Contacts of the helix formed by residues 206 - 224 (chain H) in PDB entry 4XLR
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 THR 206 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15H THR* 5.4 4.2 + - - -
17H GLY 3.7 8.8 + - - -
18H ASP* 4.2 16.6 - - - +
203H GLY 5.1 0.2 + - - -
204H SER 4.4 0.4 + - - -
205H VAL* 1.3 74.6 - - - +
207H PRO* 1.3 70.4 - - - +
208H LEU* 3.9 9.5 + - + +
209H GLU* 2.8 60.4 + - + +
210H ALA* 3.1 3.6 + - - +
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Residues in contact with PRO 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H THR* 4.8 2.7 - - + -
17H GLY 4.1 3.1 - - - +
18H ASP 3.6 8.7 - - - +
19H HIS 3.4 21.8 - - - +
20H TYR 3.4 17.9 - - - +
21H GLY* 3.6 11.0 - - - +
23H PHE* 3.9 7.1 - - + -
199H ILE* 3.6 25.1 - - + +
201H THR* 3.3 25.1 - - + +
206H THR* 1.3 91.1 - - - +
208H LEU* 1.3 62.2 + - - +
210H ALA* 3.4 3.7 + - + +
211H LEU* 3.0 24.3 + - - +
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Residues in contact with LEU 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G PRO* 4.5 28.0 - - + -
11H PHE* 4.9 5.4 - - + -
13H ALA* 4.7 11.4 - - + -
15H THR* 4.9 11.6 - - + +
23H PHE* 4.3 5.6 - - + -
206H THR* 3.2 11.2 + - + +
207H PRO* 1.3 78.2 - - - +
209H GLU* 1.3 58.0 + - + +
211H LEU* 3.4 18.9 + - + +
212H ASN* 2.9 57.2 + - - +
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Residues in contact with GLU 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88H ARG* 5.6 2.9 + - - -
204H SER 4.5 1.6 - - - +
205H VAL* 3.3 24.3 - - + +
206H THR* 2.8 47.2 + - + +
208H LEU* 1.3 71.4 - - - +
210H ALA* 1.3 65.7 + - - +
212H ASN* 3.3 5.6 + - - +
213H GLN* 2.9 26.8 + - - +
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Residues in contact with ALA 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H LEU* 3.6 10.1 - - + +
48H ILE* 4.2 9.8 - - + +
174H VAL* 4.2 24.7 - - + -
199H ILE* 4.5 3.1 - - + -
201H THR* 4.6 3.8 - - + -
205H VAL* 3.8 23.6 - - + +
206H THR 3.1 4.8 + - - +
207H PRO 3.4 8.5 + - - +
209H GLU* 1.3 77.8 - - - +
211H LEU* 1.3 64.8 + - - +
213H GLN* 3.5 6.5 - - - +
214H ALA* 3.0 23.2 + - - +
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Residues in contact with LEU 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G PHE* 5.2 9.9 - - + -
11H PHE* 4.3 19.7 - - + -
23H PHE* 3.5 42.4 - - + -
40H LEU* 4.3 23.3 - - + -
44H LEU* 4.2 9.6 - - + +
197H LEU* 4.7 8.3 - - + -
199H ILE* 4.8 1.5 - - + +
207H PRO 3.0 14.3 + - - +
208H LEU* 3.4 17.5 - - + +
209H GLU 3.2 0.2 - - - -
210H ALA* 1.3 74.7 - - - +
212H ASN* 1.3 67.4 + - - +
214H ALA* 2.8 15.6 + - - +
215H VAL* 2.9 28.6 + - + +
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Residues in contact with ASN 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G PHE* 5.0 11.1 - - - +
208H LEU* 2.9 54.1 + - - +
209H GLU* 3.9 4.4 - - - +
211H LEU* 1.3 76.7 - - - +
213H GLN* 1.3 62.6 + - - +
215H VAL* 3.1 21.5 + - - +
216H ALA* 2.9 22.0 + - - +
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Residues in contact with GLN 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H ILE* 3.2 48.5 - - + +
49H PRO* 3.7 12.1 - - - +
205H VAL* 5.0 9.4 - - - +
209H GLU 2.9 18.0 + - - +
210H ALA* 3.5 5.2 - - - +
212H ASN* 1.3 74.4 - - - +
214H ALA* 1.3 64.1 + - - +
216H ALA* 3.0 11.2 + - + +
217H ILE* 3.0 33.2 + - + +
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Residues in contact with ALA 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H LEU* 3.8 13.2 - - + -
43H ILE* 4.7 6.1 - - + -
44H LEU* 3.7 27.1 - - + -
48H ILE* 4.2 6.1 - - + +
210H ALA 3.0 12.6 + - - +
211H LEU 2.8 10.6 + - - +
213H GLN* 1.3 75.0 - - - +
215H VAL* 1.3 63.5 + - - +
217H ILE* 2.9 17.2 + - - +
218H LEU* 2.9 27.9 + - - +
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Residues in contact with VAL 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222G LEU* 4.2 6.9 - - + +
