Contacts of the helix formed by residues 209 - 221 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148E CYS* 4.1 25.1 - - - +
151E LEU* 3.4 39.0 - - + +
152E SER* 3.8 11.4 - - - +
155E GLY 3.5 9.2 - - - +
156E ASP* 2.7 28.3 + - - +
157E ALA 3.7 12.1 - - - +
158E VAL* 3.5 31.4 - - + -
207E PHE 3.5 0.6 + - - -
208E ALA* 1.3 68.7 - - - +
210E ARG* 1.3 63.9 + - - +
212E LEU* 3.2 12.5 + - + +
213E ASN* 2.9 29.8 + - - -
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Residues in contact with ARG 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E ASP 4.3 1.2 + - - -
208E ALA* 3.3 3.2 - - + -
209E LEU* 1.3 77.4 - - - +
211E TYR* 1.3 73.6 + - + +
213E ASN* 3.6 12.2 + - - +
214E PHE* 3.2 40.4 + - + -
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Residues in contact with TYR 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E LEU* 4.6 7.9 - - + -
41E ASP* 3.9 11.7 - - - -
43E SER* 2.7 28.4 + - - -
45E VAL* 3.2 36.6 - - + +
46E SER* 3.9 19.5 - - - -
208E ALA* 3.2 31.1 + - + +
209E LEU 3.1 0.6 - - - -
210E ARG* 1.3 84.1 - - + +
212E LEU* 1.3 60.7 + - - +
214E PHE* 2.8 35.5 + + - +
215E PHE* 3.4 14.5 + - + -
251E LEU* 3.7 17.5 - - + -
144F GLN* 4.7 2.7 - - + -
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Residues in contact with LEU 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E PHE* 4.2 16.1 - - + -
148E CYS* 3.9 19.1 - - - -
158E VAL* 3.7 31.2 - - + -
160E ILE* 5.0 5.4 - - + -
207E PHE* 4.2 12.3 - - + -
208E ALA 3.5 3.5 + - - +
209E LEU* 3.2 14.9 + - + +
211E TYR* 1.3 78.9 - - - +
213E ASN* 1.3 57.8 + - - +
214E PHE 3.1 4.7 + - - -
215E PHE* 3.2 28.2 + - + +
216E THR* 3.2 19.3 + - - +
235E LEU* 3.7 23.3 - - + -
237E VAL* 4.2 0.2 - - + -
251E LEU* 3.6 20.6 - - + -
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Residues in contact with ASN 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E ALA 4.5 0.9 - - - +
148E CYS* 3.3 12.5 + - - +
149E ARG* 3.2 28.9 + - - +
152E SER* 2.6 30.8 + - - -
209E LEU* 2.9 27.8 + - - +
210E ARG* 4.0 9.6 - - - +
211E TYR 3.1 0.6 + - - -
212E LEU* 1.3 73.9 - - - +
214E PHE* 1.3 60.4 + - - +
216E THR* 3.3 18.4 + - - +
217E LYS* 4.2 12.1 - - - +
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Residues in contact with PHE 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ALA 4.4 6.8 - - - +
21E ASP* 3.9 29.8 - - + -
22E LEU* 4.1 28.4 - - + +
210E ARG* 3.2 55.9 - - + -
211E TYR* 2.8 18.4 + + - +
213E ASN* 1.3 77.3 - - - +
215E PHE* 1.3 72.2 + - + +
216E THR 3.2 0.9 - - - -
217E LYS* 2.9 50.4 + - + +
249E TYR* 5.0 1.1 - - - -
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Residues in contact with PHE 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E LEU* 3.7 23.1 - - + -
46E SER* 3.8 23.1 - - - -
47E LEU 5.6 0.2 - - - -
144E PHE* 5.4 0.7 - - + -
211E TYR* 3.4 19.5 - - + -
212E LEU* 3.5 30.7 - - + +
214E PHE* 1.3 73.7 - - + +
216E THR* 1.3 53.9 + - + +
217E LYS 2.7 15.7 + - - -
218E ALA* 2.8 23.7 + - - +
237E VAL* 3.9 13.0 - - + -
239E TYR* 3.7 11.5 - - + +
249E TYR* 3.3 52.9 - + + -
250E TYR 3.8 4.7 - - - -
251E LEU* 3.6 27.4 - - + -
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Residues in contact with THR 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E PHE* 4.2 20.2 - - + -
145E ALA* 3.9 28.9 + - - +
148E CYS* 4.3 12.3 - - + -
212E LEU 3.2 16.4 - - - +
213E ASN* 3.3 22.9 + - - +
215E PHE* 1.3 73.5 - - - +
217E LYS* 1.3 58.4 + - - +
218E ALA 3.0 3.1 - - - -
219E THR* 2.5 29.5 + - - -
220E PRO* 4.8 0.2 - - - +
239E TYR* 3.6 9.2 - - - -
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Residues in contact with LYS 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E LYS 5.1 0.3 - - - +
17E GLU* 4.1 13.7 - - - +
18E ALA* 3.6 24.2 + - - +
21E ASP* 2.9 43.1 + - + +
213E ASN 4.2 11.4 - - - +
214E PHE* 2.9 40.4 + - + +
215E PHE 2.7 4.9 + - - -
216E THR* 1.3 75.8 + - - +
218E ALA* 1.3 55.7 + - - +
219E THR 3.2 3.6 + - - -
220E PRO* 3.6 13.8 - - - +
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Residues in contact with ALA 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ALA* 3.5 12.5 - - + +
215E PHE 2.8 8.6 + - - +
217E LYS* 1.3 77.9 - - - +
219E THR* 1.3 62.4 + - - +
220E PRO* 3.4 4.3 - - - -
221E LEU* 3.0 32.6 + - + +
239E TYR* 3.4 19.3 - - + -
247E LEU* 4.1 0.7 - - + -
249E TYR* 3.0 34.5 - - + +
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Residues in contact with THR 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E SER* 3.6 35.7 + - - +
142E GLY* 4.2 6.3 - - - +
145E ALA* 4.0 6.0 - - + +
216E THR* 2.5 34.1 + - - -
218E ALA* 1.3 78.5 - - - +
220E PRO* 1.4 66.7 - - + +
221E LEU 3.0 0.9 + - - -
222E SER 2.9 26.7 + - - +
239E TYR* 4.0 11.9 + - - -
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Residues in contact with PRO 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E LYS* 3.9 44.5 + - + +
17E GLU* 6.4 1.8 - - + -
216E THR 4.8 0.2 - - - +
217E LYS 3.6 15.0 - - - +
218E ALA* 3.5 1.6 - - - -
219E THR* 1.4 93.2 - - + +
221E LEU* 1.3 62.4 + - + +
222E SER 3.3 1.2 + - - -
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Residues in contact with LEU 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ILE* 4.1 12.6 - - + +
14E LYS* 3.5 31.9 - - + +
15E VAL* 4.1 17.3 - - + +
18E ALA* 4.5 1.3 - - + -
218E ALA* 3.0 23.9 + - + +
219E THR 3.0 1.4 + - - -
220E PRO* 1.3 81.8 - - + +
222E SER* 1.3 59.9 + - - +
239E TYR* 4.5 8.7 - - + -
240E LYS 3.8 7.2 - - - +
241E ILE* 4.2 34.1 - - + +
242E ALA* 4.7 4.5 + - - +
247E LEU* 3.4 35.2 - - + -
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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