Contacts of the helix formed by residues 329 - 356 (chain C) in PDB entry 1SMK
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 ASN 329 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C LEU* 6.1 0.6 - - - +
230C SER* 3.3 22.1 + - - +
243C ILE* 5.9 5.3 - - - +
328C LEU* 1.3 75.0 - - - +
330C GLU* 1.3 54.4 + - - +
331C TYR* 3.3 10.7 + - - +
332C GLU* 2.8 59.2 + - - +
333C ARG* 2.7 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C ASN* 1.3 74.6 - - - +
331C TYR* 1.3 56.2 + - - +
333C ARG* 3.1 35.5 + - - +
334C ILE* 2.9 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 4.1 19.9 + - - -
226C LEU* 6.1 4.0 - - + -
227C PRO 6.1 0.7 - - - -
243C ILE* 3.3 34.3 - - + -
244C SER* 3.5 19.8 + - - -
247C THR* 3.0 38.1 + - + +
329C ASN* 3.3 10.6 + - - +
330C GLU* 1.3 77.4 - - - +
332C GLU* 1.3 74.2 + - + +
334C ILE* 3.1 14.0 + - + +
335C GLY* 3.0 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C LEU* 3.7 11.0 - - + +
227C PRO 4.5 6.7 - - - +
228C LEU* 3.3 19.5 - - + -
229C LEU* 3.1 14.6 + - + +
230C SER* 2.7 46.6 + - - -
328C LEU* 3.4 19.5 - - + +
329C ASN* 2.8 48.0 + - - +
331C TYR* 1.3 82.9 - - + +
333C ARG* 1.3 52.2 + - - +
335C GLY 3.1 1.3 + - - +
336C LEU* 2.7 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C LEU* 3.8 25.0 + - + +
329C ASN 2.7 16.3 + - - +
330C GLU* 3.1 41.6 + - - +
332C GLU* 1.3 74.5 - - - +
334C ILE* 1.3 62.4 + - + +
336C LEU* 3.4 9.0 + - + +
337C GLU* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C GLU* 2.9 26.1 + - + +
331C TYR* 3.1 12.5 + - + +
333C ARG* 1.3 78.7 - - + +
335C GLY* 1.3 61.6 + - - +
337C GLU* 3.6 7.0 + - - +
338C LYS* 3.4 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C VAL 4.2 4.0 - - - +
226C LEU* 3.9 17.2 - - - +
251C GLN* 6.2 1.3 - - - -
331C TYR 3.0 13.6 + - - -
332C GLU 3.6 2.5 - - - -
334C ILE* 1.3 76.8 - - - +
336C LEU* 1.3 58.8 + - - +
338C LYS* 3.2 13.4 + - - +
339C ALA* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C VAL* 4.8 1.3 - - + -
226C LEU* 3.4 21.7 - - + +
308C PHE* 3.6 31.9 - - + -
325C LEU* 3.9 18.4 - - + -
328C LEU* 3.8 18.4 - - + -
332C GLU 2.7 20.5 + - - +
333C ARG* 3.6 9.2 - - + +
334C ILE 3.3 0.2 - - - -
335C GLY* 1.3 73.4 - - - +
337C GLU* 1.3 57.5 + - - +
339C ALA* 3.0 5.3 + - + +
340C LYS* 2.9 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C ARG 3.2 11.0 + - - +
334C ILE* 3.8 10.5 - - - +
336C LEU* 1.3 79.1 - - - +
338C LYS* 1.3 62.2 + - + +
340C LYS* 3.4 21.4 + - - +
341C LYS* 3.1 62.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 3.8 36.4 + - - +
223C VAL* 4.1 29.9 - - + +
334C ILE* 3.4 29.6 + - + +
335C GLY* 3.2 13.4 + - - +
336C LEU 3.2 0.2 - - - -
337C GLU* 1.3 80.6 - - + +
