Contacts of the helix formed by residues 435 - 450 (chain N) in PDB entry 5L4K
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 SER 435 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401N LYS* 3.6 25.1 - - - -
433N PRO 3.5 0.6 + - - -
434N GLY* 1.3 76.4 - - - +
436N ALA* 1.3 54.0 + - - +
437N TYR* 2.8 20.6 + - - +
438N GLN* 3.0 32.1 + - - +
439N GLU* 3.8 3.3 + - - +
18V PRO* 3.5 20.1 - - - +
20V THR 3.9 10.9 + - - -
21V ASP* 3.8 11.7 - - - +
22V ALA* 4.7 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 436 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433N PRO 3.6 0.4 + - - -
434N GLY 3.4 1.4 + - - -
435N SER* 1.3 71.2 - - - +
437N TYR* 1.3 56.7 + - - +
438N GLN 3.3 0.7 - - - -
439N GLU* 3.7 16.1 - - - +
440N GLY 2.9 24.6 + - - -
470N ASN* 3.4 33.4 - - + +
472N ILE* 3.2 25.3 - - + +
473N VAL* 4.3 2.8 - - + +
21V ASP* 2.9 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 437 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398N ASN* 3.4 49.0 - - + +
399N TRP* 3.8 42.8 + + - -
401N LYS* 4.2 22.4 - - + -
402N PHE* 3.7 13.9 - - + +
435N SER* 2.8 7.9 + - - +
436N ALA* 1.3 78.6 - - - +
438N GLN* 1.3 55.8 + - - +
441N GLY* 2.9 26.2 + - - -
472N ILE* 3.4 36.6 - - + +
21V ASP* 4.1 10.5 - - + -
22V ALA 5.2 6.5 - - - -
24V ALA* 3.6 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 438 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393N LEU* 4.5 23.8 - - - +
401N LYS* 3.5 37.3 - - + +
405N THR* 3.4 29.3 + - - +
426N TYR* 3.4 34.2 - - + +
431N THR* 6.4 1.3 - - + -
434N GLY 5.2 1.2 - - - +
435N SER* 3.0 19.5 + - - +
437N TYR* 1.3 75.5 - - - +
439N GLU* 1.3 59.7 + - + +
442N GLY* 2.9 19.3 + - - -
18V PRO* 5.5 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 439 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426N TYR 4.0 12.8 - - - +
427N LEU* 4.7 1.9 - - - +
428N PRO* 3.6 37.0 - - + +
431N THR* 4.2 2.0 - - + +
432N SER 3.3 23.1 - - - +
433N PRO* 3.5 24.7 - - - +
434N GLY 4.3 3.1 - - - +
435N SER 4.2 8.7 - - - +
436N ALA* 3.3 15.9 + - - +
437N TYR 3.3 0.4 - - - -
438N GLN* 1.3 77.0 - - + +
440N GLY* 1.3 66.5 + - - +
442N GLY* 3.0 11.3 + - - -
443N LEU* 3.0 19.9 + - + +
470N ASN* 4.3 4.5 + - - -
473N VAL* 4.0 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 440 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402N PHE* 3.7 7.9 - - - -
436N ALA 2.9 16.5 + - - -
437N TYR 4.1 0.4 - - - -
439N GLU* 1.3 71.7 - - - +
441N GLY* 1.3 58.2 + - - +
443N LEU* 3.2 3.3 + - - -
444N TYR 3.0 24.3 + - - -
472N ILE 3.6 23.6 - - - -
473N VAL* 3.9 11.9 - - - +
476N GLY* 3.3 13.3 - - - -
477N GLY 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 441 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402N PHE* 3.5 28.7 - - - -
405N THR* 3.6 15.2 - - - +
406N ALA* 4.2 1.4 + - - -
437N TYR 2.9 19.8 + - - -
438N GLN 4.2 0.9 - - - -
440N GLY* 1.3 70.8 - - - +
442N GLY* 1.3 65.1 + - - +
444N TYR* 3.8 2.6 - - - +
445N ALA* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 442 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405N THR* 3.4 11.4 - - - +
423N MET* 4.4 9.2 - - - +
426N TYR 5.3 1.3 - - - -
427N LEU* 3.8 19.0 - - - +
438N GLN 2.9 18.2 + - - -
439N GLU 3.0 5.0 + - - -
441N GLY* 1.3 75.0 - - - +
443N LEU* 1.3 62.6 + - - +
445N ALA* 3.1 5.2 + - - +
446N LEU* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 443 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427N LEU* 3.7 19.3 - - + +
428N PRO* 4.6 2.5 - - + -
439N GLU* 3.0 16.0 + - + +
440N GLY* 3.7 2.5 - - - +
