Contacts of the helix formed by residues 326 - 351 (chain I) in PDB entry 5G04
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 326 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322I MET* 3.6 16.4 - - - +
323I ASN 5.3 3.1 - - - +
324I GLN 5.9 0.2 - - - -
325I LEU* 1.3 77.0 - - - +
327I VAL* 1.3 55.5 - - - +
328I LYS* 4.0 6.7 + - - +
329I GLY* 3.0 24.0 + - - -
330I LEU* 2.7 36.3 + - - +
425I MET* 4.6 3.8 - - - -
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Residues in contact with VAL 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326I THR* 1.3 75.6 - - - +
328I LYS* 1.3 63.5 + - + +
330I LEU* 3.7 3.4 + - + +
331I LYS* 3.5 26.3 + - + +
422I TYR* 3.8 33.2 - - + -
425I MET* 4.3 26.9 - - + -
426I LEU* 5.0 10.5 - - + +
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Residues in contact with LYS 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326I THR* 3.3 5.9 + - - +
327I VAL* 1.3 82.2 - - + +
329I GLY* 1.3 63.0 + - - +
331I LYS* 3.7 5.7 + - - +
332I LYS* 3.2 25.8 + - + +
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Residues in contact with GLY 329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325I LEU* 4.2 6.1 - - - -
326I THR* 3.0 25.1 + - - -
328I LYS* 1.3 75.1 - - - +
330I LEU* 1.3 53.6 + - - +
332I LYS* 3.5 4.6 + - - +
333I LEU* 2.8 36.2 + - - +
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Residues in contact with LEU 330 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325I LEU* 3.7 21.7 - - + +
326I THR 2.7 19.7 + - - +
327I VAL* 3.9 9.9 - - + +
328I LYS 3.4 0.2 - - - -
329I GLY* 1.3 72.6 - - - +
331I LYS* 1.3 59.7 + - + +
333I LEU* 3.9 5.1 - - + +
334I GLY* 2.7 33.6 + - - -
418I PHE* 3.7 51.6 - - + +
421I LEU* 3.9 24.5 - - + -
422I TYR* 4.1 17.7 - - + +
425I MET* 4.3 12.6 - - + -
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Residues in contact with LYS 331 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327I VAL* 3.5 17.5 + - + +
328I LYS* 4.1 6.5 - - + +
329I GLY 3.5 0.2 - - - -
330I LEU* 1.3 83.1 - - + +
332I LYS* 1.3 56.8 + - - +
334I GLY* 4.1 0.8 - - - -
335I GLN* 3.1 28.1 + - - +
422I TYR* 3.0 51.7 + - + -
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Residues in contact with LYS 332 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328I LYS* 3.2 20.1 + - + +
329I GLY* 3.9 4.5 - - - +
331I LYS* 1.3 76.5 - - - +
333I LEU* 1.3 54.1 + - - +
334I GLY 3.3 0.2 - - - -
335I GLN* 3.2 9.1 + - + +
336I SER* 2.8 36.5 + - - +
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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
----------------------------------------------------------
282I GLN* 3.7 48.5 - - + +
283I MET* 4.7 8.7 - - - -
286I ARG* 6.1 1.1 - - - +
325I LEU* 3.8 38.6 - - + -
329I GLY 2.8 18.1 + - - +
330I LEU* 3.9 3.1 - - + +
332I LYS* 1.3 68.9 - - - +
334I GLY* 1.3 68.3 + - - +
336I SER* 3.2 6.1 + - - -
337I ILE* 3.1 42.8 + - + +
418I PHE* 4.0 19.3 - - + -
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Residues in contact with GLY 334 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330I LEU 2.7 22.8 + - - -
331I LYS* 4.3 1.1 - - - -
333I LEU* 1.3 70.6 - - - +
335I GLN* 1.3 58.1 + - - +
337I ILE* 2.7 24.5 + - - +
338I GLU* 3.1 20.6 + - - +
418I PHE* 3.8 22.4 - - - -
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Residues in contact with GLN 335 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331I LYS 3.1 22.4 + - - +
332I LYS* 3.2 11.6 + - + +
