Contacts of the helix formed by residues 332 - 356 (chain C) in PDB entry 3U1K
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 ASP 332 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLN* 5.3 3.5 + - - +
277C PHE* 6.1 0.7 - - - -
330C GLU 3.7 2.6 + - - -
331C ALA* 1.3 72.4 - - - +
333C PRO* 1.3 69.9 - - - +
334C TYR* 2.8 35.0 + - - +
335C GLU* 2.7 43.9 + - + +
336C ILE* 3.3 5.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 333 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C LYS* 5.6 11.7 - - + -
331C ALA 3.5 7.8 - - - +
332C ASP* 1.3 93.4 - - - +
334C TYR* 1.3 62.5 + - + +
336C ILE* 3.5 14.2 + - + +
337C ILE* 3.1 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PRO 5.0 4.1 + - - -
94C GLN* 3.2 57.4 - - + +
332C ASP* 2.8 31.5 + - - +
333C PRO* 1.3 76.4 - - + +
335C GLU* 1.3 61.7 + - - +
337C ILE* 3.3 20.4 + - + +
338C GLU* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C LYS* 5.5 9.3 + - - -
278C THR 4.6 1.4 - - - +
279C PRO* 3.8 17.6 - - + +
280C SER* 2.8 38.4 + - - -
283C ILE* 4.8 11.9 - - + -
331C ALA* 4.7 8.4 - - + +
332C ASP* 2.7 32.4 + - + +
334C TYR* 1.3 74.3 - - - +
336C ILE* 1.3 54.7 + - + +
338C GLU* 3.3 5.8 + - - +
339C SER* 2.7 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C ILE* 4.0 10.3 - - + -
287C THR* 5.3 0.7 + - - +
321C GLU* 3.6 29.8 - - + +
324C LEU* 3.8 47.4 - - + +
325C LYS* 4.0 20.2 - - + +
328C PHE* 4.6 2.0 - - + +
331C ALA* 4.4 24.5 - - + +
332C ASP 3.3 8.0 + - - +
333C PRO* 3.6 14.1 - - + +
334C TYR 3.2 0.2 - - - -
335C GLU* 1.3 76.3 - - - +
337C ILE* 1.3 64.6 + - - +
339C SER* 3.3 8.4 - - - -
340C PHE* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C ARG* 5.2 4.7 - - - +
321C GLU* 3.5 31.1 - - - +
333C PRO* 3.1 23.0 + - + +
334C TYR* 3.6 23.6 - - + +
335C GLU 3.3 0.2 - - - -
336C ILE* 1.3 74.1 - - + +
338C GLU* 1.3 65.6 + - - +
340C PHE* 3.2 4.3 + - - +
341C ASN* 3.1 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLN 4.7 4.0 - - - +
147C PHE* 4.0 22.7 - - + -
277C PHE 4.5 7.9 - - - +
279C PRO* 3.8 23.8 - - + -
334C TYR 2.9 17.2 + - - +
335C GLU* 3.7 6.3 - - - +
337C ILE* 1.3 77.3 - - - +
339C SER* 1.3 62.7 + - - +
341C ASN* 3.2 18.8 + - - +
342C VAL* 3.0 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C PRO* 4.0 14.7 - - - +
283C ILE* 3.0 32.0 + - - +
284C VAL* 3.5 8.2 - - - +
287C THR* 2.7 26.5 + - - -
335C GLU 2.7 19.1 + - - -
336C ILE 3.3 4.0 - - - -
338C GLU* 1.3 76.6 - - - +
340C PHE* 1.3 62.6 + - - +
342C VAL* 3.4 2.3 + - - +
343C VAL* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C THR* 3.9 19.2 - - + +
291C ALA* 4.2 9.2 - - + -
295C LEU* 4.0 20.6 - - + -
