Contacts of the helix formed by residues 220 - 231 (chain D) in PDB entry 6M17
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 GLY 220 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D ARG* 4.8 2.0 - - - -
218D SER* 3.2 7.6 + - - -
219D ARG* 1.3 75.8 - - - +
221D GLN* 1.3 62.3 + - - +
222D LEU 3.2 2.9 - - - -
223D ILE* 3.4 24.6 + - - +
224D GLU* 2.8 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D ASP 4.4 3.5 + - - +
217D TYR* 3.8 29.4 - - + -
218D SER* 3.3 38.2 + - - +
220D GLY* 1.3 77.2 - - - +
222D LEU* 1.3 62.2 + - - +
223D ILE 3.2 0.7 - - - -
224D GLU* 3.4 13.2 + - + +
225D ASP* 3.2 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D ARG* 4.0 27.4 - - + +
207D TYR* 3.7 51.1 - - + -
217D TYR* 4.0 22.1 - - + +
218D SER 3.7 4.7 + - - +
219D ARG* 4.3 10.8 - - - +
220D GLY 3.2 1.0 - - - -
221D GLN* 1.3 79.1 - - - +
223D ILE* 1.3 61.2 + - - +
225D ASP* 4.0 0.5 - - - -
226D VAL* 3.2 42.2 + - + +
461D TRP* 4.5 11.4 - - + -
513D ILE* 4.7 7.6 - - + -
517D THR* 4.9 8.1 - - + -
566D TRP* 6.0 0.7 - - + -
579D MET* 5.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D ARG* 3.6 47.1 - - - +
220D GLY* 3.7 17.7 - - - +
221D GLN 3.2 0.4 - - - -
222D LEU* 1.3 78.5 - - - +
224D GLU* 1.3 65.7 + - + +
226D VAL* 4.1 1.9 - - - +
227D GLU* 3.2 44.2 + - + +
461D TRP* 4.3 23.8 - - + -
465D LYS* 4.3 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D GLY 2.8 23.9 - - - +
221D GLN* 3.4 14.9 + - + +
222D LEU 3.3 0.4 - - - -
223D ILE* 1.3 79.1 - - + +
225D ASP* 1.3 64.7 + - - +
227D GLU* 3.3 8.6 + - - +
228D HIS* 2.8 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D TYR* 2.4 39.9 + - - +
221D GLN* 3.2 21.0 + - - +
222D LEU 4.1 2.9 - - - +
223D ILE 3.4 0.2 - - - -
224D GLU* 1.3 77.7 - - - +
226D VAL* 1.3 53.8 + - - +
228D HIS* 3.9 7.7 - - - +
229D THR* 2.6 39.3 + - + +
578D ASN* 4.8 11.5 - - - +
579D MET* 3.7 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D LEU* 3.2 28.5 + - + +
223D ILE* 4.1 4.3 - - - +
224D GLU 3.3 0.4 - - - -
225D ASP* 1.3 78.0 - - - +
227D GLU* 1.3 58.1 + - + +
229D THR* 3.0 16.2 + - - -
230D PHE* 3.1 17.8 + - - +
454D TYR* 3.6 29.4 - - + -
461D TRP* 5.1 8.7 - - + -
513D ILE* 4.5 20.2 - - + -
516D TYR* 3.4 24.6 + - + -
517D THR* 5.3 0.9 - - + -
579D MET* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D ILE* 3.2 31.1 + - + +
224D GLU* 3.3 9.4 + - - +
226D VAL* 1.3 75.2 - - + +
228D HIS* 1.3 62.1 - - - +
230D PHE* 3.9 7.3 - - - +
231D GLU* 3.4 27.8 + - - +
454D TYR* 3.2 34.5 + - + +
458D LYS* 3.8 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D GLU* 2.8 19.7 + - + +
225D ASP* 4.3 8.1 - - - +
227D GLU* 1.3 77.9 - - - +
229D THR* 1.3 68.8 + - + +
231D GLU* 3.4 32.1 + - + +
232D GLU* 3.6 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D ASP* 2.6 25.1 + - + +
226D VAL* 3.0 13.0 + - - -
228D HIS* 1.3 83.4 - - + +
230D PHE* 1.3 61.3 + - - +
232D GLU* 3.5 12.8 + - - +
233D ILE* 3.3 17.8 + - - +
516D TYR* 3.2 16.3 + - - -
520D LEU* 4.0 22.7 - - + -
579D MET* 4.1 20.3 - - + +
580D ASN* 4.9 0.9 - - - +
581D VAL* 3.9 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D VAL 3.1 18.3 + - - +
227D GLU* 4.1 7.9 - - - +
228D HIS 3.3 0.6 - - - -
229D THR* 1.3 74.1 + - - +
231D GLU* 1.3 58.8 + - + +
232D GLU 3.1 5.4 - - - -
233D ILE* 3.1 31.8 + - + -
234D LYS* 3.3 42.4 + - + +
237D TYR* 5.8 2.5 - + + -
450D LEU* 4.6 1.1 - - + -
451D PRO* 3.9 36.3 - - + -
454D TYR* 3.5 41.1 - + + -
484D ILE* 3.9 28.0 - - + -
516D TYR* 3.6 12.6 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D GLU 3.4 16.7 + - - +
228D HIS* 3.4 31.9 + - + +
230D PHE* 1.3 77.6 - - + +
232D GLU* 1.3 60.2 + - + +
234D LYS* 3.7 23.5 - - + +
235D PRO* 3.9 12.0 - - - +
----------------------------------------------------------
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