334I GLY* 1.3 76.0 - - - +
336I SER* 1.3 63.9 + - - +
338I GLU* 3.7 6.3 + - - +
339I SER* 3.1 34.0 + - - +
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Residues in contact with SER 336 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278I GLU* 5.8 5.4 - - - -
279I ILE* 3.3 4.9 - - - +
282I GLN* 3.9 20.9 + - - -
332I LYS* 2.8 17.9 + - - +
333I LEU* 3.3 11.0 + - - -
335I GLN* 1.3 77.3 - - - +
337I ILE* 1.3 61.6 + - - -
339I SER* 3.4 5.0 + - - -
340I SER* 3.0 29.1 + - - -
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Residues in contact with ILE 337 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279I ILE* 3.1 21.7 - - + +
282I GLN* 4.6 0.4 - - + +
283I MET* 3.9 8.7 - - + -
333I LEU* 3.1 31.3 + - + +
334I GLY* 2.7 15.1 + - - +
336I SER* 1.3 71.9 - - - +
338I GLU* 1.3 61.4 + - + +
340I SER* 3.9 1.2 - - - -
341I TYR* 2.9 49.7 + - + +
411I MET* 6.4 0.2 - - - -
414I PHE* 4.8 13.5 - - + -
418I PHE* 3.6 34.1 - - + -
473I GLU* 3.6 27.4 - - - +
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Residues in contact with GLU 338 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334I GLY* 3.1 16.8 + - - +
335I GLN* 4.5 5.6 - - - +
337I ILE* 1.3 81.1 - - + +
339I SER* 1.3 53.2 + - - +
341I TYR* 3.4 5.1 + - - +
342I SER* 2.8 34.5 + - - -
411I MET* 5.5 7.4 - - + +
414I PHE* 4.8 3.5 - - + +
415I LYS* 3.5 52.3 + - + +
418I PHE* 5.5 3.6 - - - +
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Residues in contact with SER 339 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335I GLN* 3.1 29.6 + - - +
336I SER* 3.4 6.9 + - - -
338I GLU* 1.3 75.1 - - - +
340I SER* 1.3 62.0 + - - +
342I SER* 3.3 8.8 - - - -
343I SER* 2.9 30.9 + - - -
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Residues in contact with SER 340 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275I ALA* 3.3 22.2 + - - +
278I GLU* 4.0 23.9 + - - +
279I ILE* 3.9 17.9 - - - +
336I SER* 3.0 16.4 + - - -
337I ILE 3.9 2.9 - - - -
339I SER* 1.3 80.6 + - - +
341I TYR* 1.3 65.0 + - - +
343I SER* 3.1 17.6 + - - -
344I ILE* 3.1 19.3 + - - +
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Residues in contact with TYR 341 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276I TRP* 4.6 1.0 + - - -
279I ILE* 4.1 17.6 - - + +
337I ILE* 2.9 37.0 + - + +
338I GLU* 3.8 5.2 - - - +
340I SER* 1.3 74.5 - - - +
342I SER* 1.3 58.7 + - - +
344I ILE* 3.3 18.6 + - + +
345I GLN* 2.9 33.5 + - - +
407I ILE* 4.0 9.5 - - + +
410I SER* 3.3 23.8 + - - -
411I MET* 4.3 29.8 - - + -
414I PHE* 4.6 2.2 - + - -
473I GLU* 3.5 35.4 + - - +
475I VAL* 3.1 41.9 - - + +
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Residues in contact with SER 342 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338I GLU 2.8 21.9 + - - -
339I SER* 3.3 10.8 - - - -
341I TYR* 1.3 71.9 - - - +
343I SER* 1.3 56.7 + - - -
345I GLN* 4.1 5.1 - - - +
346I LYS* 2.8 37.0 + - - +
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Residues in contact with SER 343 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275I ALA* 4.0 18.6 - - - -
339I SER 2.9 17.6 + - - -
340I SER* 3.1 12.5 + - - -
342I SER* 1.3 77.1 - - - +
344I ILE* 1.3 63.0 + - - +
346I LYS* 3.7 5.4 - - - +
347I LEU* 3.0 25.3 + - - +
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Residues in contact with ILE 344 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I MET* 4.3 13.2 - - + +
275I ALA* 4.1 16.6 - - + -
276I TRP* 3.7 29.4 - - + +
