Contacts of the helix formed by residues 308 - 323 (chain D) in PDB entry 4O9U
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 ALA 308 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D MET* 2.8 21.0 + - + +
306D SER 3.6 0.2 - - - -
307D GLN* 1.3 72.0 - - - +
309D GLN* 1.3 55.1 + - - +
310D HIS 3.2 2.9 - - - -
311D LYS* 2.7 28.4 + - - -
312D LEU* 3.1 8.4 + - - +
374D ILE* 4.5 0.4 - - + -
436D ALA* 3.6 33.0 - - + -
437D GLN* 3.6 20.4 - - + +
440D LEU* 3.8 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D MET* 3.6 25.9 - - - +
307D GLN* 2.7 60.2 + - - +
308D ALA* 1.3 77.3 + - - +
310D HIS* 1.3 90.8 + - + +
312D LEU* 3.1 17.5 + - - +
313D LYS* 3.4 10.2 + - - +
344D LEU* 3.4 46.5 - - + +
345D LEU* 6.0 3.7 - - + +
347D GLU* 5.1 0.8 + - - +
348D ALA* 4.2 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D GLN 4.9 3.1 - - - +
308D ALA 3.2 1.0 - - - -
309D GLN* 1.3 106.0 + - + +
311D LYS* 1.3 63.0 + - + +
312D LEU 3.3 1.1 + - - -
313D LYS* 4.5 2.8 - - - +
314D GLU* 3.8 24.6 + - - +
347D GLU* 3.4 28.5 + - - -
348D ALA* 4.1 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D GLN 5.9 0.4 - - - +
308D ALA 2.7 10.2 + - - +
310D HIS* 1.3 82.9 - - + +
312D LEU* 1.3 59.4 + - - +
314D GLU* 3.6 27.1 + - - +
315D LEU* 4.1 4.0 + - - +
437D GLN* 4.1 27.1 - - + +
440D LEU* 3.3 31.7 - - + +
441D THR* 3.3 37.4 - - - +
444D ILE* 3.5 25.9 - - + +
445D GLN* 5.8 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D PHE* 3.6 34.1 - - + -
299D PRO* 4.4 5.2 - - + -
303D MET* 3.7 26.5 - - + -
308D ALA 3.1 4.6 + - - +
309D GLN* 3.1 11.3 + - - +
311D LYS* 1.3 78.2 - - - +
313D LYS* 1.3 61.4 + - - +
314D GLU 3.3 1.1 - - - -
315D LEU* 3.3 6.2 + - - +
316D ALA* 3.1 23.8 + - - +
328D PHE* 3.9 23.3 - - + -
345D LEU* 4.3 9.6 - - + -
374D ILE* 4.1 22.4 - - + -
440D LEU* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D GLN 3.4 10.8 + - - +
310D HIS* 4.4 3.3 + - - +
312D LEU* 1.3 76.4 - - - +
314D GLU* 1.3 58.6 - - - +
315D LEU 3.1 0.4 - - - -
316D ALA* 3.0 9.4 + - + +
317D ASP* 2.8 61.6 + - - +
328D PHE* 5.1 2.0 - - - -
348D ALA* 4.7 11.2 - - + +
349D GLY 3.5 25.0 + - - +
350D VAL* 3.5 39.0 - - + +
351D ASP 4.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D HIS 3.8 18.9 + - - +
311D LYS* 3.6 25.5 + - - +
312D LEU 3.3 0.2 - - - -
313D LYS* 1.3 79.6 - - - +
315D LEU* 1.3 55.0 + - - +
317D ASP* 4.1 5.6 - - - +
318D LEU* 3.4 24.4 + - - +
444D ILE* 3.8 32.6 - - + +
448D LYS* 4.6 10.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D LEU* 3.9 12.1 - - + -
297D PHE* 3.6 29.8 - - + -
311D LYS 4.1 6.3 + - - +
312D LEU 3.3 9.0 + - - +
313D LYS 3.1 0.2 - - - -
314D GLU* 1.3 79.3 - - - +
