Contacts of the helix formed by residues 462 - 476 (chain D) in PDB entry 5LS6
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 462 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D GLN* 3.8 42.8 + - + +
428D GLU* 5.4 0.5 + - - -
455D ALA* 3.4 7.6 - - - -
461D LYS* 1.3 77.9 - - - +
463D CYS* 1.3 57.6 + - - +
464D ARG* 3.6 12.3 - - - +
465D GLN* 2.4 63.2 + - - +
466D VAL* 2.8 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 463 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D CYS* 3.5 11.9 - - - -
323D GLN 4.0 2.6 + - - +
324D CYS* 3.9 4.3 - - - -
325D TYR* 3.2 36.6 - - - +
451D PHE* 4.0 4.5 - - - +
452D CYS* 3.7 14.1 - - - -
455D ALA* 3.2 15.3 - - + +
462D THR* 1.3 71.7 - - - +
464D ARG* 1.3 66.1 + - - +
466D VAL* 3.5 2.4 + - - +
467D TYR* 3.3 20.1 + - - +
802D ZN 2.5 35.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 464 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D GLN* 4.0 12.7 + - + +
324D CYS 3.9 15.1 - - - +
325D TYR* 3.7 14.0 - - - +
326D GLN 5.8 3.4 - - - +
425D GLU* 4.4 14.1 + - - +
426D PRO 3.0 25.9 + - - -
427D PRO* 4.1 3.2 - - - +
428D GLU* 3.3 29.3 + - - +
462D THR* 3.6 11.4 - - - +
463D CYS* 1.3 80.3 - - - +
465D GLN* 1.3 62.7 + - + +
467D TYR* 3.3 12.3 + - - +
468D GLU* 2.3 66.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 465 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428D GLU* 4.4 14.7 + - - +
430D VAL* 3.2 45.7 - - + +
432D TRP* 3.3 16.3 + - + +
460D THR 5.5 0.2 + - - -
461D LYS* 3.6 18.8 - - + +
462D THR* 2.4 59.0 + - - +
464D ARG* 1.3 74.6 - - + +
466D VAL* 1.3 61.3 + - - +
467D TYR 3.4 0.2 - - - -
468D GLU* 3.6 18.1 + - - +
469D PHE* 3.2 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 466 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D TRP* 4.2 6.5 - - + -
440D PHE* 3.7 10.4 - - + -
451D PHE* 3.6 29.8 - - + -
454D ILE* 3.4 26.5 - - + -
455D ALA* 3.5 39.7 - - + +
458D ILE* 4.2 8.7 - - + -
461D LYS* 4.5 6.7 - - + -
462D THR 2.8 7.6 + - - +
463D CYS 3.8 7.2 - - - +
465D GLN* 1.3 75.4 - - - +
467D TYR* 1.3 51.5 - - - +
469D PHE* 3.1 6.1 + - - +
470D ARG* 2.8 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 467 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D TYR* 3.7 30.3 - + + -
330D GLY 3.3 18.4 + - - -
331D ALA* 3.7 19.5 - - - -
334D PHE* 4.0 4.0 - - - -
335D ALA* 4.5 9.9 - - + -
338D LEU* 6.2 0.2 - - + -
423D ASN* 3.4 39.3 + - - +
451D PHE* 3.8 22.0 - + + -
463D CYS 3.3 9.6 + - - +
464D ARG* 3.4 17.3 - - - +
466D VAL* 1.3 81.5 - - - +
468D GLU* 1.3 66.5 + - + +
470D ARG* 3.2 9.9 + - + +
471D VAL* 2.8 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 468 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427D PRO* 3.6 21.3 - - + +
428D GLU* 2.7 44.8 + - - +
430D VAL* 4.6 1.2 - - - +
432D TRP* 6.0 0.2 + - - -
464D ARG* 2.3 48.6 + - - +
465D GLN* 3.6 25.6 - - - +
466D VAL 3.3 0.2 - - - -
467D TYR* 1.3 85.0 - - + +
469D PHE* 1.3 57.7 + - - +
471D VAL* 3.7 6.6 + - - +
