Contacts of the helix formed by residues 295 - 315 (chain C) in PDB entry 3MY0
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 GLU 295 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C THR 4.1 2.6 + - - -
294C LEU* 1.3 71.7 - - - +
296C PRO* 1.4 86.7 - - + +
297C HIS* 2.5 47.9 + - - +
298C LEU* 2.8 23.9 + - + +
299C ALA* 3.0 10.0 + - - +
413C ILE* 4.5 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C LEU 3.6 0.8 - - - +
295C GLU* 1.4 94.0 - - + +
297C HIS* 1.3 61.5 + - - +
299C ALA* 3.2 3.9 + - + +
300C LEU* 3.0 23.5 + - - +
412C THR* 3.9 16.4 - - + -
413C ILE* 3.5 24.2 - - + +
414C VAL* 4.9 7.0 - - + -
460C VAL* 5.2 19.8 - - + +
461C LEU* 5.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B ASN* 3.4 35.9 + - + -
295C GLU* 2.5 32.5 + - - +
296C PRO* 1.3 71.4 - - - +
298C LEU* 1.3 62.9 + - - +
300C LEU* 3.4 6.6 + - - +
301C ARG* 3.1 51.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C PHE* 4.3 13.5 - - + -
292C GLN* 6.2 0.2 - - + -
293C THR 4.6 3.8 - - - +
294C LEU* 3.5 33.9 - - + -
295C GLU* 2.8 18.3 + - + +
297C HIS* 1.3 83.4 - - + +
299C ALA* 1.3 66.1 + - - +
301C ARG* 3.0 7.8 + - + -
302C LEU* 3.0 35.3 + - + +
342C LEU* 3.9 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C LEU* 4.2 4.4 - - + +
295C GLU 3.0 6.7 + - - +
296C PRO* 3.2 9.6 + - + +
298C LEU* 1.3 78.2 - - - +
300C LEU* 1.3 55.9 + - - +
302C LEU* 3.5 5.0 + - - +
303C ALA* 3.0 28.8 + - - +
408C ILE* 3.8 21.9 - - + +
409C ALA* 5.9 0.2 - - - -
412C THR* 3.2 37.7 - - + +
464C LEU* 5.6 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C PRO 3.0 12.0 + - - +
297C HIS* 3.7 10.8 - - - +
299C ALA* 1.3 73.2 - - - +
301C ARG* 1.3 60.8 + - - +
303C ALA* 3.8 3.5 - - + +
304C VAL* 2.7 41.0 + - + +
460C VAL* 4.7 17.9 - - + +
464C LEU* 4.3 21.2 - - + +
489C LEU* 3.4 44.2 - - + +
492C ILE* 4.2 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C HIS* 3.1 36.9 + - + +
298C LEU* 3.0 14.9 + - + +
300C LEU* 1.3 79.3 - - - +
302C LEU* 1.3 57.8 + - - +
304C VAL* 3.2 10.5 - - + +
305C SER* 2.9 27.4 + - - -
341C ASN* 2.7 40.6 + - - +
342C LEU* 3.2 23.3 + - - +
343C GLN* 3.7 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C LEU* 4.1 8.3 - - + -
288C PHE* 4.2 7.6 - - + -
294C LEU* 3.9 26.5 - - + -
298C LEU* 3.0 45.5 + - + +
299C ALA* 3.8 3.6 - - - +
301C ARG* 1.3 76.2 - - - +
303C ALA* 1.3 63.7 + - - +
305C SER* 3.0 17.1 + - - -
306C ALA* 3.0 11.6 + - - +
338C VAL* 3.9 28.3 - - + -
342C LEU 4.1 12.3 - - - +
344C CYS* 3.3 28.1 - - - -
408C ILE* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ALA 3.0 20.3 + - - +
300C LEU* 3.8 10.5 - - + +
302C LEU* 1.3 78.0 - - - +
304C VAL* 1.3 62.5 + - - +
306C ALA* 3.8 3.5 - - - +
307C ALA* 3.0 23.6 + - - +
401C PHE* 4.0 4.0 - - - -
405C LEU* 3.8 25.8 - - + -
408C ILE* 4.2 11.9 - - + +
464C LEU* 5.4 6.5 - - + -
489C LEU* 3.8 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C LEU* 2.7 26.2 + - + +
301C ARG* 3.2 18.6 - - + +
303C ALA* 1.3 74.9 - - - +
305C SER* 1.3 61.3 + - - +
307C ALA* 3.2 4.2 + - - +
308C CYS* 2.9 31.3 + - - -
343C GLN* 5.5 5.2 - - - +
486C LYS* 4.6 1.1 - - + +
489C LEU* 3.6 45.7 - - + +
490C GLN* 4.2 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C ASN* 3.4 28.9 - - - +
301C ARG 2.9 17.0 + - - -
302C LEU* 3.0 8.8 + - - -
304C VAL* 1.3 78.7 - - - +
306C ALA* 1.3 64.8 + - - +
308C CYS* 3.1 11.2 + - - +
309C GLY 3.0 17.8 + - - -
343C GLN* 3.7 16.8 - - - -
344C CYS* 2.9 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C LEU* 5.9 2.2 - - + -
302C LEU 3.0 13.6 + - - +
303C ALA* 3.8 5.2 - - - +
305C SER* 1.3 81.4 + - - +
