Contacts of the helix formed by residues 311 - 335 (chain A) in PDB entry 2MBG
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 PRO 311 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLU* 3.8 15.5 - - - +
280A THR* 4.7 7.6 - - + -
309A GLU 3.6 4.0 - - - +
310A LEU* 1.3 87.3 - - - +
312A GLU* 1.3 68.0 + - - +
313A CYS* 3.9 10.1 - - - -
314A ASN* 3.0 36.9 + - - +
315A TYR* 2.8 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ARG* 4.6 16.2 - - + -
310A LEU 4.0 0.2 + - - -
311A PRO* 1.3 72.7 - - - +
313A CYS* 1.3 64.2 + - - +
315A TYR* 3.1 21.2 + - - +
316A LEU* 2.9 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 3.7 30.6 - - + +
195A ALA* 4.5 9.6 - - - -
198A VAL* 4.8 6.1 - - + -
208A ARG* 3.8 31.1 - - + +
209A LEU* 4.2 4.5 - - + +
210A PRO* 6.1 0.2 - - + -
276A GLU* 5.3 1.3 - - - -
311A PRO* 3.9 12.1 - - - -
312A GLU* 1.3 78.8 - - - +
314A ASN* 1.3 78.6 + - - +
316A LEU* 3.5 1.7 + - - +
317A LEU* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 3.1 16.3 - - - +
276A GLU* 3.1 19.1 + - - +
277A ASN 3.0 18.6 + - - -
278A LEU* 3.0 32.4 + - - +
280A THR* 4.2 1.6 - - - +
310A LEU* 3.8 8.7 - - + +
311A PRO* 3.0 23.3 + - - +
313A CYS* 1.3 91.8 - - - +
315A TYR* 1.3 58.9 + - - +
317A LEU* 3.6 3.4 - - - +
318A ILE* 2.8 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 3.2 46.9 - - + +
308A LYS* 3.0 32.7 + - + +
310A LEU* 4.3 3.5 - - - +
311A PRO 2.8 12.8 + - - +
312A GLU* 3.3 24.7 - - - +
314A ASN* 1.3 77.5 - - - +
316A LEU* 1.3 58.3 + - + +
318A ILE* 3.0 17.5 - - + +
319A SER* 2.6 28.3 + - - -
368A PHE* 3.7 28.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ILE* 3.0 35.2 - - + +
208A ARG 3.7 6.3 - - - +
209A LEU* 4.3 13.5 - - + -
312A GLU* 2.9 38.8 + - + +
313A CYS 3.9 3.8 - - - +
315A TYR* 1.3 79.9 - - + +
317A LEU* 1.3 65.8 + - - +
319A SER* 3.2 9.2 + - - +
320A TRP* 3.0 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 4.7 9.6 - - + -
209A LEU* 3.5 23.7 - - + +
210A PRO* 4.3 10.8 - - + -
213A PHE* 3.8 40.0 - - + -
271A LEU* 4.3 11.9 - - + -
278A LEU* 3.6 38.8 - - + -
313A CYS 2.9 19.0 + - - +
314A ASN* 3.6 7.4 - - - +
316A LEU* 1.3 76.3 - - - +
318A ILE* 1.3 57.0 + - - +
320A TRP* 3.3 3.3 + - - -
321A LEU* 2.9 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 4.3 19.7 - - + +
279A LEU* 3.6 29.6 - - + -
307A LEU* 4.2 28.5 - - + -
310A LEU* 4.4 4.5 - - + -
314A ASN 2.8 19.0 + - - +
315A TYR* 3.0 26.5 - - - +
317A LEU* 1.3 73.3 - - - +
319A SER* 1.3 63.7 + - - +
321A LEU* 4.7 2.2 - - + -
322A ILE* 3.1 41.3 + - + +
350A VAL* 5.7 1.8 - - + -
360A PHE* 3.8 25.6 - - + -
364A VAL* 4.5 1.9 - - + +
368A PHE* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A TYR* 2.6 22.1 + - - -
