Contacts of the helix formed by residues 211 - 224 (chain B) in PDB entry 2XLR
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 SER 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B GLY 3.8 0.6 - - - -
210B SER* 1.3 81.4 - - - +
212B TYR* 1.3 82.9 + - - -
213B SER 3.3 2.0 - - - -
214B ALA* 3.1 3.9 + - - +
215B GLU* 3.0 31.9 + - - +
276B CYS 5.2 0.6 + - - -
501B NAP 2.7 53.9 + - - -
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Residues in contact with TYR 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ASP* 4.3 13.7 - - + +
211B SER* 1.3 92.5 + - - +
213B SER* 1.3 56.4 + - - +
215B GLU* 3.3 12.7 + - - +
216B ASP* 2.8 33.5 + - - +
324B TRP* 4.8 8.8 - - - -
405B TRP* 4.3 7.0 - + - -
406B LYS* 3.5 19.5 + - - -
409B LYS* 4.0 24.5 - - - -
501B NAP 3.3 89.4 + + - +
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Residues in contact with SER 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 5.7 1.3 - - - -
191B ALA* 4.3 8.7 - - - +
212B TYR* 1.3 78.3 - - - +
214B ALA* 1.3 59.7 + - - +
216B ASP* 5.1 1.1 - - - -
217B ILE* 2.7 51.0 + - - +
276B CYS* 3.8 16.4 - - - -
279B TYR* 5.0 4.0 + - - -
500B FAD 5.7 4.2 - - - +
501B NAP 2.8 37.1 + - - -
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 4.2 12.5 - - + +
209B GLY 3.2 33.0 - - - +
211B SER 3.1 11.1 + - - +
213B SER* 1.3 75.4 - - - +
215B GLU* 1.3 67.2 + - - +
218B GLY* 2.9 21.7 + - - -
238B MET* 4.1 14.8 - - + -
246B TRP* 4.2 3.5 - - - -
276B CYS* 3.7 19.1 - - + +
501B NAP 4.6 0.2 + - - -
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Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B SER 4.9 2.6 - - - +
211B SER* 3.0 24.8 + - - +
212B TYR* 3.5 16.0 + - - +
214B ALA* 1.3 74.5 - - - +
216B ASP* 1.3 60.6 + - + +
219B SER* 2.8 33.6 + - - +
238B MET* 3.8 16.3 - - - +
240B TYR* 3.6 31.6 + - + -
242B TRP* 4.4 17.7 - - + -
246B TRP* 3.9 2.9 - - - -
406B LYS* 5.9 0.2 + - - -
409B LYS* 3.0 30.0 + - - -
413B ILE* 4.5 5.6 - - + +
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Residues in contact with ASP 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 2.7 26.9 + - - +
75B LEU* 4.9 6.2 - - - +
78B ASP* 6.1 1.3 - - + -
212B TYR* 2.8 20.0 + - + +
213B SER* 4.5 1.1 - - - +
215B GLU* 1.3 73.5 - - + +
217B ILE* 1.3 65.5 + - - +
219B SER* 3.3 6.8 + - - -
220B GLN* 3.0 47.5 + - - +
416B PHE* 5.1 3.3 - - - -
417B ARG* 2.9 38.7 + - - -
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Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.9 26.7 - - + -
191B ALA* 3.4 38.8 - - + +
194B PHE* 3.8 34.8 - - + -
207B LEU* 4.0 9.6 - - + -
213B SER* 2.7 33.6 + - - +
216B ASP* 1.3 71.8 - - - +
218B GLY* 1.3 63.2 + - - +
220B GLN* 3.3 9.2 + - - +
221B CYS* 3.1 22.3 + - - -
274B ILE* 3.9 16.8 - - + -
276B CYS* 4.1 4.5 - - - -
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Residues in contact with GLY 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 3.6 19.3 - - - +
214B ALA 2.9 12.2 + - - -
217B ILE* 1.3 77.9 - - - +
219B SER* 1.3 56.3 + - - +
221B CYS* 3.1 7.9 + - - +
222B TYR* 2.9 28.8 + - - +
