Contacts of the helix formed by residues 437 - 449 (chain Y) in PDB entry 5XTE
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 ASP 437 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385Y GLU* 2.8 22.1 - - - +
388Y VAL* 4.3 4.7 - - - -
435Y GLU 3.5 5.1 + - - +
436Y VAL* 1.3 75.7 - - - +
438Y ALA* 1.3 81.6 + - - +
439Y SER* 3.2 14.2 + - - -
440Y VAL* 2.9 21.2 + - + +
441Y VAL* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 438 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383Y ALA* 3.3 25.1 - - - +
385Y GLU* 3.3 24.6 + - + +
388Y VAL* 3.7 24.7 - - + +
437Y ASP* 1.3 85.2 + - - +
439Y SER* 1.3 56.0 + - - +
441Y VAL* 3.3 3.3 + - - +
442Y ARG* 2.9 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 439 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437Y ASP* 3.2 13.7 + - - -
438Y ALA* 1.3 78.3 - - - +
440Y VAL* 1.3 60.1 + - - +
442Y ARG* 3.3 31.2 + - - +
443Y GLU* 2.9 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 440 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303Y ALA* 4.5 7.9 - - + -
435Y GLU* 4.6 6.1 - - + +
436Y VAL* 5.0 6.7 - - + -
437Y ASP* 2.9 33.5 + - + +
439Y SER* 1.3 77.2 - - - +
441Y VAL* 1.3 59.6 + - - +
443Y GLU* 3.3 12.5 + - - +
444Y ILE* 2.9 50.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 441 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303Y ALA* 4.6 11.0 - - + +
306Y VAL* 4.5 7.6 - - + -
307Y ALA* 4.4 11.4 - - + -
310Y ILE* 4.7 13.9 - - + -
379Y LEU* 4.7 8.3 - - + +
383Y ALA* 5.2 3.4 - - + -
388Y VAL* 4.1 19.3 - - + -
436Y VAL* 3.8 20.6 - - + -
437Y ASP 2.9 16.8 + - - +
438Y ALA* 3.7 7.9 - - - +
440Y VAL* 1.3 78.7 - - - +
442Y ARG* 1.3 56.5 + - - +
444Y ILE* 4.9 2.5 - - - -
445Y CYS* 2.9 47.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 442 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16T ASN* 3.5 29.8 + - - +
379Y LEU 3.9 8.7 - - - +
380Y CYS 4.1 7.1 + - - +
381Y THR* 3.8 27.3 - - - +
382Y SER 4.4 0.2 - - - +
383Y ALA* 3.5 29.4 + - + +
438Y ALA* 2.9 21.5 + - - +
439Y SER* 3.3 33.9 + - - +
440Y VAL 3.2 0.2 - - - -
441Y VAL* 1.3 77.2 - - - +
443Y GLU* 1.3 59.5 + - - +
446Y SER* 2.9 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 443 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439Y SER* 2.9 34.6 + - - +
440Y VAL* 3.7 13.6 - - - +
442Y ARG* 1.3 79.3 - - + +
444Y ILE* 1.3 60.7 + - + +
446Y SER* 3.7 4.9 - - - -
447Y LYS* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 444 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300Y ASP* 3.7 30.5 - - + +
303Y ALA* 3.6 28.7 - - + -
304Y LEU* 3.8 22.4 - - + -
440Y VAL* 2.9 30.9 + - + +
441Y VAL* 4.4 1.1 - - - +
443Y GLU* 1.3 78.9 - - + +
445Y CYS* 1.3 61.1 + - - +
447Y LYS* 2.9 10.1 + - + +
448Y TYR* 2.9 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 445 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303Y ALA 5.4 1.3 - - - -
304Y LEU* 4.6 8.5 - - - -
307Y ALA* 3.6 31.2 - - - -
379Y LEU* 4.1 24.7 - - + +
380Y CYS* 4.1 4.7 - - - +
441Y VAL* 2.9 35.0 + - - +
444Y ILE* 1.3 78.0 - - - +
446Y SER* 1.3 57.8 + - - +
449Y ILE* 2.9 54.6 + - + +
450Y TYR 3.4 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 446 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Q ARG* 2.7 41.5 + - - -
380Y CYS* 4.2 16.9 - - - +
442Y ARG 2.9 21.9 + - - -
443Y GLU* 3.8 4.9 - - - -
445Y CYS* 1.3 77.4 - - - +
447Y LYS* 1.3 62.9 + - - +
450Y TYR* 3.3 32.0 + - - +
480Y PHE* 5.6 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 447 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300Y ASP* 5.0 2.5 - - - +
443Y GLU 2.9 19.7 + - - +
444Y ILE* 2.9 11.8 + - + +
446Y SER* 1.3 80.1 - - - +
448Y TYR* 1.3 103.0 + - + +
450Y TYR 5.1 1.0 - - - +
452Y GLN* 4.4 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 448 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104P ARG* 4.5 20.0 + - - -
291Y VAL* 3.9 5.9 - - - +
292Y GLU* 3.8 23.8 - - + +
293Y GLY 4.8 0.7 - - - -
294Y PRO* 3.4 37.5 - - + +
300Y ASP* 2.6 29.7 + - - -
304Y LEU* 4.8 1.8 - - + -
354Y LEU* 4.4 13.5 - - + -
444Y ILE* 2.9 40.2 + - + +
447Y LYS* 1.3 116.9 + - + +
449Y ILE* 1.3 65.2 + - + +
452Y GLN* 3.5 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 449 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291Y VAL* 4.4 11.0 - - + -
304Y LEU* 5.0 2.7 - - + -
307Y ALA* 5.7 3.1 - - + -
354Y LEU* 4.4 21.3 - - + -
376Y TRP* 4.0 53.8 - - + +
377Y MET* 6.2 0.9 - - - -
379Y LEU* 6.4 1.3 - - + -
380Y CYS* 4.4 7.0 - - - -
445Y CYS* 2.9 36.2 + - + +
448Y TYR* 1.3 84.8 - - + +
450Y TYR* 1.3 68.3 + - - +
451Y ASP 3.4 1.9 + - - -
452Y GLN* 3.3 11.6 - - - +
475Y MET* 3.4 17.3 - - + +
----------------------------------------------------------
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