339C ALA* 1.3 63.9 + - - +
341C LYS* 3.4 6.1 + - - +
342C GLU* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C GLY* 4.8 9.4 - - - -
223C VAL* 3.4 23.5 + - - +
224C THR* 3.4 24.0 + - - +
226C LEU* 5.0 4.7 - - + -
308C PHE* 5.1 1.1 - - + -
335C GLY 2.9 11.6 + - - +
336C LEU* 3.4 15.5 - - + +
338C LYS* 1.3 77.6 - - - +
340C LYS* 1.3 55.8 + - - +
342C GLU* 4.0 0.2 - - - -
343C LEU* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C THR* 4.3 23.9 - - - +
304C GLU* 5.0 8.3 + - - -
305C LEU* 3.7 20.6 - - + +
308C PHE* 4.2 15.5 - - + -
325C LEU* 5.6 0.2 - - - +
336C LEU* 2.9 50.5 + - + +
337C GLU* 3.8 23.3 + - - +
339C ALA* 1.3 77.2 - - - +
341C LYS* 1.3 63.3 + - + +
344C ALA* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C GLU* 3.1 48.1 + - + +
338C LYS* 3.4 6.5 + - - +
340C LYS* 1.3 81.1 - - + +
342C GLU* 1.3 59.7 + - - +
344C ALA* 4.1 10.7 - - - +
345C GLY 4.2 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C ASN* 5.7 1.6 + - - +
221C ALA* 4.1 20.8 - - - +
222C GLY* 5.2 1.2 - - - -
223C VAL* 4.1 20.6 + - + +
224C THR* 4.6 7.0 - - - +
338C LYS 3.3 15.0 + - - +
339C ALA 4.1 1.6 - - - +
340C LYS 3.2 0.4 - - - -
341C LYS* 1.3 75.5 - - - +
343C LEU* 1.3 68.2 + - - +
344C ALA 3.2 0.4 - - - -
345C GLY* 3.3 11.1 + - - -
346C SER* 3.3 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C ASN* 3.3 44.9 - - + +
218C GLY* 3.8 14.4 - - - +
219C GLY* 4.3 1.3 - - - -
224C THR* 3.7 7.1 + - - +
297C PHE* 3.9 11.2 - - + -
305C LEU* 3.6 14.8 - - + -
307C PHE 3.7 8.5 - - - +
308C PHE* 3.5 36.1 - - + -
339C ALA 2.9 18.2 + - - +
340C LYS 3.3 0.2 + - - -
342C GLU* 1.3 77.3 - - - +
344C ALA* 1.3 63.3 + - - +
346C SER* 2.9 5.9 + - - -
347C ILE* 2.9 30.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
305C LEU* 4.0 22.1 - - + +
340C LYS 3.0 16.5 + - - +
341C LYS* 4.1 7.9 - - - +
342C GLU 3.2 0.4 - - - -
343C LEU* 1.3 76.5 - - - +
345C GLY* 1.3 61.1 + - - +
347C ILE* 3.3 6.0 + - - +
348C GLU* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C LYS 4.2 3.4 + - - -
342C GLU 3.3 7.7 + - - -
343C LEU 3.2 0.6 - - - -
344C ALA* 1.3 78.6 - - - +
346C SER* 1.3 56.4 + - - +
348C GLU* 3.9 5.9 - - - +
349C LYS* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ASP* 5.3 4.8 + - - -
165C ASN* 3.7 32.8 + - - +
166C SER* 2.5 34.0 + - - -
342C GLU* 3.3 19.1 + - - +
343C LEU* 2.9 11.1 + - - -
345C GLY* 1.3 75.5 - - - +
347C ILE* 1.3 61.1 + - - +
349C LYS* 3.6 5.0 + - - -
350C GLY 3.4 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C ASN 3.9 14.6 - - - +
169C PRO* 3.9 14.7 - - + +
297C PHE* 4.6 0.9 - - + -
305C LEU* 4.2 8.1 - - + -
306C PRO* 3.7 28.5 - - + -
307C PHE* 3.8 39.5 - - + +
