Contacts of the helix formed by residues 421 - 439 (chain A) in PDB entry 4LOU
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 LEU 421 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 4.2 7.6 - - + -
245A SER 3.3 24.0 - - - +
246A ASP 4.2 8.7 - - - -
247A ALA* 4.3 7.6 - - + +
388A THR* 3.7 32.8 - - + +
391A ILE* 3.9 29.6 - - + -
418A ASN* 2.8 14.5 + - + +
419A TYR 2.7 4.9 + - - -
420A GLN* 1.3 95.1 - - + +
422A ILE* 1.3 62.6 + - - -
423A LEU 3.3 2.9 - - - -
424A PRO* 3.2 13.3 - - + +
425A MET* 2.9 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ILE* 3.6 23.3 - - + -
413A LEU* 4.4 5.4 - - + -
419A TYR* 2.6 61.1 + - + +
420A GLN 3.3 1.4 - - - -
421A LEU* 1.3 70.3 - - - +
423A LEU* 1.3 63.0 + - + +
425A MET* 3.2 21.2 + - + +
426A ILE* 2.8 46.2 + - + +
193B PRO* 4.4 10.5 - - + -
194B LEU* 3.9 20.9 - - + -
230B ARG* 4.3 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 4.8 4.0 - - + -
252A LEU* 3.7 28.9 - - + -
420A GLN 5.0 0.8 + - - +
421A LEU 3.3 0.4 - - - -
422A ILE* 1.3 87.3 - - + +
424A PRO* 1.4 67.5 - - + +
426A ILE* 3.2 6.0 + - + +
427A ILE* 2.9 36.4 + - + +
193B PRO* 4.6 7.2 - - + -
223B ILE* 5.7 4.0 - - + +
226B THR* 3.5 26.2 - - + -
227B ILE* 4.0 19.5 - - + -
230B ARG* 3.3 45.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ALA* 4.0 23.8 - - + -
252A LEU* 3.9 12.8 - - + -
255A TYR* 3.2 46.4 - - + +
388A THR 6.0 0.2 - - - +
392A ALA* 4.8 1.8 - - + -
420A GLN 4.7 1.8 - - - +
421A LEU* 3.2 31.4 - - + +
423A LEU* 1.4 89.7 - - + +
425A MET* 1.3 53.8 + - + +
427A ILE* 3.8 4.0 - - + +
428A THR* 2.8 38.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ILE* 4.1 21.1 - - + +
392A ALA* 4.4 14.3 - - + +
409A ILE* 3.8 26.2 - - + +
412A VAL* 4.0 26.9 - - - -
413A LEU* 3.8 23.3 - - + -
416A THR* 5.5 1.1 - - - +
418A ASN* 4.1 11.2 - - - +
421A LEU* 2.9 27.6 + - + +
422A ILE* 3.3 40.2 - - + +
424A PRO* 1.3 73.7 - - - +
426A ILE* 1.3 65.7 + - - +
428A THR* 4.1 1.4 - - - -
429A GLY* 3.1 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ILE* 3.6 24.9 - - + -
422A ILE* 2.8 30.6 + - + +
423A LEU* 3.7 6.7 - - + +
425A MET* 1.3 68.9 - - - +
427A ILE* 1.3 59.3 + - + +
429A GLY* 2.8 21.7 + - - -
430A LEU* 2.8 14.1 + - + +
193B PRO* 3.7 37.5 - - + +
194B LEU* 4.4 7.6 - - + -
197B ILE* 5.9 0.2 - - + -
219B PHE* 3.4 31.2 - - + -
222B VAL* 6.0 0.2 - - + -
223B ILE* 3.4 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 3.9 31.0 - - + +
255A TYR* 4.2 2.9 - - + -
256A LEU* 3.5 42.9 - - + +
423A LEU* 2.9 25.7 + - + +
424A PRO* 3.8 5.6 - - + +
426A ILE* 1.3 76.4 - - - +
428A THR* 1.3 62.9 + - - +
430A LEU* 3.4 1.8 + - - +
431A GLY* 3.0 20.8 + - - -
223B ILE* 3.7 27.1 - - + -
227B ILE* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A TYR* 3.3 26.4 + - - +
258A LEU* 4.0 17.7 - - + +
259A GLY* 3.3 26.5 - - - +
392A ALA* 3.6 29.5 - - - +
396A ALA* 4.3 12.3 - - + -
424A PRO 2.8 24.9 + - - -
425A MET 4.2 0.2 - - - -
427A ILE* 1.3 73.1 - - - +
429A GLY* 1.3 57.0 + - - +
432A ALA* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ALA 5.3 0.8 + - - -
395A GLY 5.4 3.1 - - - -
396A ALA* 5.4 2.7 - - - -
399A ALA* 3.6 20.7 - - - +
405A PRO* 4.7 2.9 - - - -
409A ILE* 4.7 10.3 - - - -
425A MET 3.1 11.9 + - - -
426A ILE 2.8 14.1 + - - -
428A THR* 1.3 69.1 - - - +
430A LEU* 1.3 60.3 + - - -
