Contacts of the helix formed by residues 417 - 439 (chain D) in PDB entry 5FLZ
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 GLN 417 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D TYR* 3.9 15.8 + - - -
398D PHE* 4.0 13.5 - - + -
404D LEU* 3.3 31.5 - - - +
407D TYR* 3.3 52.8 - - + +
413D PHE* 4.0 13.0 - - + -
416D MET* 1.4 74.8 - - - +
418D ASN* 1.4 62.4 + - - +
419D VAL 3.4 0.7 - - - -
420D GLN* 3.5 42.1 + - + +
421D ASP* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 418 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D ASP 5.2 0.3 - - - +
412D LEU 3.2 19.8 - - - +
413D PHE* 4.0 3.0 - - - +
414D GLN* 3.6 3.3 + - - +
415D SER* 3.4 37.5 + - - -
416D MET 2.8 18.7 + - - +
417D GLN* 1.4 69.4 - - - +
419D VAL* 1.3 58.7 + - - +
421D ASP* 3.0 16.0 + - - +
422D GLU* 2.9 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 419 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D LEU* 3.9 16.4 - - + -
192D ARG* 3.1 36.5 + - - +
193D ARG* 4.2 11.7 - - - +
412D LEU* 3.9 23.8 - - + +
413D PHE* 3.3 39.3 - - + -
418D ASN* 1.3 71.3 - - - +
420D GLN* 1.3 57.8 + - - +
422D GLU* 3.5 10.9 + - - +
423D PHE* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D TYR* 3.6 31.2 - - - +
188D ILE* 3.4 32.2 - - + +
189D LEU* 3.5 36.8 - - + +
394D PHE* 4.0 13.6 - - + -
398D PHE* 4.1 9.6 - - + -
407D TYR* 4.0 2.6 + - - -
417D GLN* 3.5 42.7 + - + +
419D VAL* 1.3 79.3 - - - +
421D ASP* 1.4 54.8 + - - +
423D PHE* 3.3 8.5 + - - +
424D ALA* 2.9 28.8 + - - +
427D ARG* 5.0 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 421 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394D PHE* 4.2 11.4 - - - -
398D PHE* 3.7 25.6 - - - -
416D MET* 5.6 0.5 - - - +
417D GLN 2.9 21.7 - - - +
418D ASN* 3.0 16.8 + - - +
420D GLN* 1.4 75.7 - - - +
422D GLU* 1.3 63.6 + - + +
424D ALA* 3.3 8.8 + - - +
425D GLU* 3.3 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 422 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D ARG* 3.5 19.8 + - - +
412D LEU 4.8 0.7 - - - +
418D ASN* 2.9 40.0 + - + +
419D VAL* 3.4 13.0 + - - +
421D ASP* 1.3 73.6 - - + +
423D PHE* 1.4 64.9 - - - +
425D GLU* 3.4 7.3 + - - +
426D SER* 3.1 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 423 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ILE* 3.7 34.1 - - + +
191D LEU* 3.8 24.0 - - + -
192D ARG* 3.4 41.0 - - + +
195D ILE* 4.2 20.4 - - + -
387D PHE* 5.4 0.2 - + - -
419D VAL 3.0 18.3 + - - +
420D GLN* 3.4 7.6 - - - +
422D GLU* 1.4 75.6 - - - +
424D ALA* 1.4 52.3 + - - +
426D SER* 2.9 6.3 + - - -
427D ARG* 2.7 92.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 424 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D CYS* 4.9 5.1 - - - -
394D PHE* 3.7 28.9 - - + -
420D GLN 2.9 13.4 + - - +
421D ASP* 3.3 10.3 + - - +
423D PHE* 1.4 73.4 - - - +
425D GLU* 1.4 72.0 + - - +
427D ARG* 3.8 19.9 + - - +
428D GLU* 3.4 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 425 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421D ASP* 3.3 19.3 + - - +
422D GLU* 3.8 7.9 - - - +
423D PHE 3.3 0.2 - - - -
424D ALA* 1.4 85.7 - - - +
426D SER* 1.4 61.0 + - - +
428D GLU* 3.2 9.2 + - - +
429D VAL* 3.2 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 426 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D ARG* 4.2 13.5 + - - -
422D GLU 3.1 13.1 + - - -
423D PHE* 2.9 12.6 + - - -
425D GLU* 1.4 74.6 - - - +
427D ARG* 1.4 62.0 + - - +
429D VAL* 3.3 10.9 + - - +
430D VAL* 3.3 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 427 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ILE* 3.6 8.7 - - - +
191D LEU* 5.4 0.2 - - - +
195D ILE* 5.9 0.7 - - + -
387D PHE* 3.8 38.8 + - + +
390D ALA* 3.3 29.3 - - - +
391D CYS* 3.5 20.6 - - - +
394D PHE* 3.7 32.1 - - - +
420D GLN 5.0 0.6 + - - -
423D PHE* 2.7 61.8 + - + +
424D ALA* 3.8 21.9 + - - +
426D SER* 1.4 75.2 - - - +
428D GLU* 1.3 60.9 + - - +
430D VAL* 3.1 11.9 - - + +
431D GLN* 3.1 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 428 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D GLU* 5.5 1.0 - - - +
391D CYS* 3.9 22.1 - - - +
