Contacts of the helix formed by residues 298 - 315 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ASP* 2.8 16.9 + - - +
285A SER 4.6 3.1 - - - +
286A LYS* 5.7 1.6 - - - -
295A GLY* 4.6 0.2 - - - -
297A ILE* 1.3 88.4 - - + +
299A PRO* 1.3 66.8 - - - +
300A TYR* 3.2 3.0 + - + -
301A ARG* 3.4 59.3 + - + +
302A LEU* 3.5 10.6 + - - +
298D GLU* 3.4 44.2 - - + +
300D TYR* 5.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLY* 3.5 26.9 - - - +
297A ILE 3.6 5.6 - - - +
298A GLU* 1.3 87.8 - - - +
300A TYR* 1.3 61.2 + - + +
302A LEU* 3.3 7.2 + - + +
303A PHE* 3.1 20.1 + - - +
345A GLU* 4.6 8.3 - - - +
349A ALA* 5.2 1.2 - - - +
381A TYR* 3.2 28.7 - - + +
300D TYR* 3.7 20.9 - - + -
378D LYS* 4.3 8.1 - - - +
381D TYR* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLU* 3.2 1.4 - - + -
299A PRO* 1.3 79.5 - - + +
301A ARG* 1.3 59.3 + - - +
303A PHE* 3.0 25.8 + + - +
304A LEU* 2.8 55.8 + - + +
374A THR* 4.5 2.9 + - - -
377A LEU* 4.0 15.4 - - - +
378A LYS* 3.5 29.3 - - + +
381A TYR* 3.4 39.9 + + + -
187C PRO* 4.0 12.2 - - + +
296D ALA 3.6 20.0 + - - -
297D ILE 3.2 22.7 - - - +
298D GLU* 5.2 1.1 - - - -
299D PRO* 3.7 22.4 - - + -
300D TYR* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 5.2 13.2 + - + +
262A THR 5.7 2.5 + - - -
264A ILE* 4.1 30.2 - - + +
265A GLU* 4.2 15.7 - - - +
284A ASP* 3.0 27.7 + - - +
285A SER* 3.2 30.9 + - - +
298A GLU* 3.4 42.7 + - - +
299A PRO 3.4 0.4 - - - -
300A TYR* 1.3 78.3 - - - +
302A LEU* 1.3 64.1 + - - +
304A LEU* 3.1 14.1 + - - +
305A VAL* 3.0 27.9 + - + +
286D LYS* 5.9 4.5 - - - +
297D ILE 5.5 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 4.2 14.4 - - + -
282A PHE* 3.9 33.4 - - + -
294A ALA* 4.4 7.0 - - + -
295A GLY* 4.0 26.9 - - - +
298A GLU 3.5 8.4 + - - +
299A PRO* 3.3 10.7 + - + +
300A TYR 3.2 0.2 - - - -
301A ARG* 1.3 81.0 - - - +
303A PHE* 1.3 61.6 + - - +
305A VAL* 3.2 9.0 + - + +
306A PHE* 3.1 27.0 + - + -
345A GLU* 3.9 30.1 - - + +
346A ILE* 4.3 6.3 - - + -
349A ALA* 3.7 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PRO 3.1 7.9 + - - +
300A TYR* 3.0 36.9 + + - +
302A LEU* 1.3 77.2 - - - +
304A LEU* 1.3 70.7 + - + +
306A PHE* 3.2 3.0 + - - +
307A ASN* 2.8 29.8 + - + +
349A ALA* 3.9 13.2 - - + +
352A GLN* 3.6 34.1 - - + +
353A ALA* 3.6 28.0 - - + -
356A VAL* 4.0 14.8 - - + -
377A LEU* 3.5 31.2 - - + -
381A TYR* 3.7 25.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A GLU* 3.5 31.4 - - + +
300A TYR* 2.8 35.8 + - + +
301A ARG* 3.1 12.8 + - - +
303A PHE* 1.3 92.4 - - + +
305A VAL* 1.3 64.6 + - - +
307A ASN* 3.4 10.8 + - + +
308A GLU* 3.4 23.6 + - - +
377A LEU* 4.0 10.8 - - + -
187C PRO* 3.8 32.8 - - + -
228C TYR* 3.7 11.2 - - + +
297D ILE* 5.3 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 4.5 18.8 - - + -
264A ILE* 4.8 4.7 - - + -
265A GLU* 4.3 26.5 - - + +
268A VAL* 4.4 4.0 - - + +
280A PHE* 3.9 34.1 - - + -
282A PHE* 4.6 11.0 - - + -
301A ARG* 3.0 23.1 + - + +
302A LEU* 3.5 11.4 - - + +
303A PHE 3.2 0.2 - - - -
304A LEU* 1.3 78.1 - - - +
306A PHE* 1.3 63.4 + - + +
308A GLU* 3.0 16.3 + - - +
309A LEU* 3.2 16.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 3.5 26.9 - + - -
282A PHE* 3.6 29.2 - + - -
302A LEU* 3.1 24.5 + - + +
303A PHE 3.7 7.0 - - - +
305A VAL* 1.3 78.0 - - + +
307A ASN* 1.3 60.0 - - - +
