Contacts of the helix formed by residues 208 - 219 (chain A) in PDB entry 2XRG
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 LYS 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A PRO* 2.7 25.6 + - + +
207A THR* 1.4 74.4 - - - +
209A THR* 1.4 65.0 + - - +
211A PRO* 3.4 13.4 - - + +
212A ASN* 2.8 23.0 + - - +
230A ASN* 3.7 28.0 - - + +
359A HIS* 3.8 6.5 - - - -
386A PRO 5.6 3.2 + - - -
387A GLY* 5.8 1.0 - - - -
388A THR* 3.4 25.0 + - - +
389A LEU* 3.9 13.2 - - + -
473A ASP* 4.3 11.5 + - - -
474A HIS* 3.4 29.4 + - + +
475A GLY* 4.0 1.1 - - - -
1862A SWH 4.6 0.2 - - - +
1870A IOD 4.7 12.3 - - + -
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Residues in contact with THR 209 (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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171A ASP* 3.4 14.1 - - - +
208A LYS* 1.4 74.8 - - - +
210A PHE* 1.4 58.9 + - - +
212A ASN* 3.9 0.7 - - - +
213A LEU* 3.1 47.3 + - + +
230A ASN* 4.0 0.2 + - - -
306A TYR* 4.4 0.2 - - - +
358A ASP* 3.7 7.2 - - - +
1862A SWH 1.6 67.5 + - + -
1864A ZN 2.0 31.6 - - - -
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Residues in contact with PHE 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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209A THR* 1.4 74.3 - - - +
211A PRO* 1.4 67.8 - - + +
212A ASN 3.5 0.5 + - - -
213A LEU* 4.7 2.2 - - - +
214A TYR* 3.5 24.3 + - - +
227A ILE* 4.0 15.2 - - + +
229A GLY 4.7 0.2 - - - +
230A ASN* 3.3 20.9 + - - +
241A PHE* 4.7 12.3 - + - -
243A LEU* 3.7 35.7 - - + -
248A LYS* 5.0 16.4 - - + -
254A TRP* 3.6 35.4 - + - -
274A PHE* 5.7 1.8 - + - -
1862A SWH 3.7 52.8 - + - +
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Residues in contact with PRO 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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204A VAL* 4.1 2.0 - - + +
206A PRO* 4.0 26.9 - - + +
208A LYS* 3.4 17.0 - - + +
210A PHE* 1.4 90.3 - - + +
212A ASN* 1.4 51.0 + - - +
215A THR* 2.6 34.1 + - - -
222A PRO* 4.2 13.9 - - + -
225A HIS* 3.5 6.5 + - + -
227A ILE* 3.6 21.5 - - + +
229A GLY* 3.7 26.7 - - - +
230A ASN* 3.6 11.9 - - - +
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Residues in contact with ASN 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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203A PRO* 3.3 3.0 - - - +
204A VAL* 3.0 52.4 + - - +
206A PRO 3.1 10.3 + - - -
207A THR* 3.6 3.0 - - - +
208A LYS 2.8 29.0 + - - +
209A THR 3.5 2.2 + - - +
210A PHE 3.3 0.6 - - - -
211A PRO* 1.4 75.4 - - - +
213A LEU* 1.4 65.0 + - - +
214A TYR 3.4 0.4 - - - -
215A THR* 3.3 4.2 + - - -
216A LEU* 3.3 27.0 + - + +
358A ASP* 3.2 35.3 - - + +
505A ASN* 3.5 7.9 + - - +
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Residues in contact with LEU 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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169A SER* 4.3 17.5 - - - +
209A THR* 3.1 38.0 + - + +
210A PHE 4.7 0.7 - - - +
212A ASN* 1.4 75.1 - - - +
214A TYR* 1.4 60.3 + - - +
216A LEU* 3.3 23.9 + - + +
217A ALA 3.4 2.8 + - - -
306A TYR* 4.0 21.8 - - + -
357A GLY 5.9 0.4 - - - +
358A ASP* 4.7 14.1 - - + +