316A LEU* 3.3 14.1 - - - +
318A ILE* 1.3 80.6 - - - +
320A TRP* 1.3 61.9 + - - +
323A VAL* 2.9 37.2 + - - +
368A PHE* 3.6 29.5 - - - -
371A VAL* 3.9 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ILE* 4.2 20.4 - - + -
209A LEU* 3.8 10.8 - - + -
213A PHE* 3.3 31.2 - + + -
214A ARG* 3.6 25.8 - - + -
217A ILE* 4.5 7.9 - - + -
316A LEU* 3.0 28.9 + - + +
319A SER* 1.3 76.9 - - - +
321A LEU* 1.3 60.1 + - - +
324A HIS* 2.7 37.8 + - - +
371A VAL* 3.8 18.7 - - + +
372A VAL* 3.4 23.3 + - + +
373A LEU* 4.0 18.6 - - + -
374A LYS* 3.5 50.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A PHE* 3.3 25.2 - - + -
231A TYR* 5.7 0.7 - - + -
267A LEU* 4.8 6.3 - - + -
271A LEU* 4.2 21.1 - - + -
278A LEU* 3.9 14.1 - - + -
317A LEU* 2.9 18.9 + - + +
318A ILE* 4.3 3.1 - - + +
320A TRP* 1.3 77.4 - - - +
322A ILE* 1.3 72.5 + - + +
324A HIS* 4.9 0.2 - - - -
325A MET* 3.2 56.5 + - + +
346A LEU* 4.7 11.7 - - + -
349A THR* 4.8 2.9 - - + -
350A VAL* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ILE* 3.1 32.1 + - + +
321A LEU* 1.3 85.2 - - + +
323A VAL* 1.3 60.2 + - - +
325A MET 3.2 0.7 + - - -
326A ASP* 2.9 25.5 + - - +
346A LEU* 4.5 18.2 - - + -
350A VAL* 5.9 2.2 - - + -
357A LEU* 4.6 1.8 - - + -
360A PHE* 3.4 47.1 - - + +
361A PHE* 3.2 30.0 - - + -
364A VAL* 3.4 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A SER* 2.9 26.7 + - - +
320A TRP* 4.2 1.3 - - - +
322A ILE* 1.3 75.4 - - - +
324A HIS* 1.3 62.1 + - - +
326A ASP* 3.2 8.6 + - - +
327A HIS* 3.2 32.6 + - + -
364A VAL* 3.7 15.7 - - + -
365A GLN* 3.2 29.6 - - - +
368A PHE* 4.7 1.6 - - + -
371A VAL* 3.7 41.5 - - + +
373A LEU* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ILE* 3.4 38.9 + - + +
220A VAL* 3.6 36.6 - - + -
221A GLU* 2.7 40.8 + - - +
231A TYR* 4.7 0.6 + - - -
320A TRP 2.7 24.3 + - - +
321A LEU 4.2 1.8 - - - +
323A VAL* 1.3 75.0 - - - +
325A MET* 1.3 65.0 + - + +
327A HIS* 3.3 6.8 + - + +
328A VAL* 3.1 34.6 + - + +
373A LEU* 3.5 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ILE* 4.8 2.0 - - + -
231A TYR* 3.7 50.7 - - + +
321A LEU* 3.2 47.5 + - + +
322A ILE 3.2 0.2 + - - -
324A HIS* 1.3 83.2 - - + +
326A ASP* 1.3 60.2 + - - +
328A VAL* 3.1 20.5 - - + +
329A ILE* 3.0 32.1 + - - +
342A ILE* 3.6 27.4 - - + -
346A LEU* 4.2 10.8 - - + -
361A PHE* 3.4 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE 2.9 14.1 + - - +
323A VAL* 3.2 12.1 - - - +
325A MET* 1.3 74.9 - - - +
327A HIS* 1.3 90.4 + - - +
329A ILE* 2.9 34.4 + - - +
330A ALA* 3.4 4.5 + - - +
361A PHE* 3.8 22.0 - - + +
364A VAL* 4.6 2.9 - - + -
365A GLN* 4.1 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLU* 4.4 17.0 - - - +