229B LEU* 3.7 2.2 - - - +
246B TRP* 3.4 26.1 - - - -
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Residues in contact with SER 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B GLU* 2.8 23.0 + - - +
216B ASP* 3.3 13.6 + - - -
218B GLY* 1.3 75.2 - - - +
220B GLN* 1.3 58.5 + - - +
222B TYR* 3.4 5.2 + - - +
223B LYS* 2.9 29.6 + - - +
242B TRP* 4.8 1.4 - - - -
246B TRP* 3.5 7.8 - - - -
413B ILE* 5.2 5.0 + - - +
414B MET* 3.7 21.9 - - - +
416B PHE* 6.1 0.7 - - - -
417B ARG* 5.6 0.7 - - - -
437B TRP* 3.8 23.2 - - - -
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Residues in contact with GLN 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B TYR* 3.9 21.9 - - + -
73B ARG 4.8 1.6 - - - +
74B TYR* 3.6 36.6 + - + +
75B LEU* 4.9 0.6 - - - +
76B TRP* 5.4 0.8 - - - +
194B PHE* 4.5 4.9 - - + -
197B ALA* 3.6 15.4 - - + +
216B ASP* 3.0 40.4 + - - +
217B ILE* 3.7 6.5 - - - +
219B SER* 1.3 75.7 - - - +
221B CYS* 1.3 64.1 - - - +
223B LYS* 4.4 2.0 + - - +
224B TYR* 2.9 40.5 + - + +
417B ARG* 4.4 3.2 - - - +
437B TRP* 3.8 24.9 - - - +
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Residues in contact with CYS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PHE* 4.0 26.2 - - - -
197B ALA* 4.1 8.1 - - - +
200B PHE* 4.2 20.9 - - + -
205B VAL* 4.6 13.2 - - + -
207B LEU* 5.6 0.4 - - - -
217B ILE* 3.1 20.1 + - - +
218B GLY* 3.1 9.7 + - - +
220B GLN* 1.3 77.1 - - - +
222B TYR* 1.3 64.6 + - - +
224B TYR 3.3 2.3 + - - -
225B GLY 3.0 6.6 + - - -
226B ALA* 2.9 30.0 + - + +
229B LEU* 3.7 18.2 - - + -
274B ILE* 4.8 0.7 - - - -
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Residues in contact with TYR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B GLY 2.9 12.8 + - - +
219B SER* 3.5 10.1 - - - +
221B CYS* 1.3 76.0 - - - +
223B LYS* 1.3 66.2 + - + +
225B GLY* 3.1 14.2 + - - -
226B ALA* 4.2 5.5 + - - +
229B LEU* 3.7 16.9 - - + +
243B PRO* 3.6 35.6 - - + +
245B ASN* 3.7 26.5 - - - -
246B TRP* 4.6 2.2 - - + -
414B MET* 4.0 25.8 - - + -
437B TRP* 5.3 0.4 - + - -
438B ILE* 3.8 27.3 - - + +
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Residues in contact with LYS 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B TYR* 5.5 2.0 + - - +
76B TRP* 4.5 5.3 - - - +
219B SER 2.9 18.2 + - - +
220B GLN* 3.8 5.0 + - - +
222B TYR* 1.3 81.1 - - - +
224B TYR* 1.3 93.0 + - + +
225B GLY 3.7 0.3 + - - -
437B TRP* 2.8 73.1 + - + +
438B ILE* 3.8 25.7 - - + +
440B ALA* 3.0 23.8 + - - +
441B LEU* 4.1 10.6 - - + +
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Residues in contact with TYR 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TYR* 3.1 60.0 - + - +
197B ALA* 4.0 14.1 - - + -
198B LEU* 3.9 27.6 - - + +
201B LYS* 3.8 18.1 - - - +
220B GLN* 2.9 37.3 + - - +
221B CYS 3.6 2.7 - - - +
222B TYR 3.1 0.2 - - - -
223B LYS* 1.3 109.9 + - + +
225B GLY* 1.3 56.4 + - - +
440B ALA 3.9 1.6 + - - -
441B LEU* 2.7 48.4 + - + -
443B ASP* 5.3 0.5 - - - +
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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