1862A SWH 3.2 85.3 - - + +
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Residues in contact with TYR 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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210A PHE 3.5 17.1 + - - +
212A ASN 3.4 0.4 - - - -
213A LEU* 1.4 74.9 - - - +
215A THR* 1.4 56.1 + - - +
217A ALA* 3.6 7.4 + - + +
218A THR* 2.7 47.9 + - + +
225A HIS* 3.4 39.5 - + + -
227A ILE* 4.1 5.6 - - + -
254A TRP* 3.6 46.8 - + + +
255A GLY 2.9 30.0 + - - -
258A PRO* 3.4 27.1 - - + +
260A TRP* 4.6 12.6 - + - -
274A PHE* 5.8 1.6 - + - -
1862A SWH 4.2 11.8 + - - +
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Residues in contact with THR 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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204A VAL* 3.5 21.7 - - + +
211A PRO 2.6 24.4 + - - -
212A ASN 3.3 6.7 + - - -
213A LEU 3.2 0.6 - - - -
214A TYR* 1.4 74.4 - - - +
216A LEU* 1.4 58.5 + - - +
218A THR* 3.9 4.7 - - - -
219A GLY* 2.8 31.7 + - - -
220A LEU 3.4 17.8 + - - +
222A PRO* 4.4 2.8 - - - +
225A HIS* 3.1 12.1 + - - -
505A ASN* 4.0 12.6 - - - +
506A ILE* 3.7 26.0 - - + -
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Residues in contact with LEU 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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169A SER* 5.9 0.7 - - - -
201A MET* 4.5 6.1 - - + -
212A ASN* 3.6 15.0 - - + +
213A LEU* 3.3 27.3 + - + +
215A THR* 1.4 79.1 - - - +
217A ALA* 1.3 57.5 + - - +
218A THR 3.8 0.2 + - - -
356A VAL* 4.7 13.0 - - + -
357A GLY 3.9 19.7 - - - +
358A ASP* 5.3 2.2 - - - -
505A ASN* 4.0 31.6 - - + +
508A LEU* 3.8 29.6 - - + -
509A TYR* 4.2 9.2 + - - +
512A MET* 3.3 27.0 - - + +
1862A SWH 4.7 10.8 - - - -
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Residues in contact with ALA 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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213A LEU 3.4 8.5 + - - +
214A TYR* 3.9 10.3 - - + +
215A THR 3.3 0.6 - - - -
216A LEU* 1.3 78.6 - - - +
218A THR* 1.4 59.5 + - + +
258A PRO* 3.4 4.8 - - + +
259A LEU* 2.9 34.2 + - + +
260A TRP* 4.0 29.8 - - + -
273A PHE* 5.8 1.6 - - + -
509A TYR* 3.3 11.1 - - - -
512A MET* 5.3 0.9 - - - -
1862A SWH 4.1 12.1 - - + -
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Residues in contact with THR 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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214A TYR* 2.7 49.5 + - + +
215A THR 3.7 0.7 + - - -
217A ALA* 1.4 79.9 - - - +
219A GLY* 1.3 61.8 + - - +
220A LEU* 3.4 24.5 + - + +
225A HIS* 3.8 13.2 - - + +
255A GLY 4.3 5.2 - - - +
257A GLN 4.0 10.0 - - - +
258A PRO* 3.9 21.8 - - + -
509A TYR* 3.4 24.7 - - - -
523A ASN* 3.8 5.7 - - - +
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Residues in contact with GLY 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 THR 2.8 18.8 + - - -
218A THR* 1.3 72.7 - - - +
220A LEU* 1.3 60.5 + - - +
505A ASN 5.7 0.2 - - - -
506A ILE* 3.8 24.7 - - - +
509A TYR* 3.7 18.2 - - - +
523A ASN* 3.4 5.6 - - - +
524A ASN* 2.9 27.0 + - - +
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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