Contacts of the helix formed by residues 441 - 454 (chain Y) in PDB entry 5A31
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 ALA 441 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437Y LEU* 3.7 23.1 - - + +
438Y GLY 3.9 3.7 + - - +
439Y ALA 3.3 1.0 - - - -
440Y ASN* 1.3 79.1 - - - +
442Y GLN* 1.3 66.4 + - - +
443Y THR* 3.5 2.0 + - - +
444Y LEU* 3.5 38.9 + - + +
445Y THR* 3.4 18.9 + - - +
471Y GLN* 3.5 4.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 442 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F PHE* 5.7 0.8 - - - -
284Y ALA 5.8 0.2 - - - +
440Y ASN 3.7 15.2 + - - +
441Y ALA* 1.3 73.4 - - - +
443Y THR* 1.3 63.1 + - + +
445Y THR* 2.7 21.3 + - - -
446Y LEU* 3.0 19.3 + - - +
468Y ALA* 3.8 9.8 - - - +
471Y GLN* 4.0 27.5 + - + +
472Y GLU* 3.6 45.2 + - + +
475Y TYR* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 443 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285Y GLY* 6.4 0.4 - - - -
407Y LEU* 3.5 29.8 - - + +
437Y LEU* 3.3 23.4 - - - +
441Y ALA* 4.1 2.8 - - - +
442Y GLN* 1.3 81.2 + - + +
444Y LEU* 1.3 60.7 + - - +
446Y LEU* 3.5 9.3 - - + +
447Y LEU* 2.9 43.3 + - - +
475Y TYR* 3.6 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 444 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430Y ALA 5.4 0.2 - - - +
433Y VAL* 3.4 14.1 - - + +
434Y TYR* 3.0 64.2 - - + +
437Y LEU* 3.4 29.6 - - + -
438Y GLY 3.0 28.3 - - - +
441Y ALA* 3.5 17.6 + - + +
442Y GLN 3.3 0.2 - - - -
443Y THR* 1.3 79.1 + - - +
445Y THR* 1.3 58.1 + - + +
447Y LEU* 3.6 10.8 - - + +
448Y ALA* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 445 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434Y TYR* 4.6 11.9 - - + +
441Y ALA 3.4 11.5 + - - +
442Y GLN* 2.7 24.8 + - - -
444Y LEU* 1.3 79.7 - - + +
446Y LEU* 1.3 55.2 + - - +
448Y ALA* 3.5 1.2 + - - +
449Y THR* 2.9 34.9 + - - +
464Y LEU* 3.7 42.9 - - + +
467Y LYS* 4.9 10.3 - - + +
468Y ALA* 3.1 17.8 - - - +
471Y GLN* 5.2 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442Y GLN 3.0 15.4 + - - +
443Y THR* 3.5 8.7 - - - +
445Y THR* 1.3 75.1 + - - +
447Y LEU* 1.3 68.3 + - + +
449Y THR* 2.5 26.0 + - - -
450Y VAL 3.2 4.5 + - - -
465Y LEU* 5.0 1.8 - - + -
468Y ALA* 4.1 7.8 - - + +
475Y TYR* 3.8 22.2 - - + +
477Y LYS* 3.5 22.4 - - + -
478Y ALA* 3.5 37.9 - - + +
481Y LYS* 3.2 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 447 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407Y LEU* 5.7 8.7 - - + +
410Y TYR* 6.0 2.0 - - + -
411Y GLU* 4.8 13.2 - - + -
414Y ILE* 4.2 29.8 - - + -
415Y GLU* 6.5 0.2 - - + -
430Y ALA* 5.4 4.9 - - + -
433Y VAL* 4.7 17.3 - - + -
437Y LEU* 6.1 0.2 - - + -
443Y THR* 2.9 38.2 + - - +
444Y LEU* 3.6 16.8 - - + +
446Y LEU* 1.3 78.9 - - + +
448Y ALA* 1.3 61.5 + - - +
450Y VAL* 3.1 7.0 + - + +
451Y CYS* 2.8 38.3 + - - -