343C LEU* 2.9 28.5 + - + +
344C ALA* 3.6 8.5 - - - +
345C GLY 3.2 0.2 - - - -
346C SER* 1.3 75.6 - - - +
348C GLU* 1.3 61.6 + - - +
350C GLY* 3.1 3.5 + - - -
351C VAL* 2.8 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C ALA 3.1 15.8 + - - +
345C GLY* 4.0 5.8 - - - +
347C ILE* 1.3 79.3 - - - +
349C LYS* 1.3 58.1 + - - +
351C VAL* 4.3 16.8 - - - +
352C SER* 2.8 53.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ASP* 3.1 38.3 + - - +
134C PHE* 3.4 48.3 - - + +
166C SER* 4.1 2.5 - - - +
345C GLY 3.0 20.9 + - - +
346C SER* 3.6 7.9 - - - +
347C ILE 3.1 0.2 - - - -
348C GLU* 1.3 77.6 - - - +
350C GLY* 1.3 57.3 + - - +
352C SER* 3.8 3.9 - - - -
353C PHE* 3.1 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C PHE* 4.3 0.9 - - - -
166C SER* 3.5 14.8 + - - -
170C ILE* 3.3 44.3 - - - +
346C SER 3.4 4.4 + - - -
347C ILE 3.1 6.4 + - - -
349C LYS* 1.3 77.7 - - - +
351C VAL* 1.3 65.6 + - - +
353C PHE* 3.2 10.4 + - - +
354C ILE* 3.7 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C PRO* 4.0 11.7 - - + +
173C GLU* 3.8 25.4 - - + +
306C PRO* 5.8 1.1 - - + -
307C PHE* 5.1 4.7 - - + -
347C ILE* 2.8 39.8 + - + +
348C GLU* 3.9 19.5 - - - +
350C GLY* 1.3 72.6 - - - +
352C SER* 1.3 58.6 + - - +
354C ILE 3.3 0.7 + - - -
355C ARG* 3.1 58.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C GLU* 2.8 34.9 + - - -
349C LYS* 3.8 4.9 - - - -
351C VAL* 1.3 75.8 - - - +
353C PHE* 1.3 60.8 + - - +
354C ILE 3.0 7.3 + - - -
355C ARG* 3.9 5.2 - - - +
356C SER* 3.0 37.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C PHE* 3.8 27.1 - + + -
135C LYS* 5.2 8.1 - - + -
138C ALA* 3.7 31.4 - - + -
139C GLY* 3.9 13.2 - - - -
142C LYS* 4.2 16.8 + - + -
170C ILE* 3.9 15.9 - - + -
349C LYS 3.1 14.3 + - - +
350C GLY* 3.2 10.0 + - - +
352C SER* 1.3 75.8 - - - +
354C ILE* 1.3 76.6 + - + +
356C SER* 4.6 3.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LYS* 3.7 43.2 + - + +
170C ILE* 3.8 29.2 - - + +
173C GLU* 3.6 36.6 - - + +
174C VAL* 3.8 12.1 - - + +
177C LYS* 5.0 21.6 + - + +
350C GLY 3.7 3.1 + - - +
351C VAL 3.3 3.0 + - - +
352C SER 3.0 0.4 - - - -
353C PHE* 1.3 91.2 - - + +
355C ARG* 1.3 59.4 + - + +
356C SER 3.0 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C GLU* 3.0 31.6 + - + +
176C LYS* 5.1 7.4 - - - +
351C VAL* 3.1 37.1 + - + +
352C SER* 4.8 2.7 - - - -
354C ILE* 1.3 77.2 - - + +
356C SER* 1.3 60.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LYS* 6.0 0.5 + - - -
352C SER* 3.0 32.7 + - - -
353C PHE* 5.1 2.9 - - - -
354C ILE 3.0 11.4 - - - +
355C ARG* 1.3 84.1 - - - +
----------------------------------------------------------
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