Contacts of the helix formed by residues 325 - 346 (chain I) 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 THR 325 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315I VAL* 3.4 30.3 - - + +
316I GLU 2.9 27.8 + - - +
317I TYR* 3.6 15.0 - - + -
318I HIS* 3.0 22.7 + - - +
320I GLU* 3.8 25.0 + - - +
323I GLY 3.6 0.8 + - - -
324I THR* 1.3 73.2 - - - +
326I VAL* 1.3 69.8 + - + +
328I CYS* 3.3 3.6 + - - +
329I TRP* 3.1 33.5 + - - -
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Residues in contact with VAL 326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I ILE* 3.7 10.3 - - + +
44I ASN 4.4 1.8 - - - +
45I TYR* 3.6 38.1 - - + -
65I ILE* 4.1 11.7 - - + +
68I ASP* 4.2 4.0 - - + -
69I VAL* 3.7 24.4 - - + +
315I VAL* 4.4 5.4 - - + -
317I TYR* 4.0 11.7 - - + -
324I THR* 3.3 19.1 - - + -
325I THR* 1.3 88.3 - - + +
327I GLN* 1.3 63.0 + - - +
329I TRP 4.1 0.7 - - - -
330I SER* 2.8 31.2 + - - -
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Residues in contact with GLN 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I ASP* 3.1 54.7 + - + +
69I VAL* 5.4 0.2 - - - +
71I GLU* 4.9 7.1 - - - +
72I ARG* 3.6 46.2 + - + +
323I GLY* 3.6 4.0 - - - -
324I THR* 2.8 35.4 + - + +
326I VAL* 1.3 76.1 - - - +
328I CYS* 1.3 65.5 + - - +
330I SER* 3.3 5.9 + - - -
331I GLU* 3.1 24.6 + - - +
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Residues in contact with CYS 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ARG* 4.8 2.2 - - - +
320I GLU* 3.9 20.2 - - + -
322I GLY 4.3 1.8 - - - -
323I GLY* 3.7 22.0 - - - -
324I THR 3.1 19.2 + - - -
325I THR* 3.6 6.5 - - - +
327I GLN* 1.3 79.7 - - - +
329I TRP* 1.3 67.2 + - + +
331I GLU* 3.5 0.5 + - - +
332I THR* 3.3 12.5 + - - -
292K THR* 2.9 55.2 + - - +
293K CYS* 4.2 3.4 - - - +
329K TRP* 4.6 4.7 - - + -
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Residues in contact with TRP 329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I ILE* 3.9 16.6 - - + -
290I THR* 3.7 41.6 - - + +
292I THR* 3.6 24.5 - - - -
293I CYS* 3.4 36.0 - - + +
312I ASN* 4.0 7.9 - - + +
315I VAL* 3.9 21.3 - - + +
320I GLU* 5.9 2.6 + - - +
325I THR* 3.1 28.6 + - - +
328I CYS* 1.3 78.1 - - + +
330I SER* 1.3 59.7 + - - +
332I THR* 3.3 5.0 + - - -
333I LEU* 2.9 33.4 + - - +
320K GLU* 5.6 3.9 + - + -
328K CYS* 4.7 4.3 - - + -
329K TRP* 3.4 49.4 - + - +
332K THR* 4.3 9.6 - - + -
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Residues in contact with SER 330 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I PRO* 4.7 1.6 - - - +
43I ILE* 3.7 23.9 - - - +
69I VAL* 4.4 11.4 - - - +
72I ARG* 4.4 5.9 - - - +
73I MET* 4.2 20.1 - - - +
81I ILE* 5.2 2.2 - - - -
326I VAL 2.8 24.0 + - - -
327I GLN* 3.3 8.3 + - - -
329I TRP* 1.3 76.9 - - - +
331I GLU* 1.3 55.5 + - - +
333I LEU* 3.1 7.6 + - - +
334I ALA* 2.7 38.5 + - - +
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Residues in contact with GLU 331 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ARG* 2.9 22.8 + - + +
73I MET* 5.3 0.2 - - - -
76I VAL* 3.6 6.5 - - - +
78I PHE* 4.2 13.5 - - + -
327I GLN 3.1 18.2 + - - +
328I CYS 3.7 5.2 - - - +
330I SER* 1.3 76.7 + - - +
332I THR* 1.3 56.5 + - - +
334I ALA* 3.4 1.6 + - - +
335I TYR* 2.9 54.5 + - + -
288K GLY 5.4 0.9 - - - +
289K LYS* 5.6 0.2 - - - -
292K THR* 3.4 23.0 - - + +
296K SER* 2.6 25.6 + - - -
297K ASP* 3.2 29.1 + - - +