481Y LYS* 4.5 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 448 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430Y ALA* 5.5 3.5 - - + +
431Y ASN* 5.6 5.6 - - - +
434Y TYR* 4.6 13.0 - - + -
444Y LEU 2.9 18.3 + - - +
445Y THR* 3.7 7.2 - - - +
447Y LEU* 1.3 75.5 - - - +
449Y THR* 1.3 57.8 + - - +
451Y CYS* 3.3 10.5 + - - +
452Y LEU* 2.9 30.7 + - - +
461Y ALA* 5.4 0.2 - - - -
464Y LEU* 4.5 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 449 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445Y THR 2.9 21.0 + - - +
446Y LEU* 2.5 23.4 + - - -
448Y ALA* 1.3 74.9 - - - +
450Y VAL* 1.3 58.3 + - - +
452Y LEU 3.1 1.0 + - - -
453Y GLU* 2.9 34.4 + - - +
461Y ALA* 3.0 24.1 - - - +
464Y LEU* 3.4 3.1 - - + -
465Y LEU* 2.9 62.0 - - + +
481Y LYS* 4.3 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 450 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414Y ILE* 5.5 6.1 - - + -
418Y LEU* 6.1 6.0 - - + +
446Y LEU 3.2 0.2 + - - -
447Y LEU* 3.1 9.6 + - + +
449Y THR* 1.3 76.8 + - - +
451Y CYS* 1.3 67.6 + - - +
453Y GLU* 3.3 30.0 - - + +
454Y ASP* 3.4 7.8 + - - +
481Y LYS* 3.2 48.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 451 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414Y ILE* 3.3 32.1 - - - -
426Y ALA* 5.2 1.1 - - + -
427Y MET* 4.5 28.6 - - + +
430Y ALA* 3.7 18.4 - - + -
447Y LEU 2.8 34.7 + - - -
448Y ALA* 3.5 8.7 - - - +
450Y VAL* 1.3 75.8 - - - +
452Y LEU* 1.3 57.7 + - + +
454Y ASP* 3.3 9.1 + - - +
455Y PRO* 2.8 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 452 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427Y MET* 6.1 4.3 - - + -
448Y ALA 2.9 16.6 + - - +
449Y THR 3.1 0.2 + - - -
451Y CYS* 1.3 74.1 - - + +
453Y GLU* 1.3 64.5 + - - +
454Y ASP 3.2 0.7 - - - -
455Y PRO* 3.3 9.4 - - + +
457Y THR* 2.2 77.4 + - - +
460Y LYS* 2.9 24.5 - - + +
461Y ALA* 2.5 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 453 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449Y THR* 2.9 30.8 + - - +
450Y VAL* 3.3 24.6 + - + +
452Y LEU* 1.3 77.2 - - - +
454Y ASP* 1.3 57.8 + - - +
456Y VAL* 2.8 26.9 + - - +
457Y THR 5.7 0.4 - - - -
458Y GLN* 5.2 1.5 - - - +
461Y ALA* 3.2 24.0 - - - +
465Y LEU* 4.5 7.8 - - - +
481Y LYS* 5.2 3.4 - - - +
485Y LEU* 3.4 19.5 - - - +
488Y ARG* 3.5 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 454 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418Y LEU* 3.8 29.8 - - + +
421Y ASN* 4.9 2.8 - - - +
423Y ILE* 3.1 47.1 - - + +
426Y ALA* 5.5 2.3 - - - +
450Y VAL 3.4 6.5 + - - +
451Y CYS* 3.3 10.9 + - - +
452Y LEU 3.2 0.2 - - - -
453Y GLU* 1.3 80.3 - - - +
455Y PRO* 1.4 67.8 - - + +
456Y VAL* 3.4 7.3 + - - +
----------------------------------------------------------
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