Contacts of the helix formed by residues 259 - 278 (chain C) in PDB entry 6XWQ
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 ASP 259 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254C LYS* 5.5 1.7 - - - +
257C GLY 3.4 12.8 - - - +
258C ILE* 1.3 80.6 - - - +
260C PRO* 1.3 71.6 - - + +
261C ILE* 4.6 4.0 - - + +
262C LYS* 3.3 36.4 + - + +
263C PHE 3.2 14.7 + - - -
428C TRP* 4.4 5.9 - - - +
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Residues in contact with PRO 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C PHE* 3.4 62.8 - - + +
253C LEU* 4.2 9.2 - - + -
254C LYS* 4.1 23.1 - - + +
258C ILE 3.7 3.8 - - - +
259C ASP* 1.3 81.7 - - + +
261C ILE* 1.3 71.5 + - + +
263C PHE* 3.0 11.8 + - + +
264C ILE* 2.9 27.2 + - - +
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Residues in contact with ILE 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C PHE* 4.5 22.4 - - + -
259C ASP* 3.3 3.8 - - + -
260C PRO* 1.3 80.4 - - + +
262C LYS* 1.3 61.7 + - + +
264C ILE* 3.3 6.0 + - + +
265C ARG* 2.9 40.2 + - - +
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Residues in contact with LYS 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C ASP* 3.3 32.1 + - + +
260C PRO 3.3 0.4 - - - -
261C ILE* 1.3 80.3 - - + +
263C PHE* 1.3 57.9 + - - +
265C ARG* 4.1 10.3 - - - +
266C LYS* 2.9 50.2 + - - +
427C LYS 5.4 0.7 - - - +
428C TRP* 3.9 46.2 - - + +
430C SER* 5.8 0.9 + - - -
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Residues in contact with PHE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ILE* 6.3 0.4 - - + -
249C TYR* 5.1 6.1 - - + -
250C PHE* 5.7 1.3 - + - -
253C LEU* 3.3 30.1 - - + -
258C ILE* 4.1 13.6 - - + +
259C ASP 3.2 7.4 + - - +
260C PRO* 3.0 13.1 + - + +
262C LYS* 1.3 77.1 - - - +
264C ILE* 1.3 72.8 + - + +
267C ALA* 2.9 36.6 + - + +
271C MET* 5.6 0.2 - - - -
295C MET* 3.3 27.1 - - + +
407C THR* 3.3 44.6 - - + -
410C LEU* 3.7 17.5 - - + -
411C ALA* 3.4 27.6 - - + -
414C VAL* 4.8 1.8 - - + -
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Residues in contact with ILE 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ILE* 4.6 13.9 - - + -
246C VAL* 6.0 0.9 - - + -
250C PHE* 3.4 35.4 - - + -
260C PRO 2.9 13.3 + - - +
261C ILE* 3.9 5.2 - - + +
263C PHE* 1.3 91.4 - - + +
265C ARG* 1.3 64.9 + - - +
267C ALA* 4.6 3.1 - - - -
268C LYS* 2.9 29.0 + - + +
271C MET* 4.2 22.7 - - + -
407C THR* 5.6 0.7 - - + -
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Residues in contact with ARG 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C ILE* 2.9 29.9 + - + +
262C LYS* 3.7 10.5 - - - +
263C PHE 3.3 0.2 - - - -
264C ILE* 1.3 77.8 - - - +
266C LYS* 1.3 67.4 + - + +
268C LYS* 3.5 33.6 + - - +
269C ASP* 5.2 1.2 - - - +
294C GLU* 4.4 2.1 - - - +
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Residues in contact with LYS 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C LYS* 2.9 35.3 + - - +
265C ARG* 1.3 86.6 - - + +
267C ALA* 1.3 58.7 + - - +
268C LYS 3.4 0.4 + - - -
269C ASP* 4.3 4.4 + - - +
290C VAL* 3.2 23.2 - - - +
294C GLU* 3.3 50.8 + - + +
295C MET* 3.8 20.9 - - + +
427C LYS* 4.2 34.5 + - - +
428C TRP* 5.1 9.4 - - + +
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Residues in contact with ALA 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C PHE* 2.9 27.8 + - + +
264C ILE* 3.2 1.8 + - - +
266C LYS* 1.3 74.8 - - - +
268C LYS* 1.3 66.6 + - - +
269C ASP 3.1 3.4 - - - -
270C ALA* 3.0 7.9 + - - +
271C MET* 2.9 32.8 + - + +
290C VAL* 4.6 2.9 - - - -
295C MET* 3.6 14.4 - - + -
407C THR* 5.6 0.4 - - - +
410C LEU* 3.7 21.1 - - + -
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Residues in contact with LYS 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 5.7 0.8 - - - +
264C ILE* 2.9 16.4 + - + +
265C ARG* 3.5 31.1 + - - +
267C ALA* 1.3 77.0 - - - +
269C ASP* 1.3 89.1 + - - +
271C MET* 3.9 13.9 - - + -
272C ILE* 2.9 49.9 + - + +
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Residues in contact with ASP 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.9 31.6 - - + +
265C ARG 5.4 1.0 - - - +
266C LYS 4.5 3.5 - - - +
267C ALA 3.1 1.6 + - - -
268C LYS* 1.3 109.0 + - - +
270C ALA* 1.3 55.9 + - - +
272C ILE* 4.6 1.1 - - - +
273C THR* 3.8 10.9 + - - -
286C VAL* 3.6 14.0 - - + +
