Contacts of the helix formed by residues 211 - 224 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A GLY 3.9 2.0 - - - -
210A SER* 1.3 77.4 - - - +
212A TYR* 1.3 85.7 + - - -
213A SER 3.2 1.6 - - - -
214A ALA* 3.0 13.1 + - - +
215A GLU* 3.0 24.0 + - - +
276A CYS 5.4 0.4 + - - -
501A NAP 2.7 53.1 + - - -
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Residues in contact with TYR 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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78A ASP* 4.4 12.6 - - + +
211A SER* 1.3 93.3 + - - +
213A SER* 1.3 66.0 + - - +
215A GLU* 3.7 12.3 + - - +
216A ASP* 2.8 28.6 + - + +
324A TRP* 4.9 9.1 - + - -
405A TRP* 4.2 7.0 - + - -
406A LYS* 3.4 20.4 + - - -
409A LYS* 3.8 26.0 - - - -
501A NAP 3.2 87.9 + + - +
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Residues in contact with SER 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 5.6 2.0 - - - -
191A ALA* 4.1 12.5 - - - +
212A TYR* 1.3 79.5 - - - +
214A ALA* 1.3 53.1 + - - +
216A ASP* 5.1 1.1 - - - -
217A ILE* 1.9 65.1 + - - +
276A CYS* 3.8 11.9 - - - -
279A TYR* 5.0 4.0 + - - -
500A FAD 5.7 4.7 - - - +
501A NAP 3.0 37.9 + - - -
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Residues in contact with ALA 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 4.1 14.4 - - + +
209A GLY 3.2 32.1 - - - +
211A SER 3.0 10.4 + - - +
213A SER* 1.3 78.1 - - - +
215A GLU* 1.3 55.2 + - - +
217A ILE* 3.8 3.1 - - - -
218A GLY* 2.7 34.3 + - - -
238A MET* 4.2 13.7 - - + -
246A TRP* 4.2 1.0 - - - -
276A CYS* 3.7 17.6 - - + +
501A NAP 4.5 0.2 + - - -
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Residues in contact with GLU 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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210A SER 5.1 1.4 - - - +
211A SER* 3.0 24.6 + - - +
212A TYR* 3.7 17.5 + - - +
214A ALA* 1.3 75.8 - - - +
216A ASP* 1.3 57.3 + - + +
219A SER* 2.6 38.5 + - - +
238A MET* 3.8 17.7 - - - +
240A TYR* 3.6 30.4 + - + -
242A TRP* 4.2 16.8 - - + -
246A TRP* 3.8 3.2 - - - -
406A LYS* 5.9 0.3 + - - -
409A LYS* 3.0 30.1 + - - -
413A ILE* 4.7 6.0 - - + +
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Residues in contact with ASP 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 2.9 27.2 + - - +
75A LEU* 4.8 6.2 - - - +
76A TRP 5.0 0.3 + - - +
78A ASP* 6.1 0.9 - - - -
212A TYR 2.8 21.4 + - - +
213A SER* 4.3 0.9 - - - +
215A GLU* 1.3 72.8 - - + +
217A ILE* 1.3 64.1 + - - +
219A SER* 3.7 5.6 + - - -
220A GLN* 2.9 51.7 + - - +
416A PHE* 5.0 3.6 - - - -
417A ARG* 2.9 37.5 + - - -
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Residues in contact with ILE 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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72A TYR* 4.2 21.1 - - + +
191A ALA* 4.4 9.9 - - + +
194A PHE* 3.4 40.8 - - + -
207A LEU* 4.3 6.7 - - + -
213A SER* 1.9 76.4 + - - +
214A ALA 3.3 0.9 - - - +
216A ASP* 1.3 69.0 - - - +
218A GLY* 1.3 68.5 + - - +
220A GLN* 3.3 8.0 + - - +
221A CYS* 3.2 19.6 + - - -
274A ILE* 4.1 17.5 - - + -
276A CYS* 3.5 13.0 - - - -
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Residues in contact with GLY 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 3.5 18.8 - - - +
214A ALA 2.7 17.9 + - - -
217A ILE* 1.3 71.8 - - - +
219A SER* 1.3 53.1 + - - -
221A CYS* 2.7 29.6 + - - +