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Residues in contact with THR 332 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290I THR* 3.6 27.1 - - + +
328I CYS 3.3 3.1 + - - -
329I TRP* 3.3 11.5 + - + -
330I SER 3.2 0.4 - - - -
331I GLU* 1.3 75.6 - - - +
333I LEU* 1.3 60.1 + - - +
335I TYR* 3.3 5.2 + - - +
336I ASP* 2.9 31.2 + - - +
289K LYS* 2.7 37.3 + - + +
290K THR* 4.2 12.1 - - + +
292K THR* 2.9 17.3 + - - -
329K TRP* 4.4 5.9 - - + -
332K THR* 4.8 6.5 - - + -
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Residues in contact with LEU 333 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I PRO* 3.8 14.4 - - + -
42I GLU 3.8 17.0 - - - +
43I ILE* 4.2 9.4 - - + -
290I THR* 3.7 19.1 - - + -
310I TRP* 3.4 38.7 - - + +
311I SER 3.7 14.4 - - - +
312I ASN* 3.6 31.2 - - + +
329I TRP 2.9 20.2 + - - +
330I SER* 3.6 5.2 - - - +
332I THR* 1.3 77.6 - - - +
334I ALA* 1.3 57.1 + - - +
336I ASP* 3.0 5.5 + - - +
337I CYS* 2.9 31.5 + - - -
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Residues in contact with ALA 334 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I PRO* 3.8 12.5 - - + +
73I MET* 3.3 30.1 - - + -
78I PHE* 3.5 29.5 - - + -
330I SER 2.7 20.0 + - - +
333I LEU* 1.3 73.5 - - - +
335I TYR* 1.3 59.0 + - - +
337I CYS* 3.4 4.8 + - - +
338I ALA* 3.0 26.0 + - - +
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Residues in contact with TYR 335 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I VAL* 3.4 11.6 - - + +
78I PHE* 3.8 11.2 - + - -
331I GLU* 2.9 53.5 + - + +
332I THR 3.6 4.3 - - - +
334I ALA* 1.3 74.3 - - - +
336I ASP* 1.3 67.1 + - - +
338I ALA* 3.0 11.2 + - + +
339I LEU 3.1 2.4 + - - -
289K LYS* 3.7 29.4 - - + -
297K ASP* 2.9 19.8 + - - -
298K VAL* 3.3 12.5 - - - -
300K GLY* 3.2 25.4 + - - -
301K ASN* 2.9 39.4 - - - +
359K SER* 4.6 0.2 - - - -
360K ASP* 3.2 24.2 - - - -
363K ARG* 3.7 12.8 - - - -
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Residues in contact with ASP 336 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289I LYS* 3.9 12.3 - - - -
290I THR* 2.7 29.0 + - - +
304I MET* 4.5 9.0 - - - +
310I TRP* 2.7 29.3 + - + +
332I THR* 2.9 18.9 + - - +
333I LEU 3.0 2.9 + - - +
335I TYR* 1.3 76.7 - - - +
337I CYS* 1.3 62.9 + - - +
339I LEU* 3.3 6.2 + - - +
340I MET* 3.2 25.7 + - + +
289K LYS* 2.7 44.0 + - - +
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Residues in contact with CYS 337 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I THR* 3.3 30.5 + - - +
40I ILE 3.6 7.6 - - - -
41I PRO* 3.5 32.3 - - + -
310I TRP* 3.9 20.9 - - - -
333I LEU 2.9 15.2 + - - +
334I ALA 3.6 8.3 - - - +
336I ASP* 1.3 74.7 - - - +
338I ALA* 1.3 54.2 + - - +
340I MET* 3.1 5.3 + - - -
341I ASN* 2.7 42.8 + - - +
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Residues in contact with ALA 338 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I PHE* 5.0 3.4 - - + -
334I ALA 3.0 13.0 + - - +
335I TYR* 3.0 11.4 + - - +
337I CYS* 1.3 75.2 - - - +
339I LEU* 1.3 53.4 + - - +
341I ASN* 3.8 7.6 - - - +
342I THR* 2.7 39.0 + - - -
301K ASN* 4.2 1.1 - - - +
359K SER* 3.7 17.0 - - - +
363K ARG* 3.7 20.4 - - - +
12L VAL* 4.6 12.8 - - + +
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Residues in contact with LEU 339 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335I TYR 3.1 6.8 + - - +
336I ASP* 3.5 10.3 - - - +
338I ALA* 1.3 74.4 - - - +
340I MET* 1.3 59.8 + - + +
342I THR* 3.2 7.7 + - - -
343I ALA* 3.0 26.5 + - - +