307C ALA* 1.3 61.3 + - - +
309C GLY* 3.2 4.0 + - - +
310C LEU* 3.1 22.5 + - - +
331C PHE* 4.8 10.6 - - + -
336C VAL* 4.9 4.9 - - + -
344C CYS* 3.9 19.6 - - + +
345C CYS* 6.2 0.2 - - - +
346C ILE* 4.1 8.9 - - - +
401C PHE* 4.0 15.8 - - + -
404C VAL* 5.9 2.9 - - + -
408C ILE* 5.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ALA 3.0 14.7 + - - +
304C VAL 3.4 9.9 - - - +
305C SER 3.2 0.2 - - - -
306C ALA* 1.3 74.0 - - - +
308C CYS* 1.3 60.4 + - - +
310C LEU* 4.0 3.0 - - - +
311C ALA* 3.0 30.8 + - - +
401C PHE* 3.8 20.8 - - + -
482C ALA* 4.4 3.6 - - - +
485C ILE* 4.2 3.1 - - + -
486C LYS* 4.0 29.4 - - - +
489C LEU* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ASP* 4.8 4.7 - - - -
253C HIS* 4.5 7.3 + - + -
255C ASN* 3.3 22.4 - - - +
304C VAL* 2.9 25.2 + - - -
305C SER* 3.1 6.5 + - - +
307C ALA* 1.3 72.7 - - - +
309C GLY* 1.3 67.2 + - - +
311C ALA* 3.4 2.1 + - - +
312C HIS* 3.0 25.6 + - - +
486C LYS* 3.8 35.5 + - - +
490C GLN* 4.4 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C HIS* 5.0 0.4 - - - -
255C ASN* 3.5 31.1 - - - +
256C ILE* 4.2 2.8 - - - +
305C SER 3.0 10.7 + - - -
306C ALA 3.2 4.0 + - - -
308C CYS* 1.3 78.8 - - - +
310C LEU* 1.3 60.5 + - - +
312C HIS* 3.3 5.6 + - - +
313C LEU* 3.1 24.8 + - - +
346C ILE* 3.4 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ALA 3.1 15.5 + - - +
307C ALA* 4.1 6.3 - - - +
309C GLY* 1.3 71.6 - - - +
311C ALA* 1.3 66.0 + - - +
313C LEU* 3.3 12.6 + - + +
314C HIS* 3.0 45.5 + - + +
328C HIS* 4.9 1.1 - - + -
331C PHE* 4.1 21.8 - - + -
346C ILE* 3.3 10.1 - - + +
397C ASP* 3.9 19.5 - - + +
398C ILE* 4.3 11.4 - - + -
401C PHE* 3.8 35.9 - - + -
482C ALA* 4.0 16.2 - - + -
485C ILE* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C ALA 3.0 19.3 + - - +
308C CYS 3.7 4.0 - - - +
310C LEU* 1.3 76.2 - - - +
312C HIS* 1.3 58.2 + - - +
314C HIS* 3.2 2.2 + - - +
315C VAL* 2.9 35.8 + - - +
482C ALA* 3.8 24.8 - - - +
483C LEU* 4.2 10.9 - - + +
486C LYS* 3.9 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ARG* 6.0 3.6 - - + +
250C LEU 5.0 1.2 + - - -
251C LEU* 3.3 30.7 - - + -
252C ARG 4.1 3.3 + - - -
253C HIS* 3.3 36.6 - + + +
256C ILE* 3.1 20.9 - - + +
308C CYS 3.0 17.9 + - - +
309C GLY 3.5 4.9 - - - +
310C LEU 3.2 0.2 - - - -
311C ALA* 1.3 76.5 - - - +
313C LEU* 1.3 62.3 + - - +
315C VAL* 3.4 22.8 - - + +
317C ILE* 4.9 15.1 - - + +
323C LYS* 3.7 29.7 - - + +
486C LYS* 5.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C LEU* 4.5 10.1 - - + -
256C ILE* 3.8 23.3 - - + -
309C GLY 3.1 10.4 + - - +
310C LEU* 3.5 15.9 - - + +
312C HIS* 1.3 81.9 - - - +
314C HIS* 1.3 57.2 + - + +
315C VAL 4.3 0.2 - - - +
323C LYS* 5.2 0.2 - - - -
324C PRO 4.2 1.9 - - - +
325C ALA* 3.7 1.7 - - - -
326C ILE* 2.6 73.3 + - + +
328C HIS* 4.2 28.5 - - + +
346C ILE* 4.1 24.9 - - + -
349C LEU* 4.9 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C LEU* 3.0 35.5 + - + +
311C ALA* 3.2 5.6 + - - +
313C LEU* 1.3 78.6 - - + +
315C VAL* 1.3 59.2 + - - +
316C GLU 3.5 0.3 + - - -
325C ALA* 3.2 22.7 - - - +
326C ILE 3.3 18.2 - - - +
327C ALA* 4.3 0.2 - - - -
394C LYS* 3.5 65.7 + - + +
397C ASP* 2.8 31.6 + - + +
398C ILE* 4.3 10.1 - - + +
482C ALA* 4.0 13.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C ALA 2.9 20.6 + - - +
312C HIS* 3.4 21.8 - - + +
313C LEU 4.3 1.6 - - - +
314C HIS* 1.3 76.4 - - - +
316C GLU* 1.3 75.1 + - - +
317C ILE* 3.6 14.0 + - + -
323C LYS* 4.3 7.6 - - - +
324C PRO 4.5 0.3 - - - +
325C ALA* 4.4 1.3 - - - -
483C LEU* 5.2 21.5 - - + -
----------------------------------------------------------
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