223G ASN* 5.8 4.7 - - + -
225G PHE* 3.5 41.1 - - + -
40H LEU* 4.6 2.9 - - + -
211H LEU* 2.9 31.4 + - + +
212H ASN* 3.1 21.5 + - - +
214H ALA* 1.3 74.9 - - - +
216H ALA* 1.3 61.5 + - + +
218H LEU* 3.1 12.0 + - - +
219H LYS* 2.9 30.6 + - + +
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Residues in contact with ALA 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212H ASN 2.9 12.7 + - - +
213H GLN* 3.0 15.4 + - + +
215H VAL* 1.3 76.7 - - + +
217H ILE* 1.3 66.1 + - + +
218H LEU 3.0 1.5 + - - -
219H LYS* 3.4 8.2 + - - +
220H GLU* 3.0 26.2 + - - +
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Residues in contact with ILE 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G PHE* 4.2 8.1 - - + -
43H ILE* 3.8 20.6 - - + -
47H SER* 3.7 28.3 - - - +
48H ILE* 3.8 22.2 - - + +
213H GLN* 3.0 21.7 + - + +
214H ALA* 2.9 6.3 + - - +
216H ALA* 1.3 75.7 - - + +
218H LEU* 1.3 56.8 + - - +
220H GLU* 3.4 8.9 - - - +
221H HIS* 2.8 62.3 + - + +
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Residues in contact with LEU 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222G LEU* 3.5 31.4 - - + -
36H LEU* 6.3 1.1 - - + -
39H PRO* 5.0 8.3 - - + +
40H LEU* 3.6 36.6 - - + +
43H ILE* 3.5 40.8 - - + -
214H ALA 2.9 23.6 + - - +
215H VAL* 3.2 11.4 - - - +
216H ALA 3.0 0.2 - - - -
217H ILE* 1.3 75.9 - - - +
219H LYS* 1.3 61.5 + - - +
220H GLU 3.2 0.3 + - - -
221H HIS* 3.3 3.9 + - - +
222H LEU* 2.9 32.0 + - + +
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Residues in contact with LYS 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G LYS* 3.5 35.7 - - + +
222G LEU* 3.2 19.8 - - + +
223G ASN* 3.6 27.7 - - - +
215H VAL* 2.9 14.8 + - + +
216H ALA* 3.8 11.7 - - - +
218H LEU* 1.3 73.2 - - - +
220H GLU* 1.3 62.0 + - - +
222H LEU* 3.5 5.8 - - - +
223H ASN* 2.9 39.5 + - - +
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Residues in contact with GLU 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216H ALA 3.0 18.4 + - - +
217H ILE* 3.4 8.5 - - - +
219H LYS* 1.3 75.0 - - + +
221H HIS* 1.3 84.3 + - - +
222H LEU 3.0 1.1 - - - -
223H ASN* 2.8 28.7 + - - +
224H TYR* 3.1 30.8 + - + +
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Residues in contact with HIS 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G LEU* 3.7 18.4 - - + +
32G PHE* 3.2 28.4 - + - -
36G LEU* 5.0 11.4 - - + -
43H ILE* 5.8 3.8 - - + -
217H ILE* 2.8 46.8 + - + +
218H LEU* 4.0 3.1 - - - +
220H GLU* 1.3 96.0 + - - +
222H LEU* 1.3 57.8 - - - +
224H TYR* 3.2 50.8 + + + +
225H PHE* 4.9 7.4 + - - -
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Residues in contact with LEU 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215G VAL* 3.3 55.0 - - + +
218G LEU* 3.5 35.7 - - + -
219G LYS* 3.5 19.3 - - + +
222G LEU* 3.6 28.7 - - + -
218H LEU* 2.9 15.3 + - + +
219H LYS* 3.5 8.3 - - - +
220H GLU 3.0 0.2 - - - -
221H HIS* 1.3 75.2 - - - +
223H ASN* 1.3 59.5 + - - +
224H TYR 3.1 5.8 + - - -
225H PHE* 3.8 15.8 + - + +
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Residues in contact with ASN 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G LYS* 3.1 43.4 + - - +
219H LYS* 2.9 26.6 + - - +
220H GLU* 2.8 13.7 + - - +
222H LEU* 1.3 71.2 - - - +
224H TYR* 1.3 60.8 + - - +
225H PHE 3.0 14.1 + - - +
226H ALA* 4.7 3.6 + - - +
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Residues in contact with TYR 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G LYS 4.9 3.8 + - - -
9G PRO* 3.4 47.3 - - + +
11G PHE* 4.2 13.0 - - - +
25G LEU* 4.3 17.9 - - + -
28G LEU* 5.3 4.9 - - + -
220H GLU* 3.1 33.0 + - + -
221H HIS* 3.2 52.0 + + - +
222H LEU 3.1 1.4 - - - -
223H ASN* 1.3 77.5 - - - +
225H PHE* 1.3 63.8 + - + +
226H ALA* 3.6 4.0 + - - -
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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