Contacts of the helix formed by residues 209 - 221 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A CYS* 3.3 40.6 - - + +
151A LEU* 3.8 25.8 - - + +
152A SER* 4.0 9.6 - - - +
155A GLY 3.5 24.5 - - - +
156A ASP* 2.9 16.2 + - - +
157A ALA 3.7 20.6 - - - +
158A VAL* 3.9 25.6 - - + -
171A ALA* 4.6 0.7 - - + -
207A PHE 3.4 0.6 + - - -
208A ALA* 1.3 69.4 - - - +
210A ARG* 1.3 66.1 + - - +
212A LEU* 3.1 9.7 + - + +
213A ASN* 3.0 29.6 + - - -
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Residues in contact with ARG 210 (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 ASP 4.4 1.8 + - - +
208A ALA* 3.2 3.8 - - + -
209A LEU* 1.3 78.8 - - - +
211A TYR* 1.3 75.7 + - + +
213A ASN* 3.7 12.1 + - - +
214A PHE* 3.2 53.1 + - + -
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Residues in contact with TYR 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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22A LEU* 4.6 10.1 - - + -
41A ASP* 3.6 21.3 - - - -
43A SER* 2.8 21.7 + - - -
45A VAL* 3.3 35.9 - - + +
46A SER* 4.1 16.8 - - - -
208A ALA* 3.6 26.7 - - + +
209A LEU 3.2 0.6 - - - -
210A ARG* 1.3 86.8 - - + +
212A LEU* 1.3 59.8 + - - +
213A ASN 3.2 0.2 - - - -
214A PHE* 2.9 27.7 + + - +
215A PHE* 3.1 25.6 - - + -
251A LEU* 3.6 20.2 - - + -
144B GLN* 4.5 2.2 - - + -
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Residues in contact with LEU 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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144A PHE* 4.3 13.7 - - + -
148A CYS* 3.8 24.9 - - + -
158A VAL* 3.5 31.6 - - + -
160A ILE* 4.9 6.5 - - + -
207A PHE* 4.3 7.2 - - + -
208A ALA 3.5 6.7 + - - +
209A LEU* 3.1 11.5 + - + +
211A TYR* 1.3 77.2 - - - +
213A ASN* 1.3 57.2 + - - +
215A PHE* 3.2 22.5 + - + +
216A THR* 3.1 33.4 + - - +
235A LEU* 4.1 15.9 - - + -
237A VAL* 4.4 0.4 - - + -
251A LEU* 3.6 24.5 - - + -
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Residues in contact with ASN 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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145A ALA 4.5 0.9 - - - +
148A CYS* 3.3 12.0 + - - +
149A ARG* 3.3 28.8 + - - +
152A SER* 2.7 29.5 + - - -
209A LEU* 3.0 24.6 + - - +
210A ARG* 4.1 7.7 - - - +
211A TYR 3.2 0.6 - - - -
212A LEU* 1.3 74.8 - - - +
214A PHE* 1.3 58.9 + - - +
216A THR* 3.1 17.5 + - - -
217A LYS* 3.8 15.8 - - - +
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Residues in contact with PHE 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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18A ALA 4.3 8.1 - - - +
21A ASP* 4.0 28.9 - - + -
22A LEU* 3.9 32.5 - - + -
210A ARG* 3.2 59.4 + - + -
211A TYR* 2.9 16.8 + + - +
213A ASN* 1.3 78.5 - - - +
215A PHE* 1.3 67.7 + - + +
216A THR 3.2 0.2 - - - -
217A LYS* 3.1 52.5 + - + +
249A TYR* 5.0 1.3 - - - -
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Residues in contact with PHE 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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22A LEU* 3.8 20.6 - - + -
46A SER* 3.9 11.9 - - - -
144A PHE* 5.3 0.7 - - + -
211A TYR* 3.1 22.0 - - + -
212A LEU* 3.4 30.5 - - + +
214A PHE* 1.3 78.6 - - - +
216A THR* 1.3 57.4 + - + +
217A LYS 2.9 6.8 + - - -
218A ALA* 2.9 23.9 + - - +
237A VAL* 3.8 17.9 - - + -
239A TYR* 3.7 9.5 + - - +
249A TYR* 3.4 50.9 - + + -
250A TYR 3.7 18.8 - - - -
251A LEU* 3.6 25.8 - - + -
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Residues in contact with THR 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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144A PHE* 3.7 26.9 - - + -
145A ALA* 3.7 35.7 - - + +
148A CYS* 4.3 7.2 - - + -
212A LEU 3.1 13.4 + - - +
213A ASN* 3.1 28.1 + - - -
215A PHE* 1.3 70.7 - - - +
217A LYS* 1.3 56.8 - - - +
218A ALA 3.0 5.8 - - - -
219A THR* 2.7 24.4 + - - +
220A PRO* 4.8 0.3 - - - +
239A TYR* 3.7 7.6 - - - +
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Residues in contact with LYS 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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14A LYS 5.0 0.5 - - - +
17A GLU* 4.4 11.7 - - - +
18A ALA* 3.8 24.3 + - - +
21A ASP* 3.3 40.1 + - + +
213A ASN 3.8 14.1 - - - +
214A PHE* 3.1 41.3 + - + +
215A PHE 2.9 1.4 + - - -
216A THR* 1.3 76.3 - - - +
218A ALA* 1.3 56.0 + - - +
219A THR 3.2 4.0 - - - -
220A PRO* 3.5 18.5 - - - +
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Residues in contact with ALA 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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18A ALA* 3.7 12.3 - - + +
215A PHE 2.9 10.1 + - - +
217A LYS* 1.3 79.6 - - - +
219A THR* 1.3 62.4 + - - +
220A PRO* 3.4 2.5 - - - -
221A LEU* 3.1 30.3 + - + +
239A TYR* 3.3 22.2 - - + -
247A LEU* 4.2 1.1 - - + -
249A TYR* 3.2 33.9 - - + +
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Residues in contact with THR 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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141A SER* 3.6 38.3 + - - +
142A GLY* 4.2 7.0 - - - +
145A ALA* 3.8 9.3 - - + +
216A THR* 2.7 26.1 + - - -
218A ALA* 1.3 76.8 - - - +
220A PRO* 1.3 65.7 - - + +
221A LEU 2.8 6.2 + - - -
222A SER 2.7 27.3 + - - +
239A TYR* 4.0 10.4 + - - -
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Residues in contact with PRO 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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14A LYS* 3.6 46.1 + - + +
216A THR 4.8 0.2 - - - +
217A LYS 3.5 17.9 - - - +
218A ALA* 4.3 0.9 - - - -
219A THR* 1.3 95.9 - - + +
221A LEU* 1.3 60.1 + - + +
222A SER* 3.3 1.3 + - - -
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Residues in contact with LEU 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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11A ILE* 4.0 6.1 - - + +
14A LYS* 3.6 33.0 - - + +
15A VAL* 3.9 24.2 - - + -
18A ALA* 4.4 2.2 - - + -
218A ALA* 3.1 22.8 + - + +
219A THR 2.8 5.7 + - - -
220A PRO* 1.3 76.2 - - + +
222A SER* 1.3 59.0 + - - +
239A TYR* 4.7 7.0 - - + -
240A LYS 3.7 8.5 - - - +
241A ILE* 4.1 34.9 - - + +
242A ALA* 4.7 3.5 + - - +
247A LEU* 3.5 34.5 - - + -
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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