Contacts of the helix formed by residues 305 - 317 (chain D) in PDB entry 3IKM
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 SER 305 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D LEU* 1.3 75.3 - - - +
306D SER* 1.3 56.2 + - - +
307D PHE* 4.1 9.6 - - - -
308D GLN* 2.8 37.2 + - - -
309D ARG* 2.5 36.8 + - - +
850D ILE* 3.8 5.3 - - - +
1027D LYS* 4.5 1.9 - - - +
1095D SER* 3.6 2.4 + - - -
1099D TRP* 2.4 43.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D LEU 3.9 0.6 + - - -
305D SER* 1.3 73.2 + - - +
307D PHE* 1.3 72.1 + - - -
309D ARG* 3.3 8.8 - - - +
310D SER* 2.7 37.1 + - - -
850D ILE* 4.6 6.2 - - - +
1055D SER* 4.2 2.1 + - - -
1058D PHE* 2.9 55.4 - - - -
1099D TRP* 4.7 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D SER* 4.1 15.9 - - - -
306D SER* 1.3 89.3 + - - +
308D GLN* 1.3 73.1 + - + +
310D SER* 2.2 26.8 + - - +
311D LEU* 2.6 24.1 + - + +
1048D ALA* 2.5 51.6 - - + +
1049D TRP* 3.6 12.1 - - + -
1051D GLY 4.9 2.5 - - - +
1052D GLY* 3.6 13.0 - - - -
1055D SER* 4.2 14.1 - - - -
1058D PHE* 5.0 3.4 - - + -
1090D GLU 3.9 15.7 - - - -
1095D SER* 4.1 20.0 - - - -
1099D TRP* 4.7 4.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D LEU* 3.9 2.4 - - - +
305D SER* 2.8 38.9 + - - +
307D PHE* 1.3 81.9 - - - +
309D ARG* 1.3 52.2 + - - +
311D LEU* 3.1 9.4 + - - +
312D TRP* 2.4 58.9 + - + +
1025D LEU* 4.9 1.1 - - - +
1027D LYS* 2.2 38.2 + - - +
1090D GLU* 3.1 22.2 - - - +
1091D GLU* 2.6 35.1 - - + +
1095D SER* 4.8 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D MET* 4.3 15.7 + - - +
303D GLY* 3.6 9.1 - - - -
304D LEU* 2.6 65.4 + - + +
305D SER 2.5 16.4 + - - +
306D SER* 3.3 12.1 - - - +
308D GLN* 1.3 69.9 - - - +
310D SER* 1.3 64.0 + - - +
312D TRP* 2.7 10.6 + - - -
313D ILE* 2.2 47.1 + - + +
351D SER 3.1 23.2 + - - -
352D SER* 3.3 20.4 - - - +
353D VAL* 3.9 17.2 - - - +
358D GLU* 3.1 7.4 + - - -
850D ILE* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D SER 2.7 15.7 + - - -
307D PHE* 2.2 41.5 + - - +
309D ARG* 1.3 75.6 - - - +
311D LEU* 1.3 58.9 + - - +
313D ILE* 3.0 25.7 - - - +
314D ALA* 3.5 6.2 + - - +
1058D PHE* 6.2 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D PHE* 2.6 49.5 + - + +
308D GLN* 3.5 7.2 - - - +
310D SER* 1.3 71.7 - - - +
312D TRP* 1.3 68.1 + - - +
314D ALA* 3.2 15.2 + - - +
315D ALA* 3.4 12.6 + - - +
1044D VAL* 6.1 4.3 - - + -
1047D ARG* 4.8 21.5 - - + +
1048D ALA* 4.1 18.2 - - + -
1090D GLU* 4.7 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D LEU* 4.1 14.0 - - + +
308D GLN* 2.4 57.5 + - + +
309D ARG* 3.3 9.2 - - - +
311D LEU* 1.3 74.5 - - - +
313D ILE* 1.3 64.7 + - - +
315D ALA* 3.3 7.8 + - + +
316D LYS* 2.7 68.7 + - + +
345D TRP* 4.3 5.4 - - + -
346D ASP* 2.5 39.7 - - + -
347D TRP* 3.1 28.2 + - - -
348D LEU* 3.3 15.7 - - + -
1025D LEU* 5.8 0.4 - - - +
1040D LYS* 4.6 17.5 - - + -
1090D GLU* 5.0 7.5 + - - -
1091D GLU* 4.8 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D ARG* 2.2 60.4 + - + +
310D SER* 3.0 20.0 - - - +
312D TRP* 1.3 67.0 - - - +
314D ALA* 1.3 88.6 + - + +
316D LYS* 3.4 9.8 - - - +
317D GLN* 3.0 26.1 + - + +
352D SER* 4.2 16.2 - - - +
353D VAL* 5.3 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D SER 4.0 7.4 - - - +
311D LEU* 3.2 10.9 + - - +
312D TRP 3.2 0.2 + - - -
313D ILE* 1.3 95.0 - - + +
315D ALA* 1.3 63.6 + - - +
317D GLN 4.3 0.7 - - - -
318D GLY 3.5 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 315 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D LEU 3.4 6.0 + - - +
312D TRP* 3.3 12.0 + - + +
314D ALA* 1.3 80.0 - - - +
316D LYS* 1.3 65.2 + - + +
318D GLY 3.9 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D LEU* 3.1 31.5 - - - +
312D TRP* 2.7 66.3 + - + +
313D ILE* 3.4 10.3 - - - +
315D ALA* 1.3 78.5 - - + +
317D GLN* 1.3 61.2 + - + +
318D GLY 3.6 1.9 + - - -
348D LEU* 2.7 47.7 - - + +
350D ILE* 3.9 12.6 - - + +
352D SER* 4.0 12.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D ILE* 3.0 16.7 + - + +
314D ALA 4.3 2.0 - - - -
316D LYS* 1.3 74.8 - - + +
318D GLY* 1.3 55.2 + - - +
350D ILE* 6.0 4.7 - - + -
352D SER* 6.5 0.4 - - - -
360D HIS* 3.6 30.9 + - + +
----------------------------------------------------------
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