Contacts of the helix formed by residues 309 - 331 (chain D) in PDB entry 1I43
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 THR 309 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A HIS* 4.1 9.5 + - - +
309A THR* 4.0 16.0 + - - +
313A ARG* 4.0 22.9 - - + -
392A CYS* 3.7 20.0 - - - -
266D HIS* 4.4 4.3 - - - -
305D ARG 4.9 0.2 + - - -
306D GLY* 3.2 6.1 + - - -
308D LYS* 1.3 84.7 - - - +
310D LEU* 1.3 62.1 + - - -
311D HIS* 3.5 7.4 - - - -
312D LEU* 3.5 13.4 + - + -
313D ARG* 3.0 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ALA* 4.3 5.4 - - + -
126D LEU* 3.9 25.1 - - + -
241D THR* 4.6 8.3 - - + -
242D PRO* 4.8 0.4 - - + -
243D LEU* 3.8 18.2 - - + -
262D PHE* 3.8 17.7 - - + +
263D LEU* 3.9 27.1 - - + +
307D MET* 3.2 24.4 + - + +
308D LYS 3.6 0.2 - - - -
309D THR* 1.3 76.8 - - - +
311D HIS* 1.3 56.2 + - - +
313D ARG* 3.0 27.1 + - - +
314D VAL* 2.7 53.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLN* 5.4 2.0 - - - -
428A VAL* 3.1 45.0 + - + +
430A ASP* 4.7 9.9 - - - -
58D GLY* 3.4 36.7 + - - +
61D ALA* 5.0 1.8 - - + +
62D ILE* 3.9 9.1 - - + +
243D LEU* 3.3 21.9 - - + +
308D LYS 3.6 15.7 - - - -
309D THR* 4.2 0.4 - - - -
310D LEU* 1.3 80.0 + - - +
312D LEU* 1.3 78.9 + - + +
314D VAL* 3.9 0.2 - - - +
315D GLN* 2.8 45.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
312A LEU* 3.7 39.9 - - + +
313A ARG* 3.8 14.8 - - + +
316A GLN* 4.2 26.7 - - + +
428A VAL* 3.3 29.2 - - + -
309D THR* 3.7 14.1 - - + +
310D LEU 3.2 0.8 - - - -
311D HIS* 1.3 112.6 - - + +
313D ARG* 1.3 65.9 + - - +
315D GLN* 3.5 13.0 - - - +
316D GLN* 3.3 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A THR* 3.9 26.0 - - + -
312A LEU* 3.7 13.5 - - + -
262D PHE* 2.8 26.6 + - - +
263D LEU 3.5 7.5 + - - -
264D GLY 4.5 0.2 - - - -
265D GLY* 3.4 17.1 - - - -
266D HIS* 4.3 3.6 - - - -
306D GLY 3.0 22.1 + - - -
309D THR* 3.0 29.1 + - - +
310D LEU* 3.2 33.2 - - - +
312D LEU* 1.3 73.6 - - - +
314D VAL* 1.3 67.2 + - - +
316D GLN* 3.1 4.3 + - - +
317D GLN* 2.9 37.6 + - - +
390D GLY 4.2 5.7 + - - -
392D CYS* 4.0 15.7 - - - +
428D VAL* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D THR* 4.1 13.7 - - + +
243D LEU* 3.6 28.9 - - + -
244D ASN* 4.2 17.0 - - - +
262D PHE* 5.4 8.7 - - + -
310D LEU* 2.7 42.6 + - + +
311D HIS 3.9 2.7 - - - +
313D ARG* 1.3 72.8 - - + +
315D GLN* 1.3 65.6 + - - +
317D GLN* 3.1 9.6 + - - +
318D ASN* 2.8 41.5 + - - +
359D GLY* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 315 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLN* 5.3 6.2 + - - +
430A ASP* 5.3 5.3 + - - -
311D HIS* 2.8 38.9 + - - +
312D LEU* 3.5 12.5 - - - +
314D VAL* 1.3 76.2 - - - +
316D GLN* 1.3 61.6 + - - +
318D ASN* 3.4 9.8 + - - +
