Contacts of the helix formed by residues 419 - 441 (chain C) in PDB entry 6DBV
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 419 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C SER 3.9 2.0 + - - +
418C LEU* 1.3 78.7 - - - +
420C ARG* 1.3 61.9 + - - +
421C ARG* 4.3 6.1 - - - +
422C ALA* 3.3 23.4 + - - +
423C GLN* 2.8 26.7 + - - +
12F T 3.9 11.0 - - - +
13F T 3.3 38.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 420 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A LEU* 6.2 3.6 - - - -
456A LEU* 4.5 13.1 - - + +
459A ARG* 3.2 57.1 - - - +
464A HIS* 5.0 0.6 - - - -
418C LEU 5.3 1.6 - - - +
419C THR* 1.3 73.7 - - - +
421C ARG* 1.3 60.3 + - - +
423C GLN* 4.1 7.1 - - - +
424C LYS* 2.9 30.5 + - - +
31E C 3.8 5.9 + - - -
32E T 2.4 40.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 421 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C THR* 3.4 5.2 + - - +
420C ARG* 1.3 79.7 - - - +
422C ALA* 1.3 57.9 + - - +
424C LYS* 3.4 6.2 + - - +
425C HIS* 3.0 60.1 + - - +
35E A 5.7 1.6 - - - +
36E A 3.3 30.9 + - - +
37E C 4.3 5.7 - - - +
13F T 3.6 27.3 + - + +
14F G 2.3 45.7 + - + +
15F T 4.0 18.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 422 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C LEU* 5.1 0.9 - - + -
419C THR* 3.3 21.8 + - - +
420C ARG 3.4 0.2 - - - -
421C ARG* 1.3 79.3 - - - +
423C GLN* 1.3 58.1 + - - +
425C HIS* 3.3 7.7 + - - +
426C ARG* 2.9 29.0 + - - +
12F T 3.0 40.0 + - + +
13F T 4.0 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 423 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A THR* 3.2 28.7 + - + +
455A LEU* 5.8 2.9 - - - +
456A LEU* 4.6 4.3 - - + +
415C LEU* 2.2 49.8 + - + -
416C LEU* 4.2 3.6 + - - +
418C LEU* 3.0 40.0 + - + +
419C THR 2.8 20.7 + - - +
420C ARG* 4.1 6.3 - - - +
422C ALA* 1.3 70.5 - - - +
424C LYS* 1.3 60.3 + - - +
426C ARG* 3.3 5.3 + - - +
427C LEU* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 424 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LEU* 3.9 34.4 - - + +
460A ALA* 5.2 1.6 - - - +
420C ARG 2.9 19.8 + - - +
421C ARG* 3.7 7.2 - - - +
423C GLN* 1.3 76.9 - - - +
425C HIS* 1.3 56.4 + - - +
428C ARG* 2.9 35.9 + - + +
431C LYS* 3.1 37.5 - - + +
33E G 2.8 49.5 + - - +
34E G 5.0 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 425 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ARG* 3.0 38.9 + - - +
422C ALA* 3.6 6.7 + - - +
423C GLN 3.3 0.2 - - - -
424C LYS* 1.3 76.0 - - - +
426C ARG* 1.3 62.0 + - - +
428C ARG* 4.2 13.6 + - - +
429C ASP* 6.0 1.2 - - - -
36E A 6.1 2.0 - - - -
11F T 4.5 18.4 - - + -
12F T 3.8 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 426 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A PHE* 4.5 7.3 - - - -
441A GLU* 4.4 16.5 + - - +
442A GLU* 3.3 32.3 + - - +
412C ARG* 3.2 55.9 - - - +
413C GLN 3.9 10.1 + - - -
415C LEU* 5.1 1.3 - - + -
418C LEU* 3.6 20.3 - - - +
422C ALA 2.9 16.5 + - - +
423C GLN* 3.3 7.6 + - + +
424C LYS 3.2 0.4 - - - -
425C HIS* 1.3 81.5 - - - +
427C LEU* 1.3 70.4 + - + +
428C ARG 3.5 0.6 + - - -
429C ASP* 4.9 7.0 - - - +
11F T 3.9 18.1 + - - +
12F T 3.5 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 427 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A PHE* 3.5 30.3 - - + -
441A GLU* 5.5 2.9 - - + -
442A GLU* 4.8 13.5 - - - +
449A VAL* 4.3 15.5 - - + +
452A THR* 3.6 34.1 - - + -
453A LEU* 3.9 23.1 - - + +
456A LEU* 5.0 6.3 - - + -
415C LEU* 4.3 15.3 - - + -
423C GLN 2.9 15.9 + - - +
424C LYS* 3.7 1.8 - - - -
426C ARG* 1.3 84.5 - - + +
428C ARG* 1.3 58.9 + - - +
429C ASP 3.1 3.5 + - - +
430C LEU* 3.3 5.2 + - + +
431C LYS* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 428 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C LYS* 2.9 20.1 + - + +
425C HIS* 4.2 12.5 + - - +
426C ARG 3.5 2.2 - - - -
427C LEU* 1.3 76.6 - - - +
429C ASP* 1.3 76.9 + - - +
431C LYS* 3.2 25.0 - - + +
432C ASN* 2.9 47.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 429 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A PHE* 4.8 16.4 - - + -
441A GLU* 5.5 1.9 - - - +
425C HIS 6.0 1.3 - - - -
426C ARG 4.9 6.6 - - - +
427C LEU 3.1 1.0 - - - -
428C ARG* 1.3 96.3 + - - +
430C LEU* 1.3 60.2 + - - +