290C VAL* 4.5 12.3 - - + -
294C GLU* 3.8 16.8 - - - +
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Residues in contact with ALA 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C ALA 3.0 8.4 + - - +
269C ASP* 1.3 77.2 - - - +
271C MET* 1.3 64.8 + - - +
272C ILE 3.2 1.3 - - - -
273C THR* 3.3 3.0 + - - +
274C ALA* 2.9 25.3 + - - +
283C THR* 4.6 3.1 + - - +
286C VAL* 3.7 21.8 - - + -
287C THR* 4.1 14.4 - - - -
290C VAL* 3.9 22.2 - - + +
406C VAL* 4.4 9.3 - - + +
410C LEU* 4.5 2.7 - - + -
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Residues in contact with MET 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ILE* 5.0 6.3 - - + -
264C ILE* 4.2 27.1 - - + -
267C ALA* 2.9 39.9 + - + +
268C LYS* 3.2 11.4 + - + +
270C ALA* 1.3 77.7 - - - +
272C ILE* 1.3 57.0 + - + +
274C ALA* 3.4 3.4 + - - +
275C PHE* 2.9 24.5 + - - +
403C MET* 3.3 42.3 - - + +
406C VAL* 4.9 3.1 - - + +
407C THR* 3.1 36.8 - - + +
410C LEU* 5.6 1.6 - - + -
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Residues in contact with ILE 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.9 26.2 - - + +
18C ILE* 5.3 0.9 - - + -
19C LEU* 3.8 39.9 - - + -
268C LYS* 2.9 38.3 + - + +
269C ASP* 5.4 0.9 - - - +
271C MET* 1.3 76.8 - - + +
273C THR* 1.3 64.6 + - - +
275C PHE* 3.2 7.9 + - + +
276C VAL* 2.9 25.4 + - + +
403C MET* 5.8 0.2 - - - -
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Residues in contact with THR 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C VAL 5.2 0.5 + - - -
15C LEU* 3.8 21.3 - - - +
18C ILE* 4.3 17.2 - - + +
204C MET* 4.5 13.5 - - - -
269C ASP 3.8 9.5 + - - -
270C ALA* 3.3 8.7 + - - +
272C ILE* 1.3 79.7 - - - +
274C ALA* 1.3 56.0 + - - +
276C VAL* 3.3 0.9 + - - +
277C THR* 2.9 39.6 + - + +
283C THR* 3.5 25.8 - - - +
286C VAL* 4.4 17.1 - - + +
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Residues in contact with ALA 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C ALA 2.9 17.6 + - - +
271C MET 3.8 3.6 - - - +
273C THR* 1.3 74.8 - - - +
275C PHE* 1.3 66.2 + - - +
277C THR* 4.1 6.7 - - - -
278C ARG* 3.0 19.6 + - - -
283C THR* 4.4 6.3 + - + -
402C THR* 3.2 23.5 - - + +
403C MET* 3.9 6.7 - - - -
406C VAL* 3.5 34.1 - - + -
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Residues in contact with PHE 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 5.9 1.8 - - + -
22C LEU* 4.4 13.0 - - + -
238C TYR* 4.6 15.9 - + - -
271C MET 2.9 19.6 + - - +
272C ILE* 3.4 9.9 - - + +
274C ALA* 1.3 77.0 - - - +
276C VAL* 1.3 65.3 + - + +
278C ARG 4.0 0.2 + - - -
399C MET* 2.9 72.5 - - + +
400C GLY* 4.1 9.2 - - - -
403C MET* 3.5 34.2 - - + +
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Residues in contact with VAL 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 3.1 44.0 - - + +
19C LEU* 3.7 21.8 - - + -
22C LEU* 3.6 26.7 - - + -
211C VAL* 3.7 28.1 - - + +
272C ILE* 2.9 19.2 + - + +
273C THR 4.0 2.0 - - - +
275C PHE* 1.3 79.9 - - + +
277C THR* 1.3 61.8 + - - +
278C ARG* 3.1 15.3 + - - +
399C MET* 4.0 6.9 - - - +
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Residues in contact with THR 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 5.3 5.8 - - - -
52C PHE* 3.3 28.5 - - - -
56C LEU* 3.5 3.6 - - - +
204C MET* 3.7 17.0 - - + +
207C ALA* 5.4 0.7 - - - -
211C VAL* 4.6 7.6 - - - -
214C LEU* 6.0 0.2 - - - +
273C THR* 2.9 34.9 + - + +
274C ALA* 4.1 2.5 - - - -
276C VAL* 1.3 78.2 - - - +
278C ARG* 1.3 73.5 + - - +
279C SER* 3.0 33.7 + - - +
283C THR* 4.7 4.7 - - - -
359C PRO* 4.1 5.0 - - - +
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Residues in contact with ARG 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C VAL* 5.9 0.4 - - - +
214C LEU* 4.6 27.6 - - + +
218C VAL* 5.3 2.2 - - - +
274C ALA 3.0 16.1 + - - -
276C VAL 3.1 10.6 - - - +
277C THR* 1.3 84.4 - - - +
279C SER* 1.3 58.9 + - - +
359C PRO* 3.3 36.1 - - + +
360C GLY* 2.9 36.4 - - - +
394C ASP* 4.3 6.3 + - - -
395C ALA* 3.2 36.5 - - - +
398C ASP* 3.4 16.7 + - - +
399C MET* 3.8 35.2 - - + +
402C THR* 3.4 11.9 - - - +
501C ASP 3.6 3.5 + - - -
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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
------------------------------------------------------------
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