Contacts of the helix formed by residues 215 - 230 (chain S) in PDB entry 6NZO
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 ASN 215 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10J A 4.7 9.7 + - - -
116S SER* 6.0 2.1 - - - -
214S ILE* 1.3 82.5 + - - +
216S GLU* 1.3 66.1 + - - +
217S PRO* 3.7 10.1 - - + -
218S THR* 3.4 10.9 - - + +
219S PHE* 2.6 39.1 + - - +
242S ASN* 4.7 5.4 - - - +
243S GLU* 3.9 22.0 + - - +
244S PHE* 4.7 0.4 - - - -
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Residues in contact with GLU 216 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215S ASN* 1.3 81.9 - - - +
217S PRO* 1.4 70.4 - - + +
219S PHE* 3.5 10.2 - - + +
220S ARG* 2.9 32.6 + - - +
242S ASN* 3.4 34.0 + - - +
244S PHE* 4.7 8.1 - - + -
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Residues in contact with PRO 217 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I C 4.6 15.0 - - - +
215S ASN* 3.9 9.2 - - + -
216S GLU* 1.4 95.6 - - + +
218S THR* 1.3 60.9 - - + +
220S ARG* 3.2 16.9 - - + +
221S SER* 3.0 30.3 + - - -
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Residues in contact with THR 218 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142I T 4.1 18.4 + - - -
214S ILE* 3.8 11.7 - - + +
215S ASN* 3.4 33.4 - - + +
217S PRO* 1.3 81.3 - - + +
219S PHE* 1.3 58.9 + - - +
221S SER* 3.3 9.2 + - - -
222S ARG* 2.9 49.5 + - - +
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Residues in contact with PHE 219 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E GLY 4.6 4.5 - - - -
35E VAL* 5.0 2.2 - - - -
214S ILE* 3.7 19.7 - - + -
215S ASN 2.6 24.8 + - - +
216S GLU* 3.5 7.9 - - + +
217S PRO 3.2 0.4 - - - -
218S THR* 1.3 75.0 - - - +
220S ARG* 1.3 62.7 + - + +
222S ARG* 3.2 3.1 + - - +
223S MET* 2.9 49.9 + - - +
236S PHE* 3.5 42.8 - + + -
244S PHE* 3.5 62.1 - + + -
245S VAL 5.8 0.4 - - - -
301S TYR* 4.6 9.6 - - - -
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Residues in contact with ARG 220 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216S GLU 2.9 17.7 + - - +
217S PRO* 3.2 22.4 - - + +
219S PHE* 1.3 75.4 - - + +
221S SER* 1.3 59.9 + - - +
223S MET* 3.5 23.1 - - + +
224S LEU* 2.9 42.6 + - + +
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Residues in contact with SER 221 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I C 5.0 9.0 + - - -
217S PRO 3.0 17.0 + - - -
218S THR* 3.4 13.9 - - - -
219S PHE 3.2 0.2 - - - -
220S ARG* 1.3 75.6 - - - +
222S ARG* 1.3 59.9 + - - +
224S LEU* 3.4 5.2 + - - +
225S LYS* 2.9 33.5 + - - +
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Residues in contact with ARG 222 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212S GLU* 4.6 9.9 - - - +
214S ILE* 3.5 44.5 - - + +
218S THR* 2.9 28.5 + - - +
219S PHE* 3.2 7.8 + - - +
221S SER* 1.3 74.6 - - - +
223S MET* 1.3 58.7 + - - +
225S LYS* 3.3 13.4 - - - +
226S TYR* 2.9 53.1 + - + -
236S PHE* 4.1 6.5 - - + -
246S ASP* 5.1 3.4 + - + +
249S LYS* 3.5 41.8 - - - +
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Residues in contact with MET 223 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E GLY* 5.0 8.5 - - - -
34E GLY 5.0 2.2 - - - +
219S PHE* 2.9 43.6 + - + +
220S ARG* 3.5 24.7 - - + +
222S ARG* 1.3 76.3 - - - +
224S LEU* 1.3 65.3 + - + +
226S TYR* 3.3 1.2 + - - +
227S ASP* 2.9 38.3 + - - +
236S PHE* 3.6 35.5 - - + -
301S TYR* 3.6 33.4 - - + -
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Residues in contact with LEU 224 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220S ARG* 2.9 33.8 + - + +
221S SER* 3.9 5.4 - - - +
223S MET* 1.3 88.6 - - + +
225S LYS* 1.3 57.6 + - - +
227S ASP* 2.8 25.1 - - - +
228S LYS* 3.0 40.8 + - + +
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Residues in contact with LYS 225 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221S SER 2.9 17.6 + - - +
222S ARG* 3.3 25.4 - - - +
224S LEU* 1.3 76.3 - - - +
226S TYR* 1.3 81.0 + - + +
228S LYS* 3.8 3.8 - - - +
229S GLU* 2.9 69.8 + - - +
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Residues in contact with TYR 226 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104S ARG* 5.5 7.9 - - - -
222S ARG* 2.9 36.0 + - + +
223S MET 4.0 2.2 - - - +
224S LEU 3.3 0.2 - - - -
225S LYS* 1.3 102.3 - - + +
227S ASP* 1.3 57.9 + - - +
229S GLU* 3.2 16.8 + - - +
230S GLY 2.9 22.2 + - - -
231S ILE* 3.4 32.7 + - + +
236S PHE* 3.5 25.8 - + + -
246S ASP* 3.5 18.2 - - - -
248S THR* 4.2 13.9 - - + -
249S LYS* 2.4 41.8 + - - +
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Residues in contact with ASP 227 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E GLY* 4.9 14.0 + - - +
223S MET* 2.9 24.4 + - - +
224S LEU* 2.8 39.0 - - - +
226S TYR* 1.3 74.3 - - - +
228S LYS* 1.3 66.2 + - - +
230S GLY* 4.0 9.8 + - - +
231S ILE* 5.0 4.9 - - + +
234S PHE* 5.8 7.0 - - + -
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Residues in contact with LYS 228 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224S LEU* 3.0 36.8 + - + +
225S LYS* 4.0 4.7 - - - +
227S ASP* 1.3 82.6 + - - +
229S GLU* 1.3 62.5 + - - +
230S GLY* 3.4 0.4 - - - -
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Residues in contact with GLU 229 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225S LYS* 2.9 54.3 + - - +
226S TYR* 3.2 18.3 + - - +
228S LYS* 1.3 77.9 - - - +
230S GLY* 1.3 58.2 + - - +
231S ILE* 5.0 2.2 - - + +
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Residues in contact with GLY 230 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226S TYR 2.9 6.2 + - - -
227S ASP* 4.0 8.9 - - - -
228S LYS 3.4 1.8 - - - -
229S GLU* 1.3 79.9 - - - +
231S ILE* 1.3 65.8 + - - +
232S LYS* 3.9 1.4 + - - +
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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