Contacts of the helix formed by residues 388 - 410 (chain M) in PDB entry 2I2X
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 ASN 388 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385M ASP* 3.0 12.6 + - + +
386M GLY 3.3 0.2 - - - -
387M ASP* 1.3 78.4 - - + +
389M ILE* 1.3 63.3 + - - +
390M TYR* 3.0 21.0 + - - +
391M LEU* 3.1 30.0 + - + +
392M ARG* 3.0 25.6 + - - +
434M ASP 4.9 1.8 + - - -
436M MET* 3.4 26.2 - - - +
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Residues in contact with ILE 389 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M ARG* 3.6 38.4 - - - +
189M GLY 3.8 7.6 - - - +
190M CYS* 4.0 17.9 - - + +
193M SER* 4.1 21.0 + - - -
194M ILE* 3.9 28.9 - - + -
252M PRO* 5.5 0.7 - - - +
387M ASP 3.6 3.8 + - - +
388M ASN* 1.3 72.4 + - - +
390M TYR* 1.3 63.6 + - - +
392M ARG* 3.7 18.0 + - - +
393M ALA* 3.5 19.8 + - - +
436M MET* 3.5 28.3 - - + -
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Residues in contact with TYR 390 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185M LEU* 3.4 17.0 - - + +
190M CYS* 3.9 16.8 - - - -
388M ASN* 3.0 7.9 + - - +
389M ILE* 1.3 80.6 - - - +
391M LEU* 1.3 62.5 + - - +
393M ALA* 3.3 5.1 + - - +
394M LYS* 3.0 48.7 + - + +
432M LEU* 3.6 5.5 - - - +
433M PRO 2.9 28.7 + - - -
434M ASP 3.5 14.8 - - - -
435M ASP 4.0 5.2 - - - -
436M MET* 3.5 35.9 - - + -
439M PHE* 3.1 54.1 - + - -
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Residues in contact with LEU 391 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385M ASP* 3.4 33.0 - - + +
388M ASN* 3.1 26.1 + - + +
390M TYR* 1.3 78.0 - - - +
392M ARG* 1.3 58.4 + - - +
394M LYS* 3.7 29.8 - - - +
395M ASN* 2.7 50.5 + - - +
434M ASP* 3.7 38.4 - - + +
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Residues in contact with ARG 392 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M ARG* 3.9 7.8 - - - +
6M TYR 4.7 0.4 + - - +
193M SER* 5.1 0.8 + - - -
252M PRO* 2.9 42.5 + - + +
255M LEU* 3.9 11.7 - - - +
256M VAL* 3.3 10.9 - - - +
259M GLU* 2.5 46.0 + - - -
382M ILE* 3.3 36.3 - - + +
385M ASP 3.7 7.2 + - - +
386M GLY* 3.0 29.5 + - - -
388M ASN 3.0 21.0 + - - +
389M ILE* 3.7 17.4 - - - +
391M LEU* 1.3 77.6 - - - +
393M ALA* 1.3 62.9 + - - +
395M ASN* 3.5 8.9 - - - +
396M ALA* 3.0 22.7 + - - +
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Residues in contact with ALA 393 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185M LEU* 3.6 21.5 - - + -
189M GLY* 3.9 18.8 - - - +
249M ILE* 4.0 9.0 - - + +
252M PRO* 3.7 20.2 - - + -
389M ILE 3.5 14.3 + - - +
390M TYR 3.3 1.9 + - - +
391M LEU 3.3 0.4 - - - -
392M ARG* 1.3 79.3 - - - +
394M LYS* 1.3 66.0 + - - +
396M ALA* 3.1 4.2 + - - +
397M ALA* 3.0 21.8 + - - +
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Residues in contact with LYS 394 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185M LEU* 3.9 16.1 - - + +
390M TYR* 3.0 46.6 + - + +
391M LEU* 3.3 19.2 + - - +
393M ALA* 1.3 74.5 - - - +
395M ASN* 1.3 65.0 + - - +
397M ALA* 3.0 6.9 + - - +
398M ILE* 2.9 43.1 + - + +
429M LEU* 3.8 20.4 + - + +
430M GLU* 5.9 0.4 + - - +
432M LEU* 3.9 15.8 + - + -
433M PRO 3.6 13.7 - - - -
434M ASP* 2.8 25.4 + - - -
