Contacts of the helix formed by residues 307 - 320 (chain D) in PDB entry 5JLH
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 307 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D VAL* 4.2 14.5 - - - +
220D LEU* 4.6 8.2 - - - +
305D TYR 3.3 0.8 + - - -
306D PRO* 1.3 72.4 - - - +
308D ILE* 1.3 62.8 + - - +
309D ALA* 3.3 3.4 - - - -
310D ASP* 3.4 19.7 + - - +
311D ARG* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D VAL* 3.6 23.3 - - + -
260D LEU* 5.1 5.6 - - + -
261D PHE* 4.5 10.5 - - + -
273D ILE* 5.1 4.9 - - + -
298D LEU* 4.1 20.0 - - + -
302D THR 3.9 3.1 - - - +
303D THR* 3.1 45.3 - - + +
305D TYR* 3.4 34.6 + - + +
306D PRO 3.4 0.8 + - - -
307D GLY* 1.3 76.6 - - - +
309D ALA* 1.3 64.8 + - - +
311D ARG* 3.2 4.6 + - - +
312D MET* 2.9 32.9 + - + +
334D ARG* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D LEU* 4.3 8.4 - - + +
307D GLY 3.3 1.0 - - - -
308D ILE* 1.3 80.5 - - - +
310D ASP* 1.3 68.5 + - - +
312D MET* 3.3 5.4 + - - +
313D GLN* 2.9 27.0 + - - +
328D ILE* 3.9 12.9 - - + +
330D ALA* 4.3 24.2 - - + -
334D ARG* 5.2 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D LEU* 4.3 28.4 - - + +
307D GLY* 3.4 18.4 + - - +
308D ILE 3.2 0.2 - - - -
309D ALA* 1.3 79.9 - - - +
311D ARG* 1.3 63.5 + - - +
313D GLN* 3.1 12.7 + - - +
314D LYS* 2.9 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D VAL* 3.5 19.5 - - + -
219D ALA 3.3 26.6 + - - +
220D LEU* 5.3 2.6 - - - +
221D ASP* 4.1 2.0 + - - +
222D PHE* 3.9 17.8 - - - +
258D GLU* 3.1 25.6 + - - -
261D PHE* 3.4 24.5 - - + +
262D GLN* 4.5 8.7 - - - +
274D HIS* 5.6 0.2 - - - -
307D GLY 3.1 11.0 + - - +
308D ILE 3.2 5.6 + - - +
310D ASP* 1.3 80.0 - - - +
312D MET* 1.3 64.0 + - - +
314D LYS* 3.2 41.0 + - - +
315D GLU* 2.8 55.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D MET* 5.1 4.0 - - + -
261D PHE* 3.6 14.1 - - + -
273D ILE* 3.4 31.0 - - + -
274D HIS* 3.9 13.0 - - - +
277D THR* 3.9 22.4 - - + +
296D THR* 5.3 5.6 - - + -
298D LEU* 4.9 17.9 - - + -
308D ILE* 2.9 31.5 + - + +
309D ALA* 3.6 6.5 - - - +
311D ARG* 1.3 76.3 - - - +
313D GLN* 1.3 56.0 + - - +
315D GLU* 3.3 4.1 + - - -
316D ILE* 2.9 53.4 + - + +
328D ILE* 3.6 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D ALA* 2.9 14.8 + - - +
310D ASP* 3.4 16.3 - - - +
312D MET* 1.3 77.6 - - - +
314D LYS* 1.3 60.2 + - - +
316D ILE* 4.4 0.8 - - - +
317D THR* 2.6 40.2 + - - +
326D ILE* 3.5 25.9 + - - +
327D LYS* 4.9 3.2 - - - +
328D ILE* 3.3 24.8 + - + +
385G ASN* 5.0 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D LEU* 3.0 31.6 - - + +
221D ASP* 4.4 9.4 + - - +
310D ASP 2.9 10.6 + - - +
311D ARG* 3.2 53.5 + - - +
313D GLN* 1.3 76.6 - - - +
315D GLU* 1.3 69.6 + - - +
317D THR* 3.8 3.9 - - - -
318D ALA* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 315 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D PHE* 3.0 25.3 - - - -
274D HIS* 2.9 45.7 - - + +
311D ARG* 2.8 55.1 + - - +
312D MET* 3.9 2.4 - - - +
314D LYS* 1.3 92.0 - - - +
316D ILE* 1.3 67.2 + - - +
318D ALA* 3.1 6.6 + - - +
319D LEU* 2.9 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D HIS* 4.1 19.1 - - + +
277D THR* 3.9 25.8 - - + -
278D PHE* 4.4 16.4 - - + -
281D ILE* 5.9 1.6 - - + -
293D TYR* 4.2 19.5 - - + -
296D THR* 5.1 7.6 - - + +
312D MET* 2.9 43.9 + - + +
313D GLN 4.4 1.1 - - - +
315D GLU* 1.3 75.8 - - - +
317D THR* 1.3 56.5 + - - +
319D LEU* 3.1 2.9 + - + +
320D ALA* 2.8 32.9 + - - +
326D ILE* 3.6 27.8 - - + -
328D ILE* 5.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D GLN* 2.6 31.2 + - - +
314D LYS* 3.8 4.9 - - - -
316D ILE* 1.3 78.7 - - - +
318D ALA* 1.3 64.5 + - - +
320D ALA* 3.4 14.7 - - - +
321D PRO 5.1 0.4 - - - -
322D SER* 4.9 17.3 + - - -
324D MET 6.0 0.4 - - - +
326D ILE* 3.9 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D LYS 2.9 20.1 + - - +
315D GLU* 3.4 7.4 - - - +
316D ILE 3.1 0.2 - - - -
317D THR* 1.3 79.4 - - - +
319D LEU* 1.3 65.7 + - + +
320D ALA 4.0 2.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
274D HIS* 4.0 26.5 - - + +
275D GLU* 4.3 16.6 - - + +
278D PHE* 3.3 40.0 - - + -
315D GLU* 2.9 17.2 + - - +
316D ILE* 5.3 0.2 - - - -
318D ALA* 1.3 83.1 - - + +
320D ALA* 1.3 62.1 + - - +
321D PRO* 4.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D PHE* 3.4 15.9 - - + -
293D TYR* 3.7 21.8 - - + -
316D ILE 2.8 21.7 + - - +
317D THR* 3.4 10.9 - - - +
318D ALA 3.5 2.6 - - - +
319D LEU* 1.3 76.8 - - - +
321D PRO* 1.3 83.6 - - + +
322D SER* 3.2 3.8 + - - -
324D MET* 6.0 0.2 - - + -
326D ILE* 4.5 6.1 - - + -
----------------------------------------------------------
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