Contacts of the helix formed by residues 230 - 239 (chain D) in PDB entry 5MG3
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 230 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ALA 3.6 24.7 + - - +
227D VAL* 3.2 11.9 + - - +
229D GLN* 1.3 84.5 - - - +
231D ILE* 1.4 62.3 + - - +
232D ASN* 3.4 7.4 - - - -
233D ILE* 3.1 19.2 - - + +
234D LEU* 3.4 7.3 + - - +
426D ALA* 4.0 20.6 - - - -
429D LEU* 4.2 6.3 + - - +
430D ILE* 3.5 42.3 - - + +
431D ALA 4.9 1.2 + - - +
433D ILE* 4.1 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D VAL 3.6 9.9 - - - +
228D GLN 3.5 18.8 - - - +
229D GLN 3.3 1.3 - - - -
230D ASN* 1.4 79.0 - - - +
232D ASN* 1.3 59.5 + - - +
234D LEU* 3.3 8.8 + - + +
235D ARG* 2.9 31.2 + - - +
248D VAL* 3.8 32.0 - - + +
249D GLN* 4.4 2.5 - - - +
250D ARG* 4.7 3.6 - - + +
256D ILE* 3.3 43.5 - - + -
433D ILE* 4.9 0.2 - - + -
538G ASN* 3.7 32.1 - - + +
539G SER 3.9 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D GLN 3.7 6.7 + - - +
230D ASN 3.7 1.7 - - - -
231D ILE* 1.3 81.5 - - - +
233D ILE* 1.3 73.0 + - - -
235D ARG* 3.3 14.2 - - - +
236D ASN* 3.3 22.0 + - - -
248D VAL* 4.7 0.2 - - - -
297D ARG* 4.7 0.3 + - - -
419D GLN 4.3 5.7 + - - -
422D LEU* 3.6 32.7 - - - +
423D LEU* 3.8 25.3 - - + +
426D ALA* 3.1 20.7 - - - +
539G SER* 3.5 21.9 + - - +
540G ASN* 3.7 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D ASN 3.1 19.3 - - - +
232D ASN* 1.3 82.1 + - - +
234D LEU* 1.4 61.8 + - - +
236D ASN* 3.4 24.3 + - - +
237D ARG* 3.6 37.1 + - + +
369D PHE* 4.4 17.7 - - + -
393D ILE* 5.0 2.9 - - + -
423D LEU* 3.6 12.3 - - + +
426D ALA 3.8 20.2 - - - +
427D GLY* 4.0 18.4 - - - +
430D ILE* 3.5 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D ASN 3.7 9.0 - - - +
231D ILE* 3.3 9.6 + - + +
233D ILE* 1.4 79.4 - - - +
235D ARG* 1.3 55.0 + - - +
237D ARG* 3.0 24.4 + - + +
238D VAL* 3.3 16.0 + - + +
248D VAL* 5.3 2.5 - - + -
256D ILE* 3.9 21.5 - - + -
258D VAL* 5.6 1.6 - - + -
273D LEU* 4.2 17.9 - - + +
274D GLY* 5.0 1.1 - - - -
430D ILE* 4.8 5.2 - - + -
433D ILE* 3.7 57.7 - - + +
435D ILE* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 235 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D ILE 2.9 19.4 + - - +
232D ASN 3.3 7.9 - - - +
234D LEU* 1.3 70.7 - - - +
236D ASN* 1.3 89.6 + - - +
237D ARG 3.5 0.2 + - - -
238D VAL* 3.7 13.9 + - - +
239D ASN* 3.3 27.9 + - - +
246D PRO* 3.0 45.9 + - + +
248D VAL* 3.5 29.0 - - + +
258D VAL* 5.7 3.1 - - + -
297D ARG* 3.7 13.3 - - - +
301D ASP* 2.6 46.0 + - - -
540G ASN* 4.6 17.3 - - - +
44Y ILE* 5.8 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D ASN 3.3 12.9 + - - -
233D ILE* 3.4 22.2 + - - +
235D ARG* 1.3 100.5 + - - +
237D ARG* 1.4 76.3 + - - +
239D ASN* 3.2 25.1 + - - +
297D ARG* 3.4 11.1 + - - +
301D ASP* 4.5 0.5 - - - +
372D TYR* 3.8 5.9 + - - -
391D GLU* 5.8 1.0 + - - -
393D ILE* 5.1 5.7 - - - +
423D LEU* 4.1 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D ILE* 3.6 32.4 + - + +
234D LEU* 3.0 11.8 + - - +
236D ASN* 1.4 83.0 + - - +
238D VAL* 1.4 63.6 + - - +
239D ASN 3.5 1.7 - - - +
241D LEU* 5.7 0.2 - - - +
273D LEU* 4.1 35.8 - - - +
275D ALA 5.6 2.7 - - - +
369D PHE* 3.6 17.0 - - - +
370D VAL* 3.4 35.9 + - + +
372D TYR* 3.2 36.8 + - + +
386D LEU* 5.4 7.6 - - + -
391D GLU* 2.5 45.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D LEU* 3.3 14.0 + - + +
235D ARG* 4.1 9.4 - - - +
236D ASN 3.4 0.4 - - - -
237D ARG* 1.4 59.3 - - - +
239D ASN* 1.4 65.5 + - - +
241D LEU* 3.6 19.5 - - + +
243D VAL* 3.8 16.1 - - + +
246D PRO* 6.0 2.2 - - + -
258D VAL* 4.0 37.5 - - + +
259D GLU* 5.3 1.3 - - + +
260D LEU* 4.1 21.3 - - + -
273D LEU* 5.2 8.1 - - + -
435D ILE* 3.9 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D ARG* 3.3 34.0 + - - +
236D ASN* 3.2 14.3 + - - +
237D ARG 3.5 1.7 - - - +
238D VAL* 1.4 82.6 - - - +
240D GLN* 1.4 66.7 + - + +
241D LEU* 3.5 4.8 + - - +
243D VAL* 3.7 8.4 - - - +
246D PRO* 3.2 32.1 - - - +
301D ASP* 4.9 1.0 - - - +
303D GLU* 3.3 32.2 + - + +
306D GLN* 6.0 4.3 - - + +
307D THR* 5.8 0.9 - - - +
372D TYR* 3.1 15.0 + - - +
----------------------------------------------------------
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