Contacts of the helix formed by residues 543 - 553 (chain B) in PDB entry 6A5T
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 PRO 543 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLU* 5.1 2.7 - - - +
541B GLY 4.3 2.7 - - - +
542B SER* 1.3 100.9 + - - +
544B SER* 1.3 60.8 + - - +
545B GLU* 4.4 7.9 - - + +
546B PRO* 3.2 27.6 - - + +
547B ILE* 4.7 6.4 - - - +
621B THR* 4.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLU* 3.3 24.9 + - - -
542B SER 3.6 1.2 + - - -
543B PRO* 1.3 73.1 - - - +
545B GLU* 1.3 67.0 + - - +
546B PRO* 3.4 0.7 - - - -
547B ILE* 3.2 5.5 + - - +
548B ILE* 2.9 28.8 + - - +
575B VAL* 4.4 10.3 - - - -
576B ASN* 4.4 9.0 - - - -
621B THR* 3.5 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B PRO* 3.3 4.7 - - + +
544B SER* 1.3 81.0 + - - +
546B PRO* 1.3 69.8 - - + +
548B ILE* 3.2 10.0 + - + +
549B ASN* 2.8 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B SER* 5.2 3.4 - - - +
543B PRO* 3.2 30.7 - - + +
545B GLU* 1.3 94.0 - - + +
547B ILE* 1.3 57.4 + - + +
549B ASN* 3.1 12.6 + - + +
550B PHE* 2.9 48.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B SER* 5.9 1.1 - - - +
543B PRO 4.7 6.3 - - - +
544B SER* 3.2 8.9 + - - +
546B PRO* 1.3 77.5 - - + +
548B ILE* 1.3 65.4 + - - +
550B PHE* 3.1 7.5 + - + +
551B LEU* 2.9 38.3 + - + +
575B VAL* 5.0 7.4 - - + -
593B MET* 6.0 3.1 - - - -
602B ILE* 3.5 40.4 - - + -
606B VAL* 4.3 13.7 - - + -
608B ILE* 6.3 2.0 - - + -
619B ILE* 3.8 25.4 - - + -
621B THR* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B SER* 2.9 22.7 + - - +
545B GLU* 3.2 10.3 + - + +
547B ILE* 1.3 75.4 - - - +
549B ASN* 1.3 66.5 + - - +
551B LEU* 3.3 7.3 + - + +
552B GLU* 3.0 44.6 + - + +
556B MET* 6.2 3.1 - - + -
575B VAL* 3.6 38.4 - - + -
580B THR* 5.1 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B GLU* 2.8 46.8 + - - +
546B PRO* 3.4 11.1 - - + +
548B ILE* 1.3 80.7 - - - +
550B PHE* 1.3 58.3 + - + +
552B GLU* 3.7 5.3 - - - +
553B GLU* 2.8 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B PRO* 2.9 45.1 + - + -
547B ILE* 3.7 8.3 - - + +
549B ASN* 1.3 73.6 - - + +
551B LEU* 1.3 67.6 + - - +
553B GLU* 3.0 26.3 + - - +
554B TRP* 2.9 27.7 - - - -
593B MET* 4.1 20.2 - - + -
596B LEU* 4.7 20.6 - - + -
601B ALA* 4.9 17.9 - - + -
602B ILE* 4.2 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B ILE* 2.9 28.7 + - + +
548B ILE* 3.6 6.7 - - + +
550B PHE* 1.3 74.4 - - - +
552B GLU* 1.3 56.7 + - + +
554B TRP* 2.6 34.2 + - - +
555B GLY 3.4 3.6 + - - -
556B MET* 4.0 19.7 + - + +
573B ILE* 4.5 14.6 - - + -
575B VAL* 4.1 19.7 - - + -
589B LEU* 4.3 22.7 - - + +
593B MET* 4.5 10.5 - - + -
617B PHE* 4.6 9.4 - - + -
619B ILE* 3.7 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B ILE* 3.0 34.4 + - + +
549B ASN* 4.3 5.1 - - - +
551B LEU* 1.3 77.3 - - + +
553B GLU* 1.3 59.4 + - - +
554B TRP 3.1 0.8 + - - -
555B GLY* 3.5 11.8 + - - +
556B MET* 4.1 36.9 - - + +
558B PRO* 5.2 12.6 - - + +
580B THR* 5.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B ASN* 2.8 17.9 + - - +
550B PHE* 3.1 35.5 - - - +
551B LEU 3.0 0.4 + - - -
552B GLU* 1.3 77.9 - - - +
554B TRP* 1.3 78.0 + - + +
555B GLY 3.5 0.4 - - - -
----------------------------------------------------------
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