Contacts of the helix formed by residues 339 - 357 (chain L) in PDB entry 3CX5
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 339 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H PRO* 4.5 12.3 - - + -
309L TYR* 3.9 31.0 - - + -
311L LEU* 4.2 13.9 - - + +
336L ASN* 3.3 39.1 + - - +
338L THR* 1.3 90.7 - - - +
340L ILE* 1.3 64.4 + - - +
341L ASP* 3.1 9.2 - - - -
342L ASP* 3.0 31.6 + - - +
343L LEU* 3.2 11.1 + - - +
1N MET* 3.8 34.3 - - + -
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Residues in contact with ILE 340 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259L ALA* 3.7 17.0 - - + -
261L ILE* 5.3 6.5 - - + -
311L LEU 5.9 0.4 - - - -
334L THR* 4.1 13.7 - - + -
336L ASN 3.7 13.6 + - - +
337L VAL* 4.0 16.6 + - - +
338L THR 3.7 1.2 - - - -
339L MET* 1.3 76.3 - - - +
341L ASP* 1.3 63.2 + - - +
343L LEU* 3.1 12.7 + - + +
344L ILE* 3.0 28.0 + - + +
438L GLN 3.5 24.7 - - - +
439L ILE* 4.4 3.8 - - + -
441L GLY* 3.9 8.9 + - - +
442L LEU* 3.8 44.0 - - + +
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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
----------------------------------------------------------
338L THR 3.9 4.5 - - - +
339L MET* 3.6 11.3 - - - -
340L ILE* 1.3 79.5 - - - +
342L ASP* 1.3 60.9 + - - +
344L ILE* 4.0 5.0 - - - +
345L HIS* 2.9 30.7 + - - +
441L GLY 3.8 11.6 + - - +
443L LEU* 3.9 30.6 - - + +
448L ILE* 6.2 2.7 - - - -
4N ARG* 3.7 19.7 + - - +
5N LYS* 3.0 30.0 + - - +
19N ASP* 4.3 3.3 - - - +
13S TRP* 5.9 6.8 - - + +
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Residues in contact with ASP 342 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311L LEU* 4.1 16.6 - - + -
339L MET* 3.0 25.5 + - - +
341L ASP* 1.3 75.6 - - - +
343L LEU* 1.3 59.9 - - - +
345L HIS* 4.2 5.5 - - - +
346L PHE* 2.9 44.5 + - + -
1N MET* 3.9 10.9 - - - +
2N ALA* 3.1 30.3 + - - +
4N ARG* 5.3 0.9 + - - -
5N LYS* 2.7 33.5 + - - +
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Residues in contact with LEU 343 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261L ILE* 6.4 0.4 - - + -
302L LEU* 6.0 0.2 - - + -
306L ILE* 4.4 11.9 - - + -
311L LEU* 3.5 41.1 - - + +
312L CYS* 4.1 14.6 - - + -
315L PHE* 5.5 2.5 - - + -
330L PHE* 4.9 5.4 - - + -
332L THR* 3.6 36.3 - - + +
334L THR* 4.4 12.3 - - + -
339L MET 3.2 9.3 + - - +
340L ILE* 3.1 13.6 + - + +
342L ASP* 1.3 77.0 - - - +
344L ILE* 1.3 68.6 + - + +
346L PHE* 4.1 1.7 - - - +
347L THR* 2.8 40.2 + - - +
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Residues in contact with ILE 344 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261L ILE* 4.2 26.0 - - + -
263L LEU* 4.2 2.2 - - + -
330L PHE* 4.0 25.1 - - + -
340L ILE* 3.0 20.2 + - + +
341L ASP* 4.0 4.3 - - - +
343L LEU* 1.3 81.9 - - + +
345L HIS* 1.3 63.9 + - - +
347L THR* 3.4 3.2 + - - -
348L LEU* 3.0 36.8 + - + +
442L LEU* 3.9 20.2 - - + -
448L ILE* 3.7 42.0 - - + -
451L ASP* 5.8 0.9 - - - +
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Residues in contact with HIS 345 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341L ASP 2.9 21.0 + - - +
342L ASP* 3.4 7.2 + - - +
344L ILE* 1.3 77.0 - - - +
346L PHE* 1.3 72.8 + + - +
348L LEU* 3.8 1.2 - - - +
349L LYS* 2.9 56.9 + - + +
451L ASP* 2.8 41.8 + - - +
2N ALA* 4.3 24.3 - - + +
4N ARG* 4.9 12.8 + - - +
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Residues in contact with PHE 346 (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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302L LEU* 3.7 15.5 - - + -
305L ASN* 3.7 47.5 - - + +
306L ILE* 4.5 2.7 - - + -
311L LEU* 3.7 17.5 - - + -
342L ASP* 2.9 29.5 + - + +
343L LEU 4.1 1.8 - - - +
345L HIS* 1.3 83.8 - + - +
347L THR* 1.3 66.1 + - - +
349L LYS* 3.3 8.4 + - + +
350L GLN* 3.0 27.2 + - - +
1N MET* 3.7 42.6 - - - -
2N ALA* 4.0 5.4 - - - -
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Residues in contact with THR 347 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302L LEU* 3.8 23.3 - - + +
317L HIS* 4.0 8.3 - - + -
330L PHE* 3.8 38.8 - - + -
343L LEU* 2.8 28.6 + - - +
344L ILE 3.7 3.6 - - - -
346L PHE* 1.3 75.2 - - - +
348L LEU* 1.3 64.1 + - + +
350L GLN* 3.0 6.1 + - - +
351L TRP* 3.0 51.6 + - + +
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Residues in contact with LEU 348 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263L LEU* 4.1 11.7 - - + -
