Contacts of the helix formed by residues 298 - 315 (chain C) in PDB entry 3M0V
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 298 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLU* 3.3 44.4 - - + +
300B TYR* 5.2 1.1 - - + -
284C ASP* 2.9 13.6 + - - +
285C SER 4.7 2.4 - - - +
286C LYS* 5.8 1.2 - - - -
297C ILE* 1.3 90.2 - - + +
299C PRO* 1.3 66.3 - - - +
300C TYR 3.2 2.9 - - - +
301C ARG* 3.3 62.9 + - + +
302C LEU* 3.5 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TYR* 3.7 20.0 - - + -
378B LYS* 4.2 9.0 - - - +
381B TYR* 3.8 17.7 - - + -
295C GLY* 3.5 28.2 - - - +
297C ILE 3.6 7.0 - - - +
298C GLU* 1.3 89.0 - - - +
300C TYR* 1.3 60.6 + - - +
302C LEU* 3.2 7.2 + - + +
303C PHE* 3.1 19.9 + - - +
345C GLU* 4.6 6.7 - - - +
349C ALA* 5.3 1.0 - - - +
381C TYR* 3.2 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PRO* 4.2 8.4 - - + +
296B ALA 3.6 20.2 + - - -
297B ILE 3.3 20.9 - - - +
298B GLU* 5.3 1.1 - - + -
299B PRO* 3.8 22.2 - - + -
300B TYR* 5.9 0.4 - - + +
298C GLU 3.2 1.6 - - - -
299C PRO* 1.3 79.1 - - + +
301C ARG* 1.3 58.5 + - - +
303C PHE* 3.1 18.1 + + - +
304C LEU* 2.9 59.1 + - + +
374C THR* 4.5 3.5 + - - -
377C LEU* 4.0 15.4 - - - +
378C LYS* 3.5 26.9 - - + +
381C TYR* 3.4 51.1 + + + +
----------------------------------------------------------
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
----------------------------------------------------------
286B LYS* 5.9 4.7 - - - +
297B ILE 5.6 0.2 + - - -
255C LEU* 5.3 15.4 + - + +
262C THR 5.8 3.0 + - - -
264C ILE* 4.4 27.8 - - + +
265C GLU* 4.3 14.4 - - - +
283C ASN 5.7 0.2 + - - -
284C ASP* 2.9 27.1 + - - +
285C SER* 3.1 31.1 + - - +
298C GLU* 3.3 47.5 + - - +
300C TYR* 1.3 78.6 - - - +
302C LEU* 1.3 64.4 + - - +
304C LEU* 3.3 13.0 + - - +
305C VAL* 3.1 29.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
255C LEU* 4.2 14.6 - - + -
282C PHE* 3.9 33.7 - - + -
283C ASN 5.7 0.4 - - - +
284C ASP* 6.5 0.2 - - - -
294C ALA* 4.5 9.0 - - + -
295C GLY* 4.1 26.9 - - - +
298C GLU 3.5 5.6 + - - +
299C PRO* 3.2 12.7 + - + +
300C TYR 3.2 0.8 - - - -
301C ARG* 1.3 79.0 - - - +
303C PHE* 1.3 61.6 + - - +
305C VAL* 3.3 7.2 + - + +
306C PHE* 3.1 30.0 + - + -
345C GLU* 4.0 28.9 - - + +
346C ILE* 4.3 5.6 - - + +
349C ALA* 3.8 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C PRO 3.1 5.2 + - - +
300C TYR* 3.1 34.7 + + - +
302C LEU* 1.3 80.9 - - - +
304C LEU* 1.3 71.5 + - + +
306C PHE* 3.1 3.0 + - - -
307C ASN* 2.8 30.0 + - + +
349C ALA* 3.9 17.9 - - + +
352C GLN* 3.7 28.0 - - + +
353C ALA* 3.6 24.2 - - + -
356C VAL* 3.9 15.9 - - + -
377C LEU* 3.6 33.2 - - + -
381C TYR* 3.7 24.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PRO* 3.8 31.6 - - + -
228A TYR* 3.8 11.2 - - + +
297B ILE 5.3 1.6 - - - +
265C GLU* 3.5 32.8 - - + +
300C TYR* 2.9 39.6 + - + +
301C ARG* 3.3 8.5 + - - +
303C PHE* 1.3 92.9 - - + +
305C VAL* 1.3 62.0 + - - +
307C ASN* 3.3 15.6 + - + +
308C GLU* 3.3 18.7 + - - +
377C LEU* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C LEU* 4.5 18.6 - - + -
264C ILE* 4.8 3.4 - - + -
265C GLU* 4.2 27.1 - - + +
268C VAL* 4.2 6.2 - - + +
280C PHE* 3.9 32.8 - - + -
282C PHE* 4.6 12.6 - - + -
301C ARG* 3.1 21.4 + - + +
302C LEU* 3.5 10.8 - - + +
303C PHE 3.2 0.2 - - - -
304C LEU* 1.3 76.9 - - - +
306C PHE* 1.3 63.6 + - + +
308C GLU* 3.2 15.2 + - - +