279I ILE* 5.4 0.2 - - + -
340I SER* 3.1 18.9 + - - +
341I TYR* 3.6 31.0 - - + +
343I SER* 1.3 71.2 - - - +
345I GLN* 1.3 67.7 + - - +
347I LEU* 2.9 19.9 + - - +
348I VAL* 2.9 21.1 + - + +
403I LEU* 5.7 0.7 - - + -
407I ILE* 3.9 23.6 - - + -
475I VAL* 4.2 4.7 - - + -
479I LEU* 3.9 19.5 - - + -
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Residues in contact with GLN 345 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341I TYR 2.9 18.3 + - - +
342I SER* 4.1 6.0 - - - +
344I ILE* 1.3 76.6 - - - +
346I LYS* 1.3 62.5 + - - +
348I VAL* 3.1 18.8 + - - +
349I ILE* 3.4 23.2 + - + +
404I LEU* 3.7 21.8 - - + +
407I ILE* 3.6 22.8 - - + +
408I ASP* 4.2 19.3 - - - +
411I MET* 4.9 6.1 - - - +
407O LEU* 5.3 2.6 + - - +
410O TRP* 3.3 38.2 + - - +
411O LYS* 4.2 5.5 - - - +
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Residues in contact with LYS 346 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342I SER* 2.8 23.4 + - - +
343I SER* 3.7 6.1 - - - +
345I GLN* 1.3 77.7 - - - +
347I LEU* 1.3 58.3 + - - +
349I ILE* 4.5 0.3 - - - +
350I SER* 3.0 31.4 + - - -
351I HIS* 4.2 1.8 + - - -
407O LEU* 4.4 19.7 - - + -
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Residues in contact with LEU 347 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145I LEU* 4.3 12.3 - - + -
146I PRO* 4.3 13.5 - - + -
268I SER* 5.1 2.2 - - - +
271I CYS* 3.8 15.3 - - + +
272I MET* 3.6 44.9 - - + +
275I ALA* 5.4 4.3 - - + -
343I SER 3.0 13.3 + - - +
344I ILE* 2.9 12.9 + - - +
346I LYS* 1.3 77.5 - - - +
348I VAL* 1.3 63.9 + - - +
351I HIS* 3.3 57.4 + - + +
352I LEU* 3.5 3.1 + - - +
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Residues in contact with VAL 348 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I MET* 3.6 16.4 - - - -
344I ILE* 2.9 24.5 + - + +
345I GLN* 3.1 5.1 + - - +
347I LEU* 1.3 77.5 - - - +
349I ILE* 1.3 65.5 + - - +
352I LEU* 3.4 27.3 + - + +
353I GLN* 3.0 36.6 + - - +
400I ALA 4.1 15.0 - - - +
403I LEU* 4.2 9.0 - - + -
404I LEU* 4.5 10.5 - - + -
407I ILE* 3.8 24.0 - - + -
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Residues in contact with ILE 349 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345I GLN* 3.4 19.5 - - - +
346I LYS 4.5 1.6 - - - +
348I VAL* 1.3 75.8 - - - +
350I SER* 1.3 63.3 + - - +
353I GLN* 3.1 31.6 - - + +
354I SER 4.0 2.4 + - - -
404I LEU* 3.5 31.0 - - + -
403O LYS* 4.9 10.2 - - - +
406O ASP* 5.1 12.8 - - + +
407O LEU* 3.7 40.2 - - + +
410O TRP* 3.5 35.0 - - + +
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Residues in contact with SER 350 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I PRO* 3.8 13.9 - - - +
346I LYS 3.0 20.5 + - - -
348I VAL 3.4 0.8 - - - -
349I ILE* 1.3 78.9 - - - +
351I HIS* 1.3 71.7 + - - +
354I SER* 3.6 14.6 + - - -
403O LYS* 4.6 11.9 - - - +
407O LEU* 3.9 28.9 - - - +
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Residues in contact with HIS 351 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I PRO* 3.6 21.0 + - + +
144I THR 3.4 23.3 - - - -
145I LEU* 3.6 12.0 - - + +
146I PRO* 4.0 14.1 - - + +
264I TYR* 3.4 29.2 + - + +
268I SER* 4.9 0.9 - - - +
346I LYS 4.2 1.2 + - - -
347I LEU* 3.3 35.2 + - + +
349I ILE 3.4 0.2 - - - -
350I SER* 1.3 97.2 - - - +
352I LEU* 1.3 68.0 + - - +
353I GLN 3.2 1.1 - - - -
354I SER* 2.5 23.8 + - - -
355I GLY* 3.0 5.9 + - - -
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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