432C ASN* 3.2 9.2 + - - +
433C GLN* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 430 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 4.6 1.3 - - + -
434A VAL* 3.9 27.1 - - + -
437A PHE* 3.5 42.7 - - + -
449A VAL* 3.7 19.3 - - + -
453A LEU* 3.6 32.8 - - + -
427C LEU* 3.3 8.2 + - + +
429C ASP* 1.3 76.2 - - - +
431C LYS* 1.3 60.3 + - - +
433C GLN* 3.4 31.4 - - + +
434C VAL* 2.9 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU* 5.0 6.9 - - + +
456A LEU* 5.4 9.6 - - + -
424C LYS* 3.1 40.0 - - + +
427C LEU 2.9 15.0 + - - +
428C ARG* 3.2 28.2 - - + +
430C LEU* 1.3 77.9 - - - +
432C ASN* 1.3 64.5 + - - +
434C VAL* 3.5 5.2 + - - +
435C LYS* 2.9 29.6 + - + +
446C VAL* 5.8 1.6 - - - +
33E G 5.9 0.4 - - - -
34E G 4.6 16.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 432 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ARG* 2.9 54.2 + - - +
429C ASP* 3.2 8.9 + - - +
431C LYS* 1.3 79.9 - - - +
433C GLN* 1.3 61.4 + - - +
435C LYS* 3.6 9.9 - - - +
436C THR* 2.9 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 433 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLN* 3.1 43.1 + - - +
436A THR* 6.4 0.2 - - - +
437A PHE* 5.1 14.3 - - - +
440A LYS* 5.9 3.0 - - - +
429C ASP* 3.0 17.3 + - - +
430C LEU* 3.4 31.5 - - + +
432C ASN* 1.3 76.8 - - - +
434C VAL* 1.3 57.2 + - - +
436C THR* 3.1 11.6 - - + +
437C PHE* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 434 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 3.7 27.4 - - + -
434A VAL* 4.8 0.4 - - + -
453A LEU* 3.9 25.1 - - + -
430C LEU* 2.9 23.7 + - + +
431C LYS* 4.0 4.7 - - - +
433C GLN* 1.3 72.6 - - - +
435C LYS* 1.3 60.6 + - - +
437C PHE* 3.7 0.5 - - - +
438C ALA* 2.9 28.2 + - - +
446C VAL* 4.2 22.0 - - + +
449C VAL* 3.6 28.5 - - + -
450C CYS* 5.2 4.9 - - + +
453C LEU* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 435 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C LYS* 2.9 20.5 + - + +
432C ASN* 3.6 12.1 - - - +
433C GLN 3.3 0.2 - - - -
434C VAL* 1.3 77.5 - - - +
436C THR* 1.3 57.9 + - - +
438C ALA* 3.3 4.8 + - + +
439C GLU* 2.9 66.7 + - - +
444C GLY* 4.6 12.5 + - - -
446C VAL* 4.0 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 436 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLN* 6.3 0.9 - - - +
432C ASN 2.9 17.9 + - - +
433C GLN* 3.1 21.1 - - + +
435C LYS* 1.3 72.5 - - - +
437C PHE* 1.3 59.6 + - - +
439C GLU* 3.3 18.2 + - - +
440C LYS* 2.9 59.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 437 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ARG 3.8 16.8 - - - -
427A LEU* 3.5 16.6 - - + -
429A ASP* 3.7 15.7 - - + -
430A LEU* 3.5 57.9 - - + -
433A GLN* 4.9 9.4 - - - +
433C GLN 2.9 19.1 + - - +
434C VAL 3.7 3.6 - - - +
435C LYS 3.3 0.2 - - - -
436C THR* 1.3 77.4 - - + +
438C ALA* 1.3 60.0 + - - +
440C LYS* 4.9 3.8 - - - -
441C GLU* 3.0 44.7 + - + +
442C GLU* 3.0 31.9 - - + -
449C VAL* 4.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 438 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C VAL 2.9 17.2 + - - +
435C LYS* 3.7 5.2 - - + +
437C PHE* 1.3 77.8 - - - +
439C GLU* 1.3 54.8 + - - +
442C GLU* 3.1 12.8 + - + -
443C GLY 2.6 17.2 + - - -
444C GLY 2.3 24.9 + - - -
445C ASP 3.2 40.2 - - - +
446C VAL* 4.3 3.1 - - + +
449C VAL* 4.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 439 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C LYS* 2.9 59.5 + - - +
436C THR* 3.3 22.7 + - - +
437C PHE 3.3 0.4 - - - -
438C ALA* 1.3 78.4 - - - +
440C LYS* 1.3 63.3 + - + +
443C GLY* 4.3 8.9 + - - -
444C GLY* 3.6 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 440 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ARG* 5.2 1.7 + - - -
436C THR* 2.9 40.2 + - + +
437C PHE* 4.1 3.8 - - - +
439C GLU* 1.3 82.2 - - + +
441C GLU* 1.3 73.2 + - + +
443C GLY 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 441 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ARG* 2.9 45.5 + - - +
426A ARG* 5.2 2.6 + - - +
429A ASP* 4.8 8.8 - - - +
437C PHE* 3.0 32.1 + - + +
440C LYS* 1.3 90.6 - - + +
442C GLU* 1.3 81.7 + - - +
443C GLY 3.6 1.1 + - - -
----------------------------------------------------------
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