309C LEU* 3.3 17.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C PHE* 3.5 30.3 - + - -
282C PHE* 3.7 29.4 - + - -
302C LEU* 3.1 28.8 + - + +
303C PHE 3.6 7.0 - - - +
305C VAL* 1.3 75.0 - - - +
307C ASN* 1.3 60.4 + - - +
309C LEU* 3.2 22.3 + - + +
310C VAL* 2.8 36.0 + - - +
324C HIS* 4.5 0.4 - - - -
346C ILE* 3.5 37.9 - - + -
349C ALA* 3.7 26.0 - - + +
350C TYR* 3.8 26.0 - + + -
353C ALA* 3.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLY* 5.5 2.4 - - - -
303C PHE* 2.8 22.3 + - + +
304C LEU* 3.4 15.7 + - + +
305C VAL 3.1 0.4 - - - -
306C PHE* 1.3 77.8 - - - +
308C GLU* 1.3 73.4 + - - +
311C ASP* 3.0 23.8 + - - +
353C ALA* 4.2 3.4 - - + -
356C VAL* 4.2 1.7 - - - +
358C ARG* 2.8 42.6 + - - +
361C LEU* 4.9 4.2 - - - +
377C LEU* 3.6 36.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A SER 5.6 1.0 - - - +
191A ASN* 6.1 1.0 - - - -
192A PHE* 3.3 32.9 + - - +
193A THR* 5.3 0.7 + - - -
265C GLU* 3.6 24.7 - - + +
268C VAL* 4.3 14.6 - - + -
269C ALA* 3.5 19.6 - - + +
272C ILE* 4.3 3.9 - - + +
304C LEU 3.3 11.5 + - - +
305C VAL 3.2 7.7 + - - +
307C ASN* 1.3 92.8 + - - +
309C LEU* 1.3 62.0 + - - +
311C ASP* 3.4 9.6 + - - +
312C ALA* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C VAL* 4.0 7.0 - - + -
272C ILE* 4.1 0.9 - - + -
277C LEU* 3.9 7.4 - - + -
280C PHE* 3.5 40.8 - - + -
282C PHE* 4.9 0.9 - - + -
305C VAL* 3.4 15.9 - - + +
306C PHE* 3.2 35.8 + - + +
308C GLU* 1.3 77.2 - - - +
310C VAL* 1.3 57.7 + - + +
312C ALA* 3.4 4.2 + - - +
313C GLU* 3.0 27.5 + - - +
320C PHE* 3.6 34.0 - - + -
322C PRO* 4.6 2.0 - - + -
324C HIS* 3.9 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C PHE* 2.8 21.5 + - + +
309C LEU* 1.3 74.6 - - + +
311C ASP* 1.3 56.4 + - - +
313C GLU* 3.1 11.2 + - - +
314C ALA* 2.7 37.1 + - + +
350C TYR* 4.2 26.5 - - + -
353C ALA* 3.3 27.6 - - + +
354C LEU* 4.2 17.5 - - + +
358C ARG* 3.5 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASN* 3.9 11.9 + - - -
307C ASN* 3.0 19.8 + - - +
308C GLU* 3.7 11.5 - - - +
309C LEU 3.3 0.2 - - - -
310C VAL* 1.3 76.7 - - - +
312C ALA* 1.3 65.2 + - - +
314C ALA* 3.3 6.8 + - - +
315C ARG* 3.0 66.0 + - - +
358C ARG* 3.5 24.8 + - - +
361C LEU* 5.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ILE* 4.1 26.2 - - + -
308C GLU 3.1 16.8 + - - +
309C LEU 3.6 4.9 - - - +
311C ASP* 1.3 79.8 + - - +
313C GLU* 1.3 63.0 + - - +
315C ARG* 3.4 20.8 + - - +
316C GLY 3.6 0.5 + - - -
317C VAL* 3.3 34.2 - - + +
320C PHE* 4.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LYS* 4.0 20.3 + - - +
309C LEU 3.0 13.9 + - - +
310C VAL* 3.4 14.7 - - - +
312C ALA* 1.3 74.9 - - - +
314C ALA* 1.3 67.7 + - - +
316C GLY* 3.1 15.7 + - - -
317C VAL* 5.2 0.9 - - - +
320C PHE* 5.0 11.9 - - + -
350C TYR* 3.9 24.1 + - - -
354C LEU* 4.1 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C VAL* 2.7 23.4 + - + +
311C ASP* 3.6 9.0 - - - +
313C GLU* 1.3 75.3 + - - +
315C ARG* 1.3 58.4 + - + +
316C GLY 3.4 2.3 + - - -
358C ARG* 4.7 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASN* 3.5 20.4 + - - +
193A THR* 6.0 1.8 - - - -
194A ARG* 3.4 35.7 - - - +
311C ASP* 3.0 46.5 + - - +
312C ALA* 3.6 11.0 - - - +
313C GLU 3.1 0.4 - - - -
314C ALA* 1.3 78.1 - - + +
316C GLY* 1.3 67.8 + - - +
317C VAL* 4.2 4.0 - - + +
362C SER* 5.9 4.6 - - - -
365C GLN* 5.7 1.0 + - - -
----------------------------------------------------------
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