472D LYS* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 469 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D TRP* 3.4 58.3 - + + +
437D ALA* 3.8 33.7 - - + -
440D PHE* 3.3 40.6 - + - -
441D ARG* 4.3 4.0 - - - -
465D GLN 3.2 2.2 + - - +
466D VAL 3.1 6.1 + - - +
468D GLU* 1.3 75.6 - - - +
470D ARG* 1.3 56.0 + - - +
472D LYS* 3.7 30.6 - - + +
473D GLU* 2.8 61.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 470 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D ALA* 5.5 1.9 + - - +
338D LEU* 4.0 32.6 + - + +
339D THR* 3.2 29.1 + - - +
342D ARG* 5.5 13.1 - - - +
440D PHE* 3.8 17.7 - - + -
444D ILE* 4.9 17.0 - - - +
449D ASP* 3.8 13.4 + - - -
451D PHE* 3.5 33.1 - - + -
466D VAL 2.8 13.1 + - - +
467D TYR* 3.3 10.8 - - + +
469D PHE* 1.3 76.0 - - - +
471D VAL* 1.3 59.0 + - + +
473D GLU* 3.2 7.9 + - - +
474D SER* 2.8 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 471 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D PHE* 4.4 22.9 - - + -
338D LEU* 4.5 7.2 - - + -
423D ASN* 4.5 12.8 - - - +
467D TYR* 2.8 54.4 + - + +
468D GLU* 3.9 7.6 - - - +
469D PHE 3.2 0.2 - - - -
470D ARG* 1.3 70.8 - - + +
472D LYS* 1.3 70.2 + - - +
474D SER* 3.0 23.7 + - - +
475D SER* 3.2 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 472 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D TRP* 5.1 7.7 - - - +
468D GLU 3.0 19.4 + - - +
469D PHE* 3.7 34.5 - - + +
471D VAL* 1.3 75.2 - - - +
473D GLU* 1.3 60.2 + - - +
475D SER* 2.8 30.0 + - - -
476D ILE* 3.2 30.8 + - + +
51J GLU 5.6 1.6 - - - -
54J GLU* 4.0 30.2 - - + +
55J ILE* 4.4 12.3 - - + -
58J GLN* 5.2 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 473 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D GLN* 4.9 4.3 + - - -
440D PHE* 4.0 8.6 - - + -
441D ARG* 3.2 48.0 + - - +
444D ILE* 5.8 2.3 - - + +
469D PHE* 2.8 53.7 + - + +
470D ARG* 3.4 11.4 - - - +
472D LYS* 1.3 75.6 - - + +
474D SER* 1.3 61.5 + - - +
476D ILE* 3.3 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 474 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D PHE* 5.6 1.6 - - - -
338D LEU* 3.9 37.9 - - - +
470D ARG* 2.8 26.2 + - - +
471D VAL* 3.0 12.8 + - - +
473D GLU* 1.3 74.8 - - - +
475D SER* 1.3 66.4 + - - +
476D ILE 3.4 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 475 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471D VAL* 3.2 10.2 + - - +
472D LYS* 2.8 20.6 + - - -
474D SER* 1.3 81.1 + - - +
476D ILE* 1.3 57.3 + - - +
477D ILE* 5.2 0.7 - - - -
55J ILE* 3.4 29.1 - - - +
201K ARG* 2.7 33.8 + - - -
247K LEU* 5.9 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 476 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472D LYS* 3.2 24.4 + - + +
473D GLU* 3.3 19.8 + - - +
474D SER 3.3 9.7 - - - +
475D SER* 1.3 78.8 - - - +
477D ILE* 1.3 70.6 + - - +
478D ALA* 3.9 2.9 + - - +
55J ILE* 3.6 42.2 - - + +
58J GLN* 3.7 21.1 - - + -
59J GLU* 4.2 13.5 - - + +
62J GLN* 4.3 20.6 - - - +
----------------------------------------------------------
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