222A TYR* 2.9 11.6 + - - +
229A LEU* 4.0 2.9 - - - +
246A TRP* 3.3 25.5 - - - -
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Residues in contact with SER 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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215A GLU* 2.6 26.7 + - - +
216A ASP* 3.7 14.2 + - - -
217A ILE 3.4 0.2 - - - -
218A GLY* 1.3 71.3 - - - +
220A GLN* 1.3 56.9 + - - +
222A TYR* 3.2 5.7 + - - +
223A LYS* 2.9 30.7 + - - +
242A TRP* 4.6 1.7 - - - -
246A TRP* 3.4 8.4 - - - -
413A ILE* 5.1 4.5 + - - +
414A MET* 3.7 23.1 - - - +
416A PHE* 6.1 0.7 - - - -
417A ARG* 5.7 0.2 - - - -
437A TRP* 3.9 22.3 - - - -
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Residues in contact with GLN 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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72A TYR* 3.8 22.3 - - + -
73A ARG 5.0 0.4 - - - +
74A TYR* 3.4 38.0 + - + +
75A LEU* 4.9 0.6 - - - +
76A TRP 5.3 0.2 - - - +
194A PHE* 4.5 6.3 - - + -
197A ALA* 3.6 14.7 - - + +
216A ASP* 2.9 45.7 + - - +
217A ILE* 3.7 5.2 - - - +
218A GLY 3.1 0.2 - - - -
219A SER* 1.3 76.7 - - - +
221A CYS* 1.3 59.2 + - - +
223A LYS* 4.4 2.9 + - - +
224A TYR* 2.9 44.7 + - + +
417A ARG* 4.1 4.0 - - - +
437A TRP* 3.8 24.3 - - - -
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Residues in contact with CYS 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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194A PHE* 4.1 24.2 - - - -
197A ALA* 4.1 9.0 - - - +
200A PHE* 4.4 20.1 - - + -
205A VAL* 4.8 11.0 - - - -
207A LEU* 5.5 0.7 - - - -
217A ILE* 3.2 17.9 + - - +
218A GLY* 2.7 13.2 + - - +
220A GLN* 1.3 72.2 - - - +
222A TYR* 1.3 64.8 + - - +
224A TYR 3.2 1.7 + - - -
225A GLY 3.0 6.6 + - - -
226A ALA* 2.9 31.8 + - + -
229A LEU* 3.7 21.1 - - + -
274A ILE* 4.9 0.9 - - - -
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Residues in contact with TYR 222 (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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218A GLY 2.9 7.1 + - - +
219A SER* 3.4 9.6 - - - +
221A CYS* 1.3 75.7 - - - +
223A LYS* 1.3 74.5 + - + +
224A TYR 2.8 2.1 + - - -
225A GLY* 2.9 14.2 + - - -
226A ALA* 4.1 5.0 + - - +
229A LEU* 3.7 20.8 - - + +
243A PRO* 3.8 26.8 - - + +
245A ASN* 3.6 33.2 - - - -
246A TRP* 4.6 2.7 - - + -
414A MET* 4.0 27.6 - - + -
437A TRP* 5.3 0.4 - + - -
438A ILE* 3.8 25.7 - - + +
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Residues in contact with LYS 223 (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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74A TYR 5.5 1.4 + - - -
76A TRP* 4.4 6.1 - - - +
219A SER 2.9 15.9 + - - +
220A GLN* 3.8 5.9 + - - +
222A TYR* 1.3 83.3 - - - +
224A TYR* 1.3 95.2 + - + +
225A GLY 3.6 0.5 + - - -
437A TRP* 2.8 66.0 + - + +
438A ILE* 3.9 21.1 - - + +
440A ALA* 2.7 28.8 + - - +
441A LEU* 4.1 14.5 - - + +
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Residues in contact with TYR 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 3.2 59.6 - + + +
197A ALA* 3.9 15.5 - - + -
198A LEU* 3.9 29.3 - - + +
201A LYS* 3.8 18.9 - - - +
220A GLN* 2.9 32.1 + - - +
221A CYS 3.6 2.2 - - - +
222A TYR 2.8 0.6 + - - -
223A LYS* 1.3 111.4 + - + +
225A GLY* 1.4 59.5 + - - +
440A ALA 3.8 1.0 + - - -
441A LEU* 2.3 51.8 + - + -
443A 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