225A MET* 4.9 4.5 - - - -
323A VAL* 3.2 24.6 + - + +
324A HIS* 3.3 9.8 + - - +
326A ASP* 1.3 101.2 + - - +
328A VAL* 1.3 60.8 + - - +
330A ALA* 3.3 10.9 + - - +
331A LYS* 3.0 27.6 + - + +
365A GLN* 4.2 9.9 - - - -
371A VAL 5.5 1.4 + - - -
373A LEU* 4.4 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A VAL* 4.6 4.9 - - + -
225A MET* 3.8 18.4 - - + -
230A ILE* 3.8 33.7 - - + -
231A TYR* 5.0 0.7 - - + -
324A HIS* 3.1 23.7 + - + +
325A MET* 3.1 30.5 - - - +
326A ASP 3.1 0.2 - - - -
327A HIS* 1.3 74.7 - - - +
329A ILE* 1.3 52.9 + - - +
331A LYS* 3.0 10.3 + - + +
332A GLU* 2.6 33.2 + - + +
342A ILE* 4.2 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A MET 3.1 20.4 - - - +
326A ASP* 2.9 20.6 + - - +
328A VAL* 1.3 78.0 - - - +
330A ALA* 1.3 59.4 + - - +
332A GLU* 3.0 33.0 + - + +
333A LEU* 3.0 27.4 + - + +
338A ASN* 5.1 1.3 - - - +
339A ILE* 3.2 37.5 - - + +
342A ILE* 3.7 21.5 - - + -
361A PHE* 4.1 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ASP 3.4 4.4 + - - +
327A HIS* 3.3 13.6 + - - +
329A ILE* 1.3 78.8 - - - +
331A LYS* 1.3 64.0 + - + +
333A LEU* 2.9 40.5 + - + +
334A GLU* 3.4 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A MET* 3.1 76.8 - - + +
226A LYS* 4.6 6.3 - - - +
230A ILE* 5.5 1.6 - - + -
327A HIS 3.0 16.8 - - - +
328A VAL* 3.0 13.8 + - + +
330A ALA* 1.3 78.9 - - + +
332A GLU* 1.3 52.6 + - - +
334A GLU* 2.7 41.1 + - - +
335A THR* 2.6 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE* 4.7 0.6 - - + +
328A VAL* 2.6 25.2 + - + +
329A ILE* 3.0 34.7 - - - +
331A LYS* 1.3 70.8 - - - +
333A LEU* 1.3 58.0 + - - +
335A THR* 3.0 10.3 + - - +
336A LYS* 2.9 9.9 + - - -
337A MET* 2.6 74.7 + - + +
338A ASN* 2.8 34.2 + - - +
339A ILE 3.4 0.5 + - - -
341A ASN* 3.5 2.1 - - - +
342A ILE* 3.3 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ILE* 3.0 22.3 + - + +
330A ALA* 2.9 25.7 + - + +
332A GLU* 1.3 79.3 - - - +
334A GLU* 1.3 58.6 + - - +
336A LYS* 4.3 12.5 + - - +
337A MET 4.5 7.0 - - - +
338A ASN* 5.4 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LYS* 3.5 26.3 - - - +
228A GLU* 5.4 0.7 - - - +
330A ALA 3.9 3.7 - - - +
331A LYS* 2.7 64.2 + - - +
333A LEU* 1.3 78.3 - - - +
335A THR* 1.3 58.7 + - + +
336A LYS* 3.0 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A MET 3.8 8.7 - - - +
226A LYS* 3.5 27.6 - - - +
227A CYS 3.3 26.5 + - - +
228A GLU* 3.6 27.6 - - - +
230A ILE* 4.2 2.4 - - + +
331A LYS* 2.6 30.0 + - + +
332A GLU* 3.0 13.5 - - - -
334A GLU* 1.3 70.4 - - + +
336A LYS* 1.3 70.9 + - - +
337A MET* 3.6 17.2 - - - +
----------------------------------------------------------
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