 26.0 + - - +
401A 9JX 3.8 32.5 - - + -
402A PG4 4.0 19.3 - - - +
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Residues in contact with LEU 214 (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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156A ALA* 5.0 7.4 - - + +
159A PHE* 3.8 26.2 - - + -
160A LYS* 3.8 41.1 - - + -
210A GLY 2.9 15.1 + - - +
211A ILE* 3.4 15.5 - - + +
213A LEU* 1.3 73.4 - - - +
215A ASN* 1.3 66.8 + - - +
217A VAL* 3.3 8.8 + - + +
218A SER* 3.0 26.1 + - - -
402A PG4 3.8 22.9 - - - +
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Residues in contact with ASN 215 (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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92A ASP* 4.5 1.2 + - - -
93A PHE* 4.9 0.4 - - + -
211A ILE* 2.9 23.9 + - - +
212A GLN* 3.0 41.6 + - - +
214A LEU* 1.3 78.2 - - - +
216A ALA* 1.3 57.1 + - - +
218A SER* 3.2 6.6 + - - -
219A ARG* 2.8 55.6 + - - +
410A EDO 3.1 29.9 - - - -
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Residues in contact with ALA 216 (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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93A PHE* 3.6 44.6 - - + -
126A ALA* 4.7 9.2 - - + -
130A LEU* 4.4 1.1 - - + +
148A LEU* 4.8 5.4 - - + -
212A GLN 2.8 11.5 + - - +
213A LEU* 3.2 10.7 + - - +
215A ASN* 1.3 77.2 - - - +
217A VAL* 1.3 57.5 + - - +
219A ARG* 3.2 5.8 + - - +
220A VAL* 2.8 35.6 + - - +
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Residues in contact with VAL 217 (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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148A LEU* 3.9 33.7 - - + -
149A VAL 3.4 23.8 - - - +
150A LEU* 4.6 13.2 - - + -
151A ALA* 4.7 7.2 - - + +
213A LEU 3.1 15.2 + - - +
214A LEU* 3.8 11.4 - - + +
216A ALA* 1.3 74.8 - - - +
218A SER* 1.3 64.4 + - - +
220A VAL* 3.3 8.3 + - - +
221A GLU* 3.0 24.5 + - + +
402A PG4 4.7 7.2 - - - +
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Residues in contact with SER 218 (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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214A LEU 3.0 14.8 + - - -
215A ASN* 3.6 10.7 - - - -
217A VAL* 1.3 77.9 - - - +
219A ARG* 1.3 61.0 + - - +
221A GLU* 3.3 12.7 + - - +
222A ARG* 3.2 41.1 + - - +
410A EDO 4.8 3.8 - - - -
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Residues in contact with ARG 219 (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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92A ASP* 2.9 43.2 + - - -
93A PHE* 3.9 6.6 - - - +
94A HIS* 3.6 5.7 - - - +
130A LEU* 3.7 17.0 - - + +
215A ASN* 2.8 31.6 + - - +
216A ALA* 3.7 5.8 - - - +
218A SER* 1.3 72.6 - - - +
220A VAL* 1.3 67.4 + - - +
222A ARG* 3.2 19.6 + - - +
223A ALA* 2.9 23.2 + - - +
410A EDO 2.9 46.5 + - - +
411A CL 3.2 29.2 - - - +
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Residues in contact with VAL 220 (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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126A ALA* 3.9 30.7 - - + +
129A ILE* 4.3 16.4 - - + -
130A LEU* 4.0 20.0 - - + -
148A LEU 4.1 3.4 - - - +
149A VAL* 4.2 25.4 - - + +
216A ALA 2.8 20.3 + - - +
217A VAL* 3.3 7.4 + - - +
219A ARG* 1.3 75.7 - - - +
221A GLU* 1.3 63.4 + - - +
223A ALA* 3.0 4.7 + - - +
224A LEU* 3.0 40.8 + - + +
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Residues in contact with GLU 221 (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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149A VAL* 6.3 0.4 - - - -
150A LEU* 6.0 4.5 - - + +
217A VAL* 3.0 15.8 + - + +
218A SER* 3.5 13.8 - - - +
219A ARG 3.2 0.2 - - - -
220A VAL* 1.3 78.4 - - - +
222A ARG* 1.3 64.1 + - + +
224A LEU* 3.5 17.8 + - - +
225A PRO* 3.6 10.0 - - - +
249A LEU* 5.4 13.2 - - + -
253A LEU* 5.4 7.6 - - + +
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Residues in contact with ARG 222 (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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218A SER* 3.2 27.1 + - - +
219A ARG* 3.6 25.3 - - - +
220A VAL 3.2 0.4 - - - -
221A GLU* 1.3 83.1 - - + +
223A ALA* 1.3 60.7 + - - +
225A PRO* 3.6 11.5 - - - +
226A LYS* 3.5 22.6 - - - +
410A EDO 2.8 35.1 + - - -
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Residues in contact with ALA 223 (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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129A ILE* 4.5 7.9 - - + -
130A LEU* 4.0 14.6 - - + -
133A ALA* 3.7 23.5 - - + +
219A ARG 2.9 16.4 + - - +
220A VAL* 3.0 5.8 + - - +
222A ARG* 1.3 77.7 - - - +
224A LEU* 1.3 66.7 + - - +
225A PRO 3.3 0.7 - - - -
226A LYS* 2.9 28.6 + - + +
227A LEU* 3.4 7.1 + - - +
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Residues in contact with LEU 224 (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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129A ILE* 4.4 5.6 - - + -
149A VAL* 4.4 7.9 - - + -
220A VAL* 3.0 34.9 + - + +
221A GLU* 3.5 9.2 + - - +
222A ARG 3.4 0.2 - - - -
223A ALA* 1.3 74.8 - - - +
225A PRO* 1.3 66.3 - - + +
227A LEU* 3.0 27.2 + - + +
249A LEU* 4.0 34.5 - - + +
250A LEU* 3.5 41.7 - - + +
253A LEU* 3.8 20.6 - - + -
254A ALA* 3.3 17.0 - - - +
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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