313C VAL* 3.8 20.9 - - + -
316C ILE* 3.9 10.3 - - + -
317C ARG* 3.5 56.1 - - + -
320C THR* 3.4 26.2 - - - -
321C GLU* 3.9 12.3 - - + +
324C LEU* 6.3 0.2 - - + -
336C ILE 3.0 13.5 + - - +
337C ILE 3.2 7.8 + - - +
339C SER* 1.3 76.8 - - - +
341C ASN* 1.3 59.1 + - - +
343C VAL* 3.2 2.3 + - - +
344C ALA* 2.9 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C ARG* 3.0 27.8 + - - +
337C ILE* 3.1 30.8 + - - +
338C GLU* 3.2 20.0 + - - +
340C PHE* 1.3 77.1 - - - +
342C VAL* 1.3 57.7 + - - +
344C ALA* 3.9 5.7 - - - +
345C LYS* 2.9 32.8 + - - +
540C ASN* 4.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C PRO* 4.1 19.7 - - + -
284C VAL* 4.5 21.8 - - + -
338C GLU* 3.0 30.6 + - + +
339C SER* 3.7 5.8 - - - +
341C ASN* 1.3 75.5 - - - +
343C VAL* 1.3 59.9 + - - +
345C LYS* 3.7 7.9 - - + +
346C GLU* 2.9 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C VAL* 3.7 21.5 - - + +
287C THR* 3.7 14.4 - - + +
288C HIS* 3.6 48.9 - - + +
291C ALA* 4.7 2.9 - - + -
292C MET 4.9 1.1 - - - +
295C LEU* 3.7 18.6 - - + -
339C SER 3.1 13.0 + - - +
340C PHE* 3.6 7.6 - - + +
342C VAL* 1.3 75.1 - - - +
344C ALA* 1.3 67.5 + - - +
346C GLU* 3.2 7.0 + - - +
347C VAL* 2.9 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU* 3.6 26.9 - - + -
299C PHE* 3.7 11.9 - - + -
313C VAL* 5.0 4.7 - - + -
340C PHE* 2.9 32.9 + - + +
341C ASN* 3.9 7.0 - - - +
343C VAL* 1.3 73.0 - - - +
345C LYS* 1.3 64.3 + - - +
347C VAL* 3.3 0.3 + - - -
348C PHE* 2.9 26.5 + - - +
540C ASN* 4.8 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C ASN 2.9 19.0 + - - +
342C VAL* 3.7 7.2 - - - +
344C ALA* 1.3 77.5 - - - +
346C GLU* 1.3 57.1 + - - +
348C PHE* 3.3 1.2 + - - +
349C ARG* 2.9 72.0 + - - +
539C TYR 4.9 5.2 + - - +
540C ASN* 3.3 39.4 + - - +
541C GLY 5.1 4.8 + - - -
542C ASP* 5.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C HIS* 3.0 35.6 + - - -
342C VAL* 2.9 21.6 + - + +
343C VAL* 3.2 4.2 + - - +
345C LYS* 1.3 76.7 - - - +
347C VAL* 1.3 72.2 + - - +
349C ARG* 4.0 6.4 - - - +
350C SER* 2.8 51.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C HIS* 4.3 2.9 - - + -
292C MET* 4.0 31.0 - - + +
295C LEU* 3.9 11.4 - - + -
296C TYR* 3.8 36.3 - - + +
299C PHE* 4.2 4.5 - - + -
343C VAL* 2.9 25.3 + - + +
344C ALA 3.8 2.7 - - - +
346C GLU* 1.3 89.7 - - - +
348C PHE* 1.3 65.9 + - - +
350C SER* 3.5 4.0 + - - -
351C ILE* 3.3 24.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C PHE* 3.6 37.2 - + + +
344C ALA 2.9 18.0 + - - +
345C LYS 3.5 3.1 - - - +
347C VAL* 1.3 79.9 - - - +
349C ARG* 1.3 70.0 + - + +
351C ILE* 3.4 11.3 + - - +
352C VAL* 3.6 23.8 + - + +
359C CYS* 3.8 22.4 - - + -
514C VAL* 5.4 5.2 - - + -