330L PHE* 4.8 2.0 - - + -
344L ILE* 3.0 31.5 + - + +
345L HIS 4.1 0.4 - - - +
347L THR* 1.3 85.4 - - + +
349L LYS* 1.3 57.1 + - - +
351L TRP* 3.2 28.8 + - + +
352L ASN* 3.0 31.2 + - - -
448L ILE* 3.4 43.3 - - + +
451L ASP* 3.8 24.2 - - + +
452L MET* 3.9 25.0 - - - +
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Residues in contact with LYS 349 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345L HIS* 2.9 46.4 + - + +
346L PHE* 3.6 10.3 - - + +
347L THR 3.2 0.2 - - - -
348L LEU* 1.3 77.6 - - - +
350L GLN* 1.3 63.3 + - + +
352L ASN* 2.8 43.4 + - - +
353L ARG* 3.5 10.0 + - - +
451L ASP* 3.0 34.4 + - - -
453L SER 3.0 20.8 + - - -
454L MET* 3.9 24.6 - - + +
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Residues in contact with GLN 350 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285L PHE* 3.4 33.3 - - + -
301L LYS* 3.8 17.7 - - - +
302L LEU* 3.7 33.2 - - + +
305L ASN* 3.9 13.9 - - - +
346L PHE 3.0 15.0 + - - +
347L THR* 3.0 10.2 + - - +
349L LYS* 1.3 76.6 - - - +
351L TRP* 1.3 66.1 + - - +
353L ARG* 2.9 60.6 + - - +
354L LEU 3.8 0.2 + - - -
362L GLU* 4.8 0.6 + - - -
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Residues in contact with TRP 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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263L LEU* 3.7 34.8 - - + -
265L VAL* 5.1 3.6 - - + -
285L PHE* 3.6 27.3 - + - -
317L HIS* 3.0 29.3 + + - -
328L TRP* 3.6 27.8 - + - -
329L GLY* 3.8 20.9 - - - -
330L PHE* 3.7 23.6 - + - -
347L THR* 3.0 27.6 + - + +
348L LEU* 3.2 20.2 + - + +
350L GLN* 1.3 75.7 - - + +
352L ASN* 1.3 62.2 + - - +
354L LEU* 2.9 22.5 + - - +
355L THR* 4.2 1.7 + - - -
426L LEU* 4.1 17.6 - - + +
452L MET* 4.0 26.2 - - + -
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Residues in contact with ASN 352 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348L LEU 3.0 14.7 + - - -
349L LYS* 2.8 46.9 + - - +
351L TRP* 1.3 78.2 - - - +
353L ARG* 1.3 61.5 + - - +
355L THR* 3.1 18.5 + - - -
356L ILE* 3.6 12.0 + - - +
426L LEU* 6.4 0.2 - - - -
427L TRP* 3.8 9.3 - - + -
451L ASP 3.1 18.4 + - - -
452L MET* 3.3 24.4 + - - +
453L SER* 3.4 2.3 - - - +
454L MET* 3.2 27.0 - - + +
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Residues in contact with ARG 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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285L PHE* 5.0 4.2 - - + -
301L LYS* 3.8 19.0 - - - +
349L LYS 3.7 9.0 - - - +
350L GLN* 2.9 51.5 + - - +
352L ASN* 1.3 78.0 - - + +
354L LEU* 1.3 58.5 + - + +
356L ILE* 3.8 3.6 - - + -
357L SER* 2.8 59.7 + - - +
358L VAL* 2.8 14.4 + - - +
359L THR* 4.1 4.8 - - - +
362L GLU* 2.8 42.8 + - - -
454L MET* 5.3 7.0 - - + -
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Residues in contact with LEU 354 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281L ALA* 3.6 29.6 - - + -
284L ILE* 3.8 26.0 - - + -
285L PHE* 3.7 37.7 - - + -
328L TRP* 4.4 1.3 - - + -
351L TRP 2.9 12.2 + - - +
353L ARG* 1.3 79.8 - - + +
355L THR* 1.3 57.2 + - - +
358L VAL* 3.7 19.7 - - + +
418L VAL* 3.8 6.9 - - + +
419L LYS* 3.2 30.5 + - - +
421L TRP* 4.1 3.4 - - + -
422L ALA* 3.5 14.0 - - + +
426L LEU* 3.9 17.0 - - + -
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Residues in contact with THR 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 TRP 5.0 0.7 + - - -
352L ASN* 3.1 10.4 + - - -
353L ARG 3.1 0.6 - - - -
354L LEU* 1.3 79.8 - - - +
356L ILE* 1.3 63.7 + - + +
419L LYS* 3.6 24.1 - - - +
422L ALA* 3.2 31.0 + - - +
423L GLY* 3.7 18.1 - - - -
426L LEU* 4.9 1.2 - - - +
427L TRP* 3.7 32.3 + - + +
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Residues in contact with ILE 356 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352L ASN 3.8 9.4 - - - +
353L ARG* 3.3 2.4 + - + -
355L THR* 1.3 89.8 - - + +
357L SER* 1.3 73.1 + - - +
419L LYS* 3.5 18.3 + - - +
427L TRP* 4.1 19.3 - - + -
454L MET* 3.5 33.4 - - + -
456L ARG* 3.7 40.2 - - - +
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Residues in contact with SER 357 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353L ARG* 2.8 51.4 + - - +
356L ILE* 1.3 84.7 - - - +
358L VAL* 1.3 67.1 + - - +
359L THR* 3.2 9.7 + - - +
419L LYS* 4.4 3.8 - - - +
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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