442N GLY* 1.3 73.8 - - - +
444N TYR* 1.3 64.1 + - - +
446N LEU* 3.0 6.4 + - - +
447N GLY 3.0 18.4 + - - -
460N TYR* 4.7 2.5 - - + -
461N LEU* 3.9 18.7 - - + +
464N GLN* 3.5 44.6 - - + +
465N LEU* 4.5 3.8 - - + -
473N VAL* 3.7 39.9 - - + +
476N GLY 3.9 1.3 - - - -
477N GLY* 3.7 18.8 - - - -
480N GLY* 3.5 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 444 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402N PHE* 3.6 27.8 - + + -
406N ALA* 3.7 14.4 - - + -
440N GLY 3.0 14.5 + - - +
441N GLY 3.8 2.9 - - - +
443N LEU* 1.3 75.1 - - - +
445N ALA* 1.3 62.5 + - - +
447N GLY* 3.1 3.8 + - - -
448N LEU* 3.0 38.1 + - + +
476N GLY* 3.1 21.9 + - - +
479N LEU* 3.4 34.8 - - + -
480N GLY 3.7 2.5 - - - +
483N LEU* 3.9 11.0 - - + -
774N PRO 4.3 8.5 + - - -
777N HIS* 3.5 39.9 - + - +
778N PHE* 3.9 23.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 445 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405N THR 3.3 26.2 - - - +
406N ALA* 3.9 3.4 - - - +
409N GLY* 3.5 26.8 - - - +
423N MET* 4.0 11.9 - - + -
441N GLY 2.9 12.6 + - - +
442N GLY 3.4 4.3 - - - +
444N TYR* 1.3 76.2 - - - +
446N LEU* 1.3 58.9 + - - +
448N LEU* 2.9 25.8 + - - +
449N ILE* 3.0 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419N ALA* 4.7 8.1 - - + +
420N LEU* 3.6 24.5 - - + +
423N MET* 5.2 6.9 - - + +
427N LEU* 4.7 8.5 - - + -
442N GLY 3.0 12.7 + - - +
443N LEU* 3.0 9.8 + - - +
445N ALA* 1.3 75.3 - - - +
447N GLY* 1.3 62.4 + - - +
449N ILE* 3.4 13.8 + - + +
450N HIS* 3.1 45.5 + - + +
457N ILE* 4.0 13.5 - - + +
460N TYR* 3.2 42.6 - - + -
461N LEU* 4.1 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 447 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443N LEU 3.0 10.7 + - - -
444N TYR 3.1 1.0 + - - -
446N LEU* 1.3 75.7 - - - +
448N LEU* 1.3 61.0 + - - +
450N HIS 3.6 2.5 - - - +
451N ALA* 3.4 15.6 + - - +
461N LEU* 4.5 4.8 - - - +
480N GLY* 3.2 31.6 - - - -
483N LEU* 3.1 23.8 - - - +
484N ALA* 4.6 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 448 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406N ALA 3.8 23.3 - - - +
409N GLY 3.2 14.7 - - - +
410N VAL* 3.8 14.8 - - + -
413N LYS* 3.7 13.0 + - - +
444N TYR* 3.0 48.1 + - + +
445N ALA* 2.9 12.2 + - - +
447N GLY* 1.3 76.7 - - - +
449N ILE* 1.3 66.5 + - - +
451N ALA* 3.6 13.1 - - - +
483N LEU* 3.7 17.5 - - + -
777N HIS* 4.1 19.5 - - + +
778N PHE* 5.1 4.0 - - + +
780N SER* 4.5 7.1 + - - +
781N LEU* 4.9 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 449 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408N LEU 3.9 8.3 - - - +
409N GLY* 3.3 33.0 - - - +
412N HIS* 3.9 20.0 - - + +
413N LYS* 3.6 18.5 + - - +
414N GLY 4.4 5.3 + - - +
415N HIS 2.9 29.6 - - - +
416N GLU* 4.5 9.0 - - - +
419N ALA* 3.9 18.2 - - + -
423N MET* 4.4 17.0 - - + -
445N ALA 3.0 8.2 + - - +
446N LEU* 4.0 6.1 - - + +
448N LEU* 1.3 76.4 - - - +
450N HIS* 1.3 72.4 + - + +
451N ALA 3.5 2.8 + - - -
453N HIS* 5.3 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 450 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415N HIS 4.0 1.7 + - - -
416N GLU* 3.3 55.7 + - - -
419N ALA* 4.1 6.3 - - - +
420N LEU* 5.4 0.6 - - - +
446N LEU* 3.1 28.8 + - + +
447N GLY 3.6 4.0 - - - -
449N ILE* 1.3 88.9 - - + +
451N ALA* 1.3 59.1 + - - +
452N ASN 3.6 0.5 + - - -
453N HIS* 4.4 11.3 + - - +
454N GLY* 3.8 12.4 + - - +
455N GLY 5.9 0.2 + - - -
457N ILE* 3.5 45.5 - - + +
484N ALA* 3.3 23.2 - - - +
----------------------------------------------------------
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