536C ILE* 3.7 40.2 - - + -
537C GLU* 3.6 34.5 - - + -
540C ASN* 3.7 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C LYS* 2.9 46.6 + - - +
346C GLU* 4.1 5.2 - - - +
348C PHE* 1.3 81.1 - - + +
350C SER* 1.3 63.7 + - - +
352C VAL* 3.2 8.5 + - - +
353C LEU* 3.1 28.6 + - + +
513C LEU 4.6 1.2 + - - -
514C VAL* 3.6 19.0 - - + +
515C THR* 3.0 33.6 + - - +
540C ASN 2.9 34.3 + - - +
541C GLY* 3.6 6.7 - - - -
542C ASP* 2.9 40.9 + - - -
563C LEU* 5.3 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C GLU* 2.8 42.0 + - - +
347C VAL* 3.9 5.2 - - - -
348C PHE 3.3 0.2 - - - -
349C ARG* 1.3 78.3 - - - +
351C ILE* 1.3 57.2 + - - +
353C LEU* 3.4 10.9 + - - +
354C ASN* 2.9 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C TYR* 3.7 41.1 - - + -
299C PHE* 3.6 34.5 - - + +
300C THR* 4.1 13.9 - - + -
302C TYR* 5.8 1.6 - - + +
347C VAL* 3.3 18.5 + - + +
348C PHE 3.7 6.1 - - - +
349C ARG 3.2 0.6 - - - -
350C SER* 1.3 75.3 - - - +
352C VAL* 1.3 68.4 + - + +
354C ASN* 4.8 1.8 - - - +
355C GLU* 2.8 49.2 + - - +
356C TYR 3.8 0.2 + - - -
357C LYS 3.9 13.9 - - - +
358C ARG 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C PHE* 3.8 26.5 - - + +
349C ARG* 3.2 8.0 + - - +
351C ILE* 1.3 77.6 - - + +
353C LEU* 1.3 57.5 + - - +
356C TYR* 2.9 28.6 + - - -
357C LYS 3.9 15.3 - - - +
358C ARG* 4.8 13.9 - - + -
359C CYS 5.7 0.9 - - - +
364C LEU* 4.2 8.3 - - + -
514C VAL* 4.5 18.4 - - + -
528C ARG* 3.6 28.3 + - + -
530C LEU* 4.0 21.1 - - + -
537C GLU* 5.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C ARG* 3.1 26.3 + - + +
350C SER* 3.8 8.7 - - - +
352C VAL* 1.3 79.2 - - - +
354C ASN* 1.3 64.7 + - - +
356C TYR* 3.5 5.5 - - - -
514C VAL* 3.8 33.9 - - + +
515C THR 4.1 5.2 - - - +
516C LYS* 4.1 35.2 - - + +
526C ASP* 4.4 2.7 - - + -
527C TYR* 4.3 7.6 - - - +
528C ARG* 2.6 50.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C SER* 2.9 33.7 + - - +
351C ILE* 4.8 1.3 - - - +
353C LEU* 1.3 81.3 - - - +
355C GLU* 1.3 70.8 + - + +
356C TYR* 3.7 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C TYR* 2.5 36.6 + - - -
300C THR* 4.1 6.6 - - - +
302C TYR* 4.4 8.0 + - - -
351C ILE* 2.8 33.8 + - + +
354C ASN* 1.3 88.7 - - + +
356C TYR* 1.3 76.0 + - - +
357C LYS* 2.9 15.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C VAL 2.9 17.5 + - - -
353C LEU 3.5 16.2 - - - -
354C ASN 3.9 8.7 - - - -
355C GLU* 1.3 82.4 - - - +
357C LYS* 1.3 58.4 + - - +
363C ASP* 4.2 14.0 - - - +
364C LEU* 4.0 32.0 - - + +
526C ASP* 4.5 2.1 + - - -
528C ARG* 3.0 44.2 + - - -
----------------------------------------------------------
Back to top of page
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