Contacts of the helix formed by residues 209 - 221 (chain C) in PDB entry 1AXC
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 LEU 209 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C CYS* 3.7 35.9 - - + +
151C LEU* 3.6 28.5 - - + +
152C SER* 3.8 10.3 - - - +
155C GLY 3.3 25.4 - - - +
156C ASP* 2.8 21.6 + - - +
157C ALA 3.8 13.2 - - - +
158C VAL* 3.8 27.8 - - + +
207C PHE 3.4 1.0 + - - -
208C ALA* 1.3 71.8 - - - +
210C ARG* 1.3 58.9 + - - +
212C LEU* 3.3 9.3 + - + +
213C ASN* 2.7 34.3 + - - -
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Residues in contact with ARG 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C ASP 4.4 1.2 + - - -
208C ALA* 3.1 3.9 + - + -
209C LEU* 1.3 79.0 - - - +
211C TYR* 1.3 74.9 + - + +
213C ASN* 3.6 12.3 + - - +
214C PHE* 3.5 21.5 + - + -
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Residues in contact with TYR 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU* 4.7 8.5 - - + -
41C ASP* 3.8 11.4 - - - -
43C SER* 2.7 27.8 + - - -
45C VAL* 3.4 35.8 - - + +
46C SER* 4.0 19.5 - - - -
208C ALA* 3.2 24.6 + - + +
210C ARG* 1.3 82.7 - - + +
212C LEU* 1.3 61.0 + - - +
214C PHE* 2.9 34.5 + + - +
215C PHE* 3.2 17.1 + - + -
251C LEU* 3.6 21.5 - - + -
144D GLN* 4.5 3.6 - - + -
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Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 3.9 22.9 - - + -
148C CYS* 3.8 22.4 - - - -
158C VAL* 3.6 31.4 - - + -
160C ILE* 5.0 7.2 - - + -
207C PHE* 4.3 10.5 - - + -
208C ALA 3.5 5.3 + - - +
209C LEU* 3.3 10.8 + - + +
211C TYR* 1.3 78.7 - - - +
213C ASN* 1.3 56.8 + - - +
214C PHE 2.9 5.4 + - - -
215C PHE* 3.0 34.8 + - + +
216C THR* 3.0 20.3 + - - +
235C LEU* 4.0 13.2 - - + -
237C VAL* 4.3 0.4 - - + -
251C LEU* 3.7 17.5 - - + -
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Residues in contact with ASN 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ALA 4.8 0.7 - - - +
148C CYS* 3.2 8.4 + - - +
149C ARG* 3.2 30.5 + - - +
152C SER* 2.7 28.0 + - - -
209C LEU* 2.7 28.7 + - - +
210C ARG* 3.9 9.2 - - - +
211C TYR 3.2 0.6 - - - -
212C LEU* 1.3 72.4 - - - +
214C PHE* 1.3 56.9 - - - +
216C THR* 3.2 19.8 + - - +
217C LYS* 4.1 15.1 - - - +
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Residues in contact with PHE 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ALA 4.6 6.6 - - - +
21C ASP* 4.0 26.0 - - + -
22C LEU* 3.9 32.9 - - + +
210C ARG* 3.5 22.6 + - + -
211C TYR* 2.9 18.5 + + - +
213C ASN* 1.3 77.0 - - - +
215C PHE* 1.3 68.0 + - + +
216C THR 3.2 0.7 - - - -
217C LYS* 3.0 55.3 + - + +
249C TYR* 5.1 1.3 - - - -
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Residues in contact with PHE 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU* 3.9 17.7 - - + -
46C SER* 3.8 11.7 - - - -
47C LEU 5.5 0.2 - - - -
144C PHE* 5.3 0.7 - - + -
211C TYR* 3.3 16.4 - - + -
212C LEU* 3.3 29.8 - - + +
214C PHE* 1.3 77.5 - - - +
216C THR* 1.3 53.2 + - + +
217C LYS 2.7 11.8 + - - -
218C ALA* 2.8 24.6 + - - +
237C VAL* 3.8 15.9 - - + -
239C TYR* 3.7 10.4 + - + +
249C TYR* 3.4 56.6 - + + -
250C TYR 3.7 20.4 - - - -
251C LEU* 3.8 27.4 - - + -
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Residues in contact with THR 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 4.2 21.5 - - + -
145C ALA* 3.8 34.5 - - + +
148C CYS* 4.3 9.9 - - + -
212C LEU 3.0 15.2 + - - +
213C ASN* 3.2 26.0 + - - +
215C PHE* 1.3 70.1 - - - +
217C LYS* 1.3 56.3 + - - +
218C ALA 2.8 9.8 + - - -
219C THR* 2.5 25.8 + - - -
220C PRO* 4.7 0.2 - - - +
239C TYR* 3.6 9.2 + - - +
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Residues in contact with LYS 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LYS 5.0 0.3 - - - +
17C GLU* 4.1 18.4 - - - +
18C ALA* 3.7 18.9 + - - +
21C ASP* 3.0 33.7 + - + +
213C ASN 4.1 11.2 - - - +
214C PHE* 3.0 54.7 + - + +
215C PHE 2.7 5.3 + - - -
216C THR* 1.3 72.0 + - - +
218C ALA* 1.3 56.9 + - - +
219C THR 3.4 0.7 - - - -
220C PRO* 3.9 12.4 - - - +
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Residues in contact with ALA 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ALA* 3.7 10.8 - - + -
215C PHE 2.8 8.6 + - - +
216C THR 2.8 0.2 + - - -
217C LYS* 1.3 76.9 - - - +
219C THR* 1.3 66.2 + - - +
220C PRO* 3.2 5.8 - - - -
221C LEU* 2.9 30.7 + - + +
239C TYR* 3.7 18.5 - - + -
249C TYR* 3.2 34.1 - - + +
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Residues in contact with THR 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C SER* 3.4 34.2 + - - +
142C GLY* 3.8 8.5 - - - +
145C ALA* 3.9 15.7 - - + +
216C THR* 2.5 25.7 + - - -
218C ALA* 1.3 75.3 - - - +
220C PRO* 1.4 63.8 - - + +
221C LEU 2.9 4.9 + - - -
222C SER 2.7 28.8 + - - +
239C TYR* 3.9 12.5 + - - -
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Residues in contact with PRO 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LYS* 3.5 46.4 + - + +
17C GLU* 6.3 2.0 - - + -
217C LYS 3.9 13.7 - - - +
218C ALA* 3.2 5.4 - - - -
219C THR* 1.4 91.5 - - - +
221C LEU* 1.3 59.4 + - + +
222C SER 3.4 0.7 - - - -
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Residues in contact with LEU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 4.1 13.0 - - + +
14C LYS* 3.4 35.0 - - + -
15C VAL* 4.2 5.4 - - + +
18C ALA* 4.5 4.7 - - + -
218C ALA* 2.9 24.0 + - + +
219C THR 2.9 1.2 + - - -
220C PRO* 1.3 78.2 - - + +
222C SER* 1.3 61.0 + - - +
239C TYR* 4.5 8.1 - - + -
240C LYS 3.5 10.6 - - - +
241C ILE* 4.0 40.0 - - + +
242C ALA* 4.3 5.5 + - - +
247C LEU* 3.5 34.8 - - + -
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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