319D SER* 3.2 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A HIS* 5.1 2.4 + - - -
312A LEU* 4.2 21.2 - - + +
315A GLN* 5.4 4.7 + - - +
312D LEU 3.3 8.4 + - - +
313D ARG 3.1 8.6 + - - +
315D GLN* 1.3 76.9 - - - +
317D GLN* 1.3 68.9 + - - +
319D SER* 3.2 9.5 + - - -
320D THR* 3.1 36.8 + - - +
428D VAL* 3.6 28.8 + - + +
429D GLU 3.4 24.2 + - - -
430D ASP* 4.5 8.9 + - - +
431D PHE* 4.5 3.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
262D PHE* 3.6 32.6 - - + -
313D ARG* 2.9 33.7 + - - +
314D VAL* 3.7 5.8 + - + +
316D GLN* 1.3 73.0 - - - +
318D ASN* 1.3 66.2 + - - +
320D THR* 4.1 3.9 - - - -
321D ALA* 3.1 27.9 + - - +
360D GLY* 3.7 16.2 - - - +
390D GLY* 3.6 10.6 + - - +
391D GLY 4.0 11.0 + - - -
426D PHE* 2.7 30.2 + - - +
427D GLY 3.4 21.6 + - - +
428D VAL* 4.2 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D ASN* 3.0 31.2 + - - +
314D VAL* 2.8 26.8 + - - +
315D GLN* 3.5 8.7 - - - +
316D GLN 3.2 0.2 - - - -
317D GLN* 1.3 77.1 - - - +
319D SER* 1.3 64.1 + - - +
322D LEU* 3.1 22.9 + - - +
339D TYR* 3.4 5.0 + - - -
356D THR 5.0 0.6 + - - -
357D GLY* 3.5 9.8 - - - -
358D PHE 4.0 7.4 - - - +
359D GLY* 3.0 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 319 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D GLN 3.2 13.5 + - - -
316D GLN* 3.2 11.6 + - - -
318D ASN* 1.3 74.9 - - - +
320D THR* 1.3 70.2 + - - +
322D LEU* 2.9 9.3 + - - +
323D ARG* 2.8 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D GLN* 3.1 29.9 + - - +
317D GLN* 4.1 4.7 - - - -
319D SER* 1.3 76.8 - - - +
321D ALA* 1.3 53.8 + - - +
323D ARG* 3.7 2.8 + - - +
324D MET* 2.7 41.5 + - + +
426D PHE* 3.7 30.3 - - + -
427D GLY 5.2 2.4 + - - -
429D GLU 4.7 1.9 + - - -
431D PHE* 3.9 32.3 - - + +
434D LEU* 3.7 19.9 - - + +
----------------------------------------------------------
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 GLN 3.1 17.9 + - - +
320D THR* 1.3 79.8 - - - +
322D LEU* 1.3 53.5 + - - +
324D MET* 3.6 0.7 - - - +
325D ALA* 2.7 37.6 + - - +
339D TYR* 3.5 3.8 - - - +
359D GLY 3.4 20.9 - - - +
360D GLY* 3.7 11.7 - - - +
362D VAL* 3.7 21.4 - - + +
426D PHE* 3.8 13.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D ASN 3.1 15.2 + - - +
319D SER* 2.9 10.7 + - - +
321D ALA* 1.3 75.3 - - - +
323D ARG* 1.3 66.8 + - + +
325D ALA* 3.0 17.4 + - - +
326D GLU* 3.2 22.3 + - - +
339D TYR* 3.4 29.5 + - + +
341D GLY* 3.9 23.6 - - - +
342D LEU* 4.7 6.1 - - + +
358D PHE* 4.5 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 323 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D SER* 2.8 41.1 + - - +
320D THR* 3.8 2.6 + - - +
322D LEU* 1.3 78.8 - - + +
324D MET* 1.3 61.5 + - - +
326D GLU* 3.4 12.0 + - - +
327D ILE* 3.3 25.2 + - + +
