Contacts of the helix formed by residues 338 - 356 (chain L) in PDB entry 1KYO
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 MET 338 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H PRO* 4.8 13.9 - - + -
308L TYR* 4.0 28.7 - - + +
310L LEU* 4.4 12.4 - - + +
335L ASN* 3.2 35.6 + - - +
337L THR* 1.3 91.7 - - - +
339L ILE* 1.3 65.5 + - - +
340L ASP* 3.1 6.7 - - - -
341L ASP* 3.0 35.0 + - - +
342L LEU* 3.4 6.4 + - - +
1N MET* 3.8 39.3 - - + -
5N LYS* 5.4 2.7 - - - +
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Residues in contact with ILE 339 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258L ALA* 4.1 15.5 - - + -
260L ILE* 5.2 7.0 - - + -
310L LEU 5.7 0.7 - - - -
333L THR* 4.2 14.1 - - + -
335L ASN 3.7 10.5 + - - +
336L VAL* 3.6 20.4 - - - +
337L THR 3.7 1.8 - - - -
338L MET* 1.3 75.5 - - - +
340L ASP* 1.3 59.5 + - - +
342L LEU* 2.8 30.8 + - + +
343L ILE* 3.1 16.0 + - + +
437L GLN 3.7 23.6 - - - +
438L ILE* 4.3 6.3 - - + -
440L GLY* 3.6 23.5 + - - +
441L LEU* 4.2 25.8 - - + +
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Residues in contact with ASP 340 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337L THR 4.0 16.1 - - - +
338L MET 4.2 1.1 - - - -
339L ILE* 1.3 79.5 + - - +
341L ASP* 1.3 57.8 + - - +
343L ILE* 3.8 7.4 + - - +
344L HIS* 3.0 26.0 + - - +
440L GLY* 3.6 15.7 + - - +
441L LEU* 5.8 0.2 - - - +
442L LEU* 4.1 30.3 - - + +
446L ARG* 5.6 0.2 - - - +
4N ARG* 3.7 13.4 + - - +
5N LYS* 3.2 33.8 + - - +
19N ASP* 4.4 2.8 - - - +
13S TRP* 5.0 9.1 - - - +
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Residues in contact with ASP 341 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310L LEU* 3.9 16.4 - - + -
338L MET* 3.0 31.3 + - + +
340L ASP* 1.3 77.5 - - - +
342L LEU* 1.3 68.5 + - - +
343L ILE 3.2 0.2 - - - -
344L HIS* 3.8 6.2 - - - +
345L PHE* 2.8 35.3 + - + -
1N MET* 3.9 4.3 - - - -
2N ALA* 3.3 26.1 + - - +
4N ARG* 4.8 1.2 + - - -
5N LYS* 3.0 40.6 + - - -
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Residues in contact with LEU 342 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260L ILE* 5.4 2.5 - - + -
301L LEU* 6.2 0.2 - - + -
305L ILE* 4.9 9.1 - - + +
310L LEU* 3.8 34.2 - - + +
311L CYS* 4.1 23.3 - - + -
314L PHE* 5.9 2.0 - - + -
329L PHE* 4.8 5.6 - - + -
331L THR* 3.6 33.4 - - + +
333L THR* 4.6 12.8 - - + -
338L MET 3.4 3.9 + - - +
339L ILE* 2.8 19.4 + - + +
341L ASP* 1.3 79.8 - - - +
343L ILE* 1.3 67.2 + - + +
345L PHE* 4.1 0.9 - - - +
346L THR* 2.6 40.7 + - - +
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Residues in contact with ILE 343 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260L ILE* 3.4 30.5 - - + -
262L LEU* 4.5 7.0 - - + -
329L PHE* 4.0 19.1 - - + -
339L ILE* 3.1 12.7 + - + +
340L ASP* 4.0 7.6 - - - +
342L LEU* 1.3 84.0 - - + +
344L HIS* 1.3 60.4 + - - +
346L THR* 3.3 2.8 + - - -
347L LEU* 2.8 42.7 + - + +
441L LEU* 4.1 19.5 - - + -
447L ILE* 3.6 37.7 - - + -