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Residues in contact with ASN 395 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381M SER* 2.9 34.0 + - - +
384M LYS* 3.7 16.4 - - - +
385M ASP* 2.8 32.2 + - - +
391M LEU* 2.7 41.7 + - - +
392M ARG* 3.5 3.5 - - - +
394M LYS* 1.3 74.2 + - - +
396M ALA* 1.3 53.5 + - - +
398M ILE* 3.3 5.1 + - - +
399M GLU* 2.7 37.8 + - - +
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Residues in contact with ALA 396 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248M ALA* 3.5 28.4 - - - +
252M PRO* 4.4 0.7 - - + -
378M VAL* 4.1 9.8 - - + +
381M SER* 3.6 11.0 + - - -
382M ILE* 3.8 17.9 - - + -
392M ARG 3.0 11.3 + - - +
393M ALA* 3.1 12.3 + - - +
395M ASN* 1.3 77.9 - - - +
397M ALA* 1.3 57.3 + - - +
399M GLU* 3.9 0.9 - - - +
400M CYS* 2.9 29.3 + - - +
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Residues in contact with ALA 397 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245M ILE* 4.1 6.2 - - + +
248M ALA* 4.5 2.2 - - - -
249M ILE* 3.7 23.6 - - + -
393M ALA 3.0 12.8 + - - +
394M LYS* 3.0 8.9 + - - +
396M ALA* 1.3 77.4 - - - +
398M ILE* 1.3 62.2 + - - +
400M CYS* 3.3 9.0 - - - +
401M CYS* 3.1 24.6 + - - -
429M LEU* 3.6 30.8 - - + +
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Residues in contact with ILE 398 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394M LYS* 2.9 36.9 + - + +
395M ASN* 4.1 3.8 - - - +
397M ALA* 1.3 75.0 - - - +
399M GLU* 1.3 65.8 + - - +
401M CYS* 3.0 8.8 + - - +
402M ASN* 3.0 33.0 + - - +
426M LYS* 4.3 8.7 - - + +
429M LEU* 3.6 45.3 - - + +
430M GLU* 3.7 29.2 - - + +
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Residues in contact with GLU 399 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377M ARG* 2.5 52.9 + - - +
378M VAL* 4.3 3.1 - - - -
381M SER* 3.6 26.8 - - - +
384M LYS* 5.2 5.2 + - - -
395M ASN 2.7 23.1 + - - +
396M ALA 3.9 2.0 - - - +
398M ILE* 1.3 73.1 - - - +
400M CYS* 1.3 57.9 + - - +
402M ASN* 3.0 14.3 + - - +
403M ILE* 2.8 43.4 + - + +
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Residues in contact with CYS 400 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244M VAL* 3.7 46.0 - - - -
245M ILE* 4.1 10.1 - - + -
248M ALA* 3.6 13.2 - - + -
369M MET* 4.1 11.4 - - + -
378M VAL* 4.7 2.5 - - + +
396M ALA 2.9 16.1 + - - +
397M ALA* 3.3 11.7 - - - +
399M GLU* 1.3 73.9 - - - +
401M CYS* 1.3 64.3 + - - +
403M ILE* 3.1 11.9 + - - +
404M ILE* 2.9 30.8 + - - +
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Residues in contact with CYS 401 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245M ILE* 3.7 27.8 - - - -
397M ALA 3.1 16.0 + - - -
398M ILE* 3.0 10.1 + - - +
400M CYS* 1.3 78.8 - - - +
402M ASN* 1.3 58.3 + - - +
404M ILE* 3.4 1.7 + - - +
405M GLU* 3.0 32.8 + - - +
422M LEU* 4.0 18.4 - - + +
426M LYS* 4.0 44.0 - - + +
429M LEU* 4.2 6.5 - - - -
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Residues in contact with ASN 402 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377M ARG* 4.1 13.9 - - - +
398M ILE* 3.0 28.0 + - - +
399M GLU* 3.0 16.4 + - - +
401M CYS* 1.3 73.2 - - - +
403M ILE* 1.3 65.2 + - - +
405M GLU* 3.3 14.1 + - - +
406M GLU* 3.0 34.4 + - - +
426M LYS* 2.6 29.3 + - - +