352I LEU* 4.1 15.3 - - + -
356I MET* 6.5 0.4 - - - -
289K LYS* 4.4 14.6 - - - +
301K ASN* 3.8 17.4 + - - +
304K MET* 5.3 1.6 - - + -
339K LEU* 4.5 17.3 - - + -
352K LEU* 4.3 15.9 - - + -
355K LEU* 3.9 14.4 - - + +
356K MET* 3.8 44.2 - - + +
359K SER* 4.7 1.6 - - - -
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Residues in contact with MET 340 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I PHE* 3.2 50.2 - - + -
39I THR* 3.8 20.6 - - + +
304I MET* 4.0 26.5 - - - +
307I CYS* 3.8 31.0 - - - -
310I TRP* 4.5 6.3 - - + -
336I ASP 3.2 20.5 + - - +
337I CYS* 3.1 18.7 + - - +
339I LEU* 1.3 78.8 - - + +
341I ASN* 1.3 58.6 + - - +
343I ALA* 3.2 1.2 + - - +
344I LEU* 2.9 24.6 + - - +
352I LEU* 4.2 8.3 - - + -
356I MET* 4.6 4.7 - - - -
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Residues in contact with ASN 341 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I GLY 5.6 0.4 - - - +
38I TYR* 3.7 17.4 - - + +
39I THR* 2.8 52.8 + - - +
79I PRO* 5.7 6.1 - - - +
337I CYS* 2.7 26.4 + - - +
338I ALA* 4.0 6.3 - - - +
340I MET* 1.3 70.0 - - - +
342I THR* 1.3 60.8 + - - +
344I LEU* 3.5 10.9 + - + +
345I GLU* 2.9 38.2 + - + +
11L LYS 5.8 1.0 + - - -
12L VAL* 4.3 19.5 + - + +
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Residues in contact with THR 342 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338I ALA 2.7 22.6 + - - -
339I LEU* 3.3 6.3 - - - -
341I ASN* 1.3 73.6 - - - +
343I ALA* 1.3 63.1 + - - +
346I THR* 2.9 30.7 + - - +
355K LEU* 3.6 31.9 - - + +
358K LEU* 3.9 18.2 - - + -
359K SER* 3.4 16.6 - - - +
4L PHE* 3.7 30.4 - - + -
12L VAL* 4.1 3.7 - - - +
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Residues in contact with ALA 343 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I PHE* 3.8 1.1 - - + -
339I LEU 3.0 6.6 + - - +
340I MET 3.2 9.8 + - - +
342I THR* 1.3 77.9 - - - +
344I LEU* 1.3 62.8 + - - +
346I THR* 3.3 4.2 + - - -
347I LYS 3.1 3.6 + - - -
348I ASN 2.9 29.3 + - - +
349I ASP* 3.8 23.3 - - - +
352I LEU* 3.7 28.9 - - + -
355K LEU* 4.2 10.9 - - + +
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Residues in contact with LEU 344 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I PHE* 3.6 36.6 - - + +
20I GLY* 4.3 2.7 - - - -
21I VAL* 4.2 15.5 - - + -
37I GLY* 3.5 31.2 - - - +
38I TYR* 4.2 2.5 - - - -
340I MET 2.9 13.1 + - - +
341I ASN* 3.6 28.5 - - - +
343I ALA* 1.3 76.3 - - - +
345I GLU* 1.3 65.7 + - - +
347I LYS* 3.2 22.2 + - - -
349I ASP* 3.9 26.2 - - + +
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Residues in contact with GLU 345 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I GLY 4.2 9.4 - - - +
38I TYR* 5.8 0.5 - - - +
341I ASN* 2.9 26.9 + - + +
342I THR 3.3 0.4 + - - +
343I ALA 3.3 0.4 - - - -
344I LEU* 1.3 78.3 - - - +
346I THR* 1.3 59.4 + - - +
347I LYS* 3.4 8.1 + - - +
4L PHE* 4.0 12.1 - - + -
8L SER* 2.7 47.5 + - - +
11L LYS* 3.0 42.5 + - + +
12L VAL* 3.8 17.9 - - + -
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Residues in contact with THR 346 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342I THR 2.9 20.8 + - - +
343I ALA 3.6 2.4 + - - -
345I GLU* 1.3 80.1 - - - +
347I LYS* 1.3 67.0 + - - +
348I ASN* 3.0 24.9 + - - +
355K LEU* 3.7 10.7 - - - +
358K LEU* 3.8 28.5 - - + -
2L LEU* 4.5 9.0 - - + +
3L ASP 4.0 13.5 - - - +
4L PHE* 4.0 10.1 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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