450L ASP* 5.3 2.5 - - - +
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Residues in contact with HIS 344 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340L ASP 3.0 21.8 + - - +
341L ASP* 3.1 9.6 + - - +
343L ILE* 1.3 77.5 - - - +
345L PHE* 1.3 79.8 + + - +
347L LEU* 3.8 1.2 - - - +
348L LYS* 2.9 56.7 + - + +
450L ASP* 3.3 29.6 + - - +
2N ALA* 3.9 26.9 - - + +
4N ARG* 4.8 9.9 + - - +
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Residues in contact with PHE 345 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301L LEU* 3.7 9.4 - - + -
304L ASN* 3.6 50.4 - - + +
305L ILE* 5.0 2.7 - - + -
310L LEU* 3.7 15.7 - - + -
341L ASP* 2.8 27.4 + - + +
342L LEU 4.2 1.3 - - - +
344L HIS* 1.3 90.9 - + - +
346L THR* 1.3 63.3 - - - +
348L LYS* 3.0 18.5 + - + +
349L GLN* 3.1 16.8 + - - +
1N MET* 3.4 48.0 - - - -
2N ALA* 3.8 7.0 - - - -
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Residues in contact with THR 346 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301L LEU* 3.7 22.5 - - + +
316L HIS* 4.3 7.2 - - + +
329L PHE* 3.5 41.3 - - + -
342L LEU* 2.6 38.2 + - - +
343L ILE 3.8 3.1 - - - -
345L PHE* 1.3 78.1 - - - +
347L LEU* 1.3 62.9 + - + +
349L GLN* 3.3 6.0 + - + +
350L TRP* 3.3 36.5 + - + +
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Residues in contact with LEU 347 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262L LEU* 4.4 10.8 - - + -
329L PHE* 4.7 2.2 - - + -
343L ILE* 2.8 34.9 + - + +
344L HIS 4.0 0.4 - - - +
346L THR* 1.3 79.9 - - + +
348L LYS* 1.3 62.9 + - - +
349L GLN 3.1 1.8 - - - -
350L TRP* 3.3 36.1 + - + +
351L ASN* 2.9 30.4 + - - -
447L ILE* 3.6 42.6 - - + +
450L ASP* 3.9 21.8 - - + +
451L MET* 4.0 16.3 - - - +
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Residues in contact with LYS 348 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344L HIS* 2.9 45.7 + - + +
345L PHE* 3.0 12.5 + - + +
347L LEU* 1.3 77.6 - - - +
349L GLN* 1.3 60.3 + - + +
351L ASN* 3.1 36.8 + - - +
352L ARG* 3.6 10.3 - - - +
450L ASP* 3.2 31.2 + - - -
452L SER 3.0 27.3 + - - -
453L MET* 3.9 18.6 - - + +
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Residues in contact with GLN 349 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284L PHE* 3.4 34.2 - - + -
300L LYS* 4.2 14.7 - - - +
301L LEU* 3.7 33.9 + - + +
304L ASN* 4.1 13.6 - - - +
345L PHE 3.1 14.5 + - - +
346L THR* 3.4 10.1 - - - +
348L LYS* 1.3 75.3 - - - +
350L TRP* 1.3 61.0 + - + +
351L ASN 3.0 1.8 - - - -
352L ARG* 2.9 65.3 + - - +
353L LEU 3.9 0.2 + - - -
361L GLU* 4.9 0.2 + - - -
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Residues in contact with TRP 350 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262L LEU* 3.5 34.3 - - + -
264L VAL* 5.1 4.5 - - + -
284L PHE* 3.5 26.4 - + - -
316L HIS* 3.0 30.0 + + - -
327L TRP* 3.6 24.8 - + - -
328L GLY* 3.8 17.3 - - - -
329L PHE* 3.6 29.2 - + - -
346L THR* 3.3 19.5 + - + +
347L LEU* 3.3 25.7 + - + +