431D PHE* 3.0 58.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 324 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D THR* 2.7 21.1 + - + +
321D ALA 3.8 0.9 - - - +
323D ARG* 1.3 70.0 - - - +
325D ALA* 1.3 65.8 + - - +
327D ILE* 3.4 14.1 + - + -
328D LEU* 2.9 43.8 + - + +
426D PHE* 3.5 30.5 - - + -
431D PHE* 3.3 30.1 - - + -
434D LEU* 5.5 0.2 - - + -
435D LYS* 3.6 29.4 - - + +
438D ILE* 3.4 31.4 - - + -
439D LEU* 5.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 325 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D ALA 2.7 18.1 + - - +
322D LEU 3.0 11.6 + - - +
324D MET* 1.3 73.9 - - - +
326D GLU* 1.3 57.4 + - - +
328D LEU* 3.6 4.2 - - - +
329D GLU* 3.0 28.2 + - - +
337D VAL* 3.9 5.9 - - + +
339D TYR* 4.0 31.0 - - + -
342D LEU* 4.0 13.0 - - + +
362D VAL* 4.4 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D LEU* 3.2 23.2 + - + +
323D ARG* 3.7 12.0 - - - +
324D MET 3.2 0.2 - - - -
325D ALA* 1.3 74.3 - - - +
327D ILE* 1.3 68.4 + - + +
329D GLU* 2.8 17.3 + - - +
330D ALA* 2.9 15.2 + - - +
342D LEU* 3.8 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D ARG* 3.3 15.6 + - + +
324D MET* 3.8 17.9 - - + +
326D GLU* 1.3 77.9 - - + +
328D LEU* 1.3 59.6 + - + +
330D ALA* 3.4 7.7 + - - +
331D HIS* 3.1 26.8 + - + +
431D PHE* 4.0 15.0 - - + -
435D LYS* 3.7 31.2 - - + +
439D LEU* 4.4 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D MET* 2.9 34.7 + - + +
325D ALA 3.6 4.3 - - - +
327D ILE* 1.3 75.8 - - + +
329D GLU* 1.3 65.0 + - - +
331D HIS* 3.1 11.8 + - + +
334D VAL* 3.1 41.1 - - + +
337D VAL* 3.9 10.1 - - + -
362D VAL* 4.4 13.2 - - + -
364D PHE* 3.6 39.9 - - + -
426D PHE* 4.8 6.5 - - + -
438D ILE* 4.0 23.8 - - + -
439D LEU* 6.1 0.7 - - + -
442D LEU* 4.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D ALA 3.0 13.5 + - - +
326D GLU* 2.8 11.2 + - - +
328D LEU* 1.3 76.7 - - - +
330D ALA* 1.3 62.1 + - - +
331D HIS 3.5 5.5 + - - +
334D VAL* 4.6 5.6 - - - +
336D HIS* 5.7 1.7 + - - -
337D VAL* 3.7 24.0 + - + +
342D LEU* 3.7 19.8 - - + +
343D GLN 5.4 0.5 + - - -
344D SER* 2.9 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D GLU 2.9 14.0 + - - +
327D ILE* 3.8 7.0 - - - +
329D GLU* 1.3 77.4 - - - +
331D HIS* 1.3 63.7 + - - +
332D PRO* 3.5 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 331 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D ILE* 3.1 14.6 + - + +
328D LEU* 3.1 17.2 + - + +
329D GLU 3.9 2.6 - - - +
330D ALA* 1.3 78.7 - - - +
332D PRO* 1.3 79.2 - - + +
333D LYS* 2.9 52.8 + - + +
334D VAL* 3.3 26.5 + - + +
439D LEU* 3.9 20.2 - - + +
442D LEU* 3.8 36.2 - - + +
443D ASP* 4.5 8.4 + - - -
----------------------------------------------------------
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