316D ALA* 1.3 60.7 + - - +
317D ASP 3.3 0.4 - - - -
318D LEU* 4.0 3.5 - - + +
319D LEU* 3.3 32.4 + - + +
440D LEU* 3.8 22.7 - - + -
443D LEU* 3.8 17.5 - - + -
444D ILE* 4.0 32.9 - - + +
447D LEU* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D PHE* 3.9 9.4 - - + -
312D LEU 3.1 8.9 + - - +
313D LYS* 3.0 13.6 + - + +
315D LEU* 1.3 78.3 - - - +
317D ASP* 1.3 60.3 + - - +
320D GLU* 3.3 32.5 + - - +
326D VAL* 3.8 16.7 - - + +
328D PHE* 3.5 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D LYS* 2.8 56.0 + - - +
314D GLU* 4.4 5.5 - - - +
316D ALA* 1.3 80.4 - - - +
318D LEU* 1.3 59.2 + - - +
319D LEU 3.3 0.4 - - - -
320D GLU* 3.2 15.9 + - - +
321D ALA* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D GLU 3.4 17.1 + - - +
315D LEU* 4.3 4.9 - - + +
316D ALA 3.6 0.2 - - - -
317D ASP* 1.3 74.9 - - - +
319D LEU* 1.3 64.0 + - - +
321D ALA* 3.5 10.3 + - + +
322D ARG* 3.3 30.2 + - + +
444D ILE* 3.9 32.1 - - + +
447D LEU* 4.1 28.7 - - + -
448D LYS* 4.0 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D LEU* 3.3 61.0 - - + +
290D ALA* 4.4 2.2 - - - +
295D VAL* 3.9 13.2 - - + -
297D PHE* 3.9 9.6 - - + -
315D LEU* 3.3 22.2 + - + +
316D ALA 4.1 0.2 - - - +
317D ASP 3.3 0.2 - - - -
318D LEU* 1.3 80.7 - - - +
320D GLU* 1.3 51.2 + - - +
322D ARG* 3.4 3.7 + - - +
323D GLY 2.9 8.8 + - - -
324D VAL* 2.7 50.8 + - + +
326D VAL* 3.7 21.5 - - + -
447D LEU* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D ALA* 3.3 19.9 + - - +
317D ASP* 3.2 18.8 + - - +
319D LEU* 1.3 77.6 - - - +
321D ALA* 1.3 61.6 + - - +
323D GLY* 3.3 12.7 + - - +
324D VAL 3.7 17.5 - - - +
325D GLU* 5.6 0.4 - - - -
326D VAL* 4.2 13.7 + - + +
354D LYS* 3.2 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D ASP 2.8 20.0 + - - +
318D LEU* 3.8 13.2 - - + +
319D LEU 3.3 0.2 - - - -
320D GLU* 1.3 72.1 - - - +
322D ARG* 1.3 61.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 322 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ALA* 3.9 33.8 + - - +
291D TYR* 6.3 0.8 - - - -
318D LEU* 3.3 18.8 + - + +
319D LEU* 3.6 11.7 - - - +
320D GLU 3.3 0.2 - - - -
321D ALA* 1.3 78.5 - - + +
323D GLY* 1.3 57.1 + - - +
324D VAL* 3.7 6.3 - - + +
447D LEU* 3.6 28.6 + - - +
450D LEU 2.8 36.2 + - - -
192E GLN* 5.7 3.8 - - - +
212E LYS* 3.4 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 323 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D LEU 2.9 2.9 + - - -
320D GLU* 3.3 13.1 + - - +
322D ARG* 1.3 79.8 - - - +
324D VAL* 1.3 67.9 + - - +
325D GLU* 3.2 4.9 + - - +
212E LYS* 5.0 8.7 - - - -
----------------------------------------------------------
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