309A LEU* 3.1 25.1 + - + +
310A VAL* 2.9 33.6 + - - +
324A HIS* 4.5 0.4 - - - -
346A ILE* 3.5 39.9 - - + -
349A ALA* 3.7 17.5 - - + +
350A TYR* 3.9 21.5 - + + -
353A ALA* 3.8 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PHE* 2.8 19.4 + - + +
304A LEU* 3.4 18.9 + - + +
305A VAL 3.1 0.2 - - - -
306A PHE* 1.3 77.0 - - - +
308A GLU* 1.3 70.6 + - - +
310A VAL 3.5 0.2 + - - -
311A ASP* 2.9 28.2 + - - +
353A ALA* 4.0 4.0 - - + +
356A VAL* 4.1 3.6 - - - +
358A ARG* 2.9 39.6 + - - +
361A LEU* 5.3 2.6 - - - +
377A LEU* 4.0 34.8 - - - +
188C GLY* 5.5 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A GLU* 3.5 24.9 - - + +
268A VAL* 4.3 15.0 - - + -
269A ALA* 3.4 20.3 - - + +
272A ILE* 4.2 4.2 - - + +
304A LEU 3.7 11.3 - - - +
305A VAL 3.0 9.2 + - - +
307A ASN* 1.3 93.2 + - - +
309A LEU* 1.3 64.7 + - - +
311A ASP* 3.3 13.1 + - - +
312A ALA* 3.0 22.9 + - - +
315A ARG* 4.6 5.7 + - - -
190C SER 5.7 0.5 - - - +
191C ASN* 6.0 0.7 - - - -
192C PHE* 3.4 31.6 + - - +
193C THR* 5.1 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 4.0 6.3 - - + -
272A ILE* 4.2 0.2 - - + -
277A LEU* 4.0 4.3 - - + -
280A PHE* 3.3 42.6 - - + -
282A PHE* 4.8 0.2 - - + -
305A VAL* 3.5 14.1 - - + +
306A PHE* 3.1 43.7 + - + +
308A GLU* 1.3 77.4 - - - +
310A VAL* 1.3 62.5 + - + +
312A ALA* 3.4 16.5 - - - +
313A GLU* 3.5 6.2 + - - +
320A PHE* 3.8 33.5 - - + -
322A PRO* 4.8 2.0 - - + -
324A HIS* 4.0 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE 2.9 18.9 + - - +
309A LEU* 1.3 74.8 - - + +
311A ASP* 1.3 61.0 + - - +
313A GLU* 3.2 14.7 + - - +
314A ALA* 2.9 24.2 + - + +
350A TYR* 4.4 14.6 - - + -
353A ALA* 3.6 23.3 - - + +
354A LEU* 4.1 26.7 - - + -
358A ARG* 3.5 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ASN* 2.9 21.0 + - - +
308A GLU* 3.6 15.0 - - - +
309A LEU 3.3 0.2 - - - -
310A VAL* 1.3 77.1 - - - +
312A ALA* 1.3 58.3 + - - +
314A ALA* 2.9 13.3 + - - +
315A ARG* 2.8 57.5 + - - +
358A ARG* 4.0 16.0 + - - +
191C ASN* 2.9 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 4.0 11.4 - - + -
308A GLU 3.0 13.3 + - - +
309A LEU 3.4 11.9 - - - +
311A ASP* 1.3 76.7 - - - +
313A GLU* 1.3 60.7 + - - +
315A ARG* 3.3 11.3 + - - +
316A GLY 3.3 3.6 + - - -
317A VAL* 3.1 40.9 + - + +
320A PHE* 3.5 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 3.2 27.0 + - - -
309A LEU 3.5 7.2 + - - +
310A VAL* 3.2 17.6 + - - +
311A ASP 3.1 0.6 - - - -
312A ALA* 1.3 75.8 - - - +
314A ALA* 1.3 67.6 + - - +
316A GLY* 3.0 14.4 + - - +
317A VAL 4.8 3.1 - - - +
320A PHE* 4.9 5.5 - - + -
350A TYR* 5.5 0.5 + - - -
354A LEU* 5.3 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A VAL* 2.9 13.7 + - + +
311A ASP* 2.9 20.6 + - - +
313A GLU* 1.3 80.2 - - - +
315A ARG* 1.3 58.5 + - + +
316A GLY 3.2 0.9 + - - -
358A ARG* 4.4 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ALA* 5.3 1.8 + - - +
272A ILE* 4.4 13.1 - - - +
273A GLN* 5.0 4.9 - - - +
308A GLU* 4.6 7.3 + - - -
311A ASP* 2.8 49.9 + - - +
312A ALA* 3.8 20.5 - - - +
313A GLU 3.1 0.4 - - - -
314A ALA* 1.3 76.9 - - + +
316A GLY* 1.3 63.6 + - - +
317A VAL* 3.6 18.1 + - + +
191C ASN* 4.2 8.7 - - - +
193C THR* 3.2 44.2 + - - +
194C ARG* 3.9 32.8 + - + +
----------------------------------------------------------
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