432A ALA* 3.2 4.3 + - - +
433A THR* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PRO* 4.9 3.8 - - + -
409A ILE* 5.3 0.2 - - + -
426A ILE* 2.8 19.2 + - + +
427A ILE 3.9 2.9 - - - +
429A GLY* 1.3 69.6 - - - -
431A GLY* 1.3 61.2 + - - +
433A THR* 3.2 12.8 + - + +
434A LEU* 2.8 43.1 + - + +
216B LYS* 4.9 3.4 - - + +
219B PHE* 3.4 43.1 - - + -
220B ILE* 3.4 44.2 - - + +
223B ILE* 3.4 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 4.5 16.8 - - - +
259A GLY* 3.6 14.4 - - - +
260A ILE 4.5 0.4 - - - -
427A ILE 3.0 15.4 + - - -
428A THR 4.0 0.9 - - - -
430A LEU* 1.3 76.8 - - - +
432A ALA* 1.3 61.4 + - - +
434A LEU* 4.4 7.4 - - - -
435A LEU* 3.0 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLY 3.1 16.1 + - - +
262A PHE* 3.8 18.6 - - + -
263A GLY* 3.1 10.1 - - - +
396A ALA* 4.0 10.3 - - + +
399A ALA* 4.0 4.3 - - + -
400A ALA* 3.6 11.9 - - + +
428A THR 3.0 18.5 + - - +
429A GLY 3.4 5.2 - - - +
430A LEU 3.1 0.4 - - - -
431A GLY* 1.3 78.9 - - - +
433A THR* 1.3 56.8 + - - +
436A ALA* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ALA 3.5 16.2 + - - -
403A ARG* 3.4 27.0 + - - +
405A PRO* 4.1 23.1 - - + +
429A GLY 3.0 15.5 + - - +
430A LEU* 3.4 17.0 - - + +
432A ALA* 1.3 76.7 - - - +
434A LEU* 1.3 59.5 + - - +
435A LEU 3.5 0.2 - - - -
436A ALA* 3.9 3.8 - - - -
437A GLN* 3.3 13.7 + - - +
29B ASP* 4.0 4.7 + - - -
216B LYS* 3.0 39.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 2.8 28.2 + - + +
431A GLY* 3.9 6.3 - - - +
433A THR* 1.3 76.2 - - + +
435A LEU* 1.3 68.2 + - + +
436A ALA 3.4 0.2 - - - -
437A GLN* 3.9 0.7 - - - +
438A PHE* 3.0 49.4 + - + -
36B LEU* 3.5 32.3 - - + -
216B LYS* 3.8 19.5 - - + +
220B ILE* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 6.3 0.2 - - + -
260A ILE* 3.8 40.8 - - + +
263A GLY* 3.2 20.5 - - - +
264A ILE* 4.4 10.3 - - + -
431A GLY* 3.0 23.1 + - - +
434A LEU* 1.3 83.6 - - + +
436A ALA* 1.3 63.5 + - - +
438A PHE* 3.9 15.7 - - + -
439A THR* 3.1 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLY 3.2 11.8 + - - +
267A PRO* 3.5 12.5 - - + +
400A ALA* 3.3 27.1 - - - +
403A ARG* 3.9 21.8 - - - +
432A ALA 3.0 20.2 + - - +
433A THR 4.1 0.9 - - - +
435A LEU* 1.3 76.6 - - - +
437A GLN* 1.3 66.5 + - - +
439A THR 3.8 2.1 + - - -
441A GLY* 3.2 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ARG* 3.4 15.8 - - - +
433A THR 3.3 5.3 + - - +
434A LEU 3.9 3.8 - - - +
436A ALA* 1.3 78.9 - - - +
438A PHE* 1.3 78.7 + - + +
440A GLY* 2.9 24.3 + - - -
441A GLY 3.9 2.5 + - - +
29B ASP 3.3 17.0 - - - +
30B LYS* 3.6 12.3 - - + +
31B THR 2.6 39.5 + - - +
33B LEU 5.2 0.4 - - - +
36B LEU* 4.2 2.9 - - - +
216B LYS* 2.5 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LEU* 3.0 33.4 + - + +
435A LEU* 4.2 19.1 - - + +
436A ALA 3.5 0.6 - - - -
437A GLN* 1.3 102.4 - - + +
439A THR* 1.3 63.2 + - + +
440A GLY 3.3 2.8 + - - -
33B LEU* 3.6 40.6 - - + -
36B LEU* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLY 3.9 2.6 + - - -
264A ILE* 4.3 18.2 + - + -
267A PRO* 3.8 20.3 - - - +
271A LYS* 5.1 5.4 + - - -
435A LEU* 3.1 36.3 + - + +
436A ALA 4.1 0.2 - - - -
437A GLN 3.1 0.2 + - - -
438A PHE* 1.3 79.0 - - + +
440A GLY* 1.3 65.1 + - - +
441A GLY 3.8 0.2 - - - -
----------------------------------------------------------
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