424D ALA 3.4 12.9 + - - +
425D GLU* 3.2 11.4 + - - +
427D ARG* 1.3 75.1 - - + +
429D VAL* 1.3 67.3 + - - +
431D GLN* 3.5 31.2 + - - +
432D SER* 3.1 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 429 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D GLU* 3.2 17.1 + - + +
426D SER* 3.3 9.6 + - - +
428D GLU* 1.3 80.6 - - + +
430D VAL* 1.3 62.8 + - + +
432D SER* 3.5 6.4 + - - -
433D LEU* 3.1 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 430 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ILE* 5.4 14.8 - - + -
387D PHE* 5.0 11.9 - - + -
426D SER* 3.3 8.0 + - - +
427D ARG* 3.1 33.0 - - + +
429D VAL* 1.3 78.6 - - + +
431D GLN* 1.3 60.5 + - - +
433D LEU* 3.2 15.7 + - + +
434D MET* 3.1 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 431 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D VAL* 3.9 29.7 - - + +
387D PHE* 3.7 21.6 + - + +
388D GLU* 3.2 47.3 - - - +
391D CYS* 4.9 0.6 - - - +
427D ARG* 3.1 31.5 + - - +
428D GLU* 3.5 34.2 + - - +
429D VAL 3.4 0.2 - - - -
430D VAL* 1.3 74.7 - - - +
432D SER* 1.4 64.5 + - - +
433D LEU 3.4 0.3 + - - -
434D MET* 3.4 4.4 + - - +
435D GLU* 3.3 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 432 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428D GLU* 3.1 22.7 + - - +
429D VAL* 3.8 5.9 - - - -
431D GLN* 1.4 74.8 - - - +
433D LEU* 1.4 62.6 + - - +
435D GLU* 3.3 11.1 + - - +
436D ASP* 3.0 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 433 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B ASN* 5.5 7.0 - - - +
429D VAL* 3.1 36.9 + - + +
430D VAL* 3.4 19.5 - - + +
432D SER* 1.4 77.5 - - - +
434D MET* 1.3 59.9 + - + +
436D ASP* 3.2 26.7 + - + +
437D TYR* 3.5 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 434 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D GLU* 3.4 29.8 - - + +
265D LEU* 3.8 31.9 - - + -
315D TYR* 4.4 0.9 - - - -
381D SER* 3.4 22.9 + - - +
383D VAL* 6.3 0.9 - - + -
384D VAL* 3.6 27.1 - - + -
387D PHE* 4.8 13.7 - - + -
430D VAL* 3.1 39.4 + - + +
431D GLN 3.8 4.5 - - - +
432D SER 3.4 0.2 - - - -
433D LEU* 1.3 71.6 - - + +
435D GLU* 1.4 66.5 + - - +
437D TYR* 3.6 20.1 + - + +
438D VAL* 3.4 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 435 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D THR* 3.8 22.4 - - - +
381D SER* 4.0 5.9 + - - +
384D VAL* 3.5 28.3 - - - +
431D GLN* 3.3 20.1 - - + +
432D SER* 3.5 9.2 - - - +
433D LEU 3.3 0.6 - - - -
434D MET* 1.4 79.9 - - - +
436D ASP* 1.4 63.3 + - - +
438D VAL* 3.3 21.6 + - - +
439D ALA* 3.7 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 436 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D SER* 3.0 19.3 - - - +
433D LEU* 3.2 24.7 + - + +
435D GLU* 1.4 74.8 - - - +
437D TYR* 1.4 62.1 + - + +
439D ALA* 3.0 33.9 + - - +
441D GLU* 4.3 17.5 + - + +
442D GLN 4.0 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 437 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B SER* 3.8 15.8 + - - -
636B ILE* 4.2 28.0 - - + -
264D GLU* 3.3 24.6 + - + -
265D LEU* 4.4 19.5 - - + -
315D TYR* 3.1 22.5 + + - +
348D SER* 3.4 4.5 - - - -
433D LEU* 3.7 46.3 - - + +
434D MET* 3.8 14.1 - - + +
435D GLU 3.3 0.6 - - - -
436D ASP* 1.4 75.3 - - + +
438D VAL* 1.4 56.6 + - - +
439D ALA 3.2 1.6 - - - -
442D GLN* 2.9 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 438 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D PRO 4.9 1.1 - - - +
314D THR* 3.6 46.4 - - + +
315D TYR* 3.7 16.1 - - + -
347D TRP 4.7 1.6 - - - +
348D SER* 3.3 28.8 - - - -
349D SER* 3.5 6.1 + - - -
381D SER* 3.9 6.7 - - - +
434D MET 3.4 13.9 - - - +
435D GLU* 3.3 20.6 + - - +
437D TYR* 1.4 73.0 - - - +
439D ALA* 1.4 58.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 439 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349D SER* 3.8 7.9 - - - -
435D GLU 3.7 4.0 + - - +
436D ASP* 3.0 18.9 + - - +
438D VAL* 1.4 78.9 - - + +
440D ALA* 1.4 62.8 + - - +
441D GLU* 3.3 6.3 - - + +
442D GLN* 3.0 29.6 - - - +
----------------------------------------------------------
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