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Residues in contact with ILE 403 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368M TYR* 3.5 17.8 - - + -
369M MET* 4.7 8.3 - - + -
374M ASN* 3.5 43.5 - - + +
377M ARG* 3.6 37.2 - - + +
378M VAL* 3.6 31.4 - - + -
399M GLU* 2.8 22.8 + - + +
400M CYS* 3.1 7.4 + - - +
402M ASN* 1.3 76.5 - - - +
404M ILE* 1.3 56.2 + - + +
406M GLU* 3.4 5.4 + - - +
407M GLY 3.0 23.0 + - - -
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Residues in contact with ILE 404 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241M THR* 4.2 10.8 - - + -
244M VAL* 4.3 9.9 - - + -
365M PRO* 3.6 31.2 - - + +
368M TYR* 4.1 17.0 - - + -
369M MET* 4.0 17.9 - - + -
400M CYS* 2.9 31.0 + - - +
401M CYS 3.9 3.4 - - - +
403M ILE* 1.3 77.2 - - + +
405M GLU* 1.3 55.7 + - - +
407M GLY* 3.3 1.4 + - - +
408M ALA* 2.9 26.7 + - - +
412M LEU* 4.1 9.7 - - + +
414M LEU* 3.9 18.2 - - + -
422M LEU* 3.8 23.3 - - + -
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Residues in contact with GLU 405 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401M CYS* 3.0 17.8 + - - +
402M ASN* 3.4 25.0 - - - +
404M ILE* 1.3 73.4 - - - +
406M GLU* 1.3 66.2 + - + +
408M ALA* 3.1 9.0 + - - +
409M ALA* 3.0 22.7 + - - +
422M LEU* 4.1 15.1 - - + +
423M ALA* 6.1 0.9 - - - -
426M LYS* 3.4 31.2 + - - +
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Residues in contact with GLU 406 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368M TYR* 4.5 2.5 - - - +
377M ARG* 2.8 45.8 + - - -
402M ASN* 3.0 18.5 + - - +
403M ILE* 3.6 4.7 - - - +
405M GLU* 1.3 78.9 - - + +
407M GLY* 1.3 64.8 + - - +
409M ALA* 3.2 9.0 + - - +
410M GLY* 3.2 16.3 + - - -
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Residues in contact with GLY 407 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362M TYR* 5.4 0.4 - - - -
368M TYR* 3.2 36.5 + - - -
403M ILE 3.0 11.1 + - - -
404M ILE 3.7 3.1 - - - -
405M GLU 3.3 0.2 - - - -
406M GLU* 1.3 75.2 - - - +
408M ALA* 1.3 56.1 + - - +
410M GLY* 2.9 17.1 + - - -
411M LYS 3.2 2.9 + - - -
412M LEU* 2.9 26.0 + - - -
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Residues in contact with ALA 408 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404M ILE 2.9 18.4 + - - +
405M GLU* 3.1 9.8 + - - +
407M GLY* 1.3 77.9 - - - +
409M ALA* 1.3 59.6 + - - +
410M GLY 3.4 4.9 + - - +
412M LEU* 3.3 23.7 - - + +
414M LEU* 4.1 23.1 - - + -
419M THR* 6.0 0.4 - - - +
422M LEU* 6.0 0.4 - - + -
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Residues in contact with ALA 409 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405M GLU 3.0 12.1 + - - +
406M GLU* 3.2 10.3 + - - +
408M ALA* 1.3 75.5 - - - +
410M GLY* 1.3 61.1 + - - +
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Residues in contact with GLY 410 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406M GLU 3.2 8.2 + - - -
407M GLY* 2.9 10.0 + - - -
408M ALA 3.7 5.0 - - - +
409M ALA* 1.3 80.9 - - - +
411M LYS* 1.3 66.0 + - - +
412M LEU 4.7 0.3 - - - +
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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
------------------------------------------------------------
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