349L GLN* 1.3 77.5 - - + +
351L ASN* 1.3 64.2 + - - +
353L LEU* 3.2 18.9 + - - +
354L THR* 4.4 3.1 + - - -
425L LEU* 4.0 21.7 - - + +
451L MET* 4.1 20.4 - - + -
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Residues in contact with ASN 351 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347L LEU 2.9 17.7 + - - -
348L LYS* 3.1 45.2 + - - +
349L GLN 3.0 0.6 - - - -
350L TRP* 1.3 79.8 - - - +
352L ARG* 1.3 62.4 + - - +
354L THR* 3.1 17.0 + - - -
355L ILE* 3.6 12.1 + - - +
426L TRP* 3.8 10.5 - - + -
450L ASP 3.2 14.9 + - - +
451L MET* 3.4 20.6 + - - +
452L SER* 4.1 2.4 - - - +
453L MET* 3.3 27.3 - - + +
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Residues in contact with ARG 352 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284L PHE* 5.1 2.9 - - + -
300L LYS* 3.6 18.8 - - - +
348L LYS 3.6 10.8 - - - +
349L GLN* 2.9 49.6 + - - +
351L ASN* 1.3 77.1 - - + +
353L LEU* 1.3 58.3 + - + +
354L THR 2.9 4.6 + - - -
355L ILE* 4.1 4.5 - - + -
356L SER* 2.7 62.7 + - - +
357L VAL* 3.0 9.9 + - + +
358L THR* 3.9 8.7 - - - +
361L GLU* 2.8 44.6 + - - -
453L MET* 6.4 0.9 - - - -
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Residues in contact with LEU 353 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280L ALA* 4.0 20.4 - - + -
283L ILE* 3.6 30.1 - - + -
284L PHE* 3.5 36.3 - - + -
327L TRP* 4.1 1.3 - - + -
350L TRP 3.2 8.0 + - - +
351L ASN 3.2 1.0 - - - -
352L ARG* 1.3 75.0 - - + +
354L THR* 1.3 56.3 + - - +
357L VAL* 3.8 15.2 - - + +
417L VAL* 3.8 14.3 - - + -
418L LYS* 3.1 31.7 + - - +
420L TRP* 4.5 3.1 - - + -
421L ALA* 3.4 14.4 - - + +
425L LEU* 3.8 22.2 - - + -
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Residues in contact with THR 354 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350L TRP 4.7 2.9 + - - -
351L ASN 3.1 3.1 + - - -
352L ARG 3.0 0.6 - - - -
353L LEU* 1.3 77.7 - - - +
355L ILE* 1.3 67.6 + - + +
418L LYS* 3.9 20.3 - - - +
421L ALA* 3.5 24.2 + - - +
422L GLY* 4.2 17.5 - - - +
425L LEU* 5.1 0.5 - - - +
426L TRP* 3.6 41.8 + - + +
455L ARG* 5.6 3.4 - - - +
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Residues in contact with ILE 355 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351L ASN 3.6 14.1 - - - +
352L ARG* 4.1 5.6 - - + +
354L THR* 1.3 86.9 - - + +
356L SER* 1.3 67.5 + - - +
357L VAL 4.0 1.1 - - - -
418L LYS* 3.3 19.7 + - - -
426L TRP* 4.3 15.7 - - + -
453L MET* 3.4 33.9 - - + -
455L ARG* 4.2 24.5 - - - +
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Residues in contact with SER 356 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352L ARG* 2.7 49.9 + - - +
355L ILE* 1.3 82.6 - - - +
357L VAL* 1.3 64.7 + - - -
358L THR* 3.1 8.8 + - - +
418L LYS* 4.8 1.1 - - - +
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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) + - + + + + + -
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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