Contacts of the helix formed by residues 544 - 552 (chain Z) in PDB entry 5WTI
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 GLU 544 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525Z LYS* 4.8 19.3 + - - -
543Z LYS* 1.3 75.3 - - - +
545Z LEU* 1.3 63.9 + - - +
547Z GLU* 3.5 9.4 + - + +
548Z TRP* 3.3 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 545 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525Z LYS* 6.1 0.2 - - - +
543Z LYS 4.0 7.1 - - - +
544Z GLU* 1.3 77.0 - - - +
546Z THR* 1.3 63.0 + - - +
548Z TRP* 3.1 10.6 + - + +
549Z ILE* 3.1 41.6 + - + +
568Z LEU* 3.5 33.9 - - + -
588Z VAL* 4.5 5.8 - - + -
603Z ILE* 4.2 24.7 - - + -
606Z THR* 4.5 6.3 - - + -
608Z LEU* 3.7 20.0 - - + -
964Z TRP* 4.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 546 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543Z LYS* 3.0 24.7 + - - -
545Z LEU* 1.3 79.2 - - - +
547Z GLU* 1.3 58.5 + - - +
549Z ILE* 4.0 2.6 + - - +
550Z LYS* 3.6 18.9 + - - +
605Z GLY 5.0 0.2 + - - -
606Z THR* 3.8 22.2 - - - +
607Z GLU* 5.5 5.6 - - + +
608Z LEU* 4.1 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 547 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543Z LYS 3.5 5.5 + - - +
544Z GLU* 3.5 11.5 + - + +
545Z LEU 3.2 0.4 - - - -
546Z THR* 1.3 77.2 - - - +
548Z TRP* 1.3 59.8 + - - +
549Z ILE 3.5 0.2 - - - -
550Z LYS* 3.9 8.3 - - - +
551Z ASP* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 548 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522Z PRO* 3.5 30.5 - - + -
523Z VAL* 3.4 20.4 - - + +
525Z LYS* 4.4 20.0 - - - +
544Z GLU 3.3 11.9 + - - +
545Z LEU* 3.1 14.2 + - + +
547Z GLU* 1.3 76.1 - - - +
549Z ILE* 1.3 58.8 + - + +
550Z LYS 3.3 0.2 - - - -
551Z ASP* 3.3 28.7 + - + +
552Z SER* 2.6 46.4 + - - -
555Z LYS* 5.7 2.7 - - - -
565Z GLU 3.1 30.5 - - - -
566Z ILE* 3.8 11.9 - - + -
567Z GLY 2.6 35.5 + - - +
568Z LEU* 4.8 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 549 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545Z LEU* 3.1 25.6 + - + +
546Z THR 4.3 3.6 - - - +
548Z TRP* 1.3 78.6 - - + +
550Z LYS* 1.3 62.3 + - - +
552Z SER* 3.2 13.5 + - - -
553Z LYS* 3.2 12.1 + - - +
567Z GLY* 4.4 8.3 - - - -
568Z LEU 4.2 17.0 - - - +
588Z VAL* 3.7 34.3 - - + +
589Z VAL* 4.6 2.0 - - - -
590Z ASP* 4.3 33.6 - - + +
608Z LEU* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 550 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546Z THR 3.6 15.7 + - - +
547Z GLU* 3.9 8.5 - - - +
548Z TRP 3.3 0.4 - - - -
549Z ILE* 1.3 76.3 - - - +
551Z ASP* 1.3 65.3 + - - +
553Z LYS* 3.3 20.8 - - - +
590Z ASP* 5.5 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 551 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547Z GLU 3.1 16.9 + - - +
548Z TRP* 3.4 35.2 - - + +
550Z LYS* 1.3 77.2 - - - +
552Z SER* 1.3 57.0 + - - +
553Z LYS 2.9 10.2 + - - +
555Z LYS* 2.8 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 552 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548Z TRP* 2.6 34.5 + - - -
549Z ILE* 3.2 10.2 + - - -
551Z ASP* 1.3 72.8 - - - +
553Z LYS* 1.3 62.4 + - - +
554Z GLY 3.5 0.2 + - - -
555Z LYS* 3.2 27.8 + - - +
566Z ILE* 3.9 9.4 - - - +
567Z GLY* 2.9 38.8 + - - -
----------------------------------------------------------
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