Contacts of the helix formed by residues 537 - 551 (chain B) in PDB entry 5KJH
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 GLY 537 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B LEU* 2.9 36.4 + - - +
533B GLU* 3.4 27.2 - - - +
535B ILE 4.2 1.0 - - - +
536B GLY* 1.3 79.3 - - - +
538B LEU* 1.3 63.9 + - - +
539B MET 3.6 0.2 - - - -
540B PRO* 3.6 4.9 - - - +
541B SER* 3.7 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B MET* 5.9 0.4 - - - -
496B VAL* 4.0 20.4 - - + -
497B ILE* 3.9 38.3 - - + +
500B LEU* 4.2 21.1 - - + -
504B THR* 4.4 19.5 - - + +
532B LEU* 4.5 14.3 - - + +
533B GLU* 4.5 2.2 + - - -
537B GLY* 1.3 69.4 - - - +
539B MET* 1.3 57.4 + - - +
541B SER* 3.4 5.2 + - - -
542B LEU* 2.8 65.6 + - + +
604B THR* 4.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B MET* 3.6 28.7 - - + -
497B ILE* 3.7 38.6 - - + -
537B GLY 3.6 0.2 - - - -
538B LEU* 1.3 84.4 - - - +
540B PRO* 1.4 66.0 - - + +
542B LEU* 4.3 5.8 - - + -
543B ARG* 2.8 69.1 + - + +
546B TRP* 4.0 23.3 - - + -
640B PRO* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B ILE 4.3 2.2 - - - +
536B GLY* 3.3 35.7 - - - +
537B GLY 3.6 7.4 - - - +
539B MET* 1.4 93.0 - - + +
541B SER* 1.3 57.9 + - - +
543B ARG* 3.9 16.8 - - - +
544B ARG* 2.9 40.5 + - - +
686B HIS* 5.3 6.1 - - + +
714B LEU* 3.6 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B LEU* 3.3 31.2 - - - +
535B ILE* 4.1 4.0 + - - +
537B GLY 3.7 2.9 + - - -
538B LEU 3.4 6.3 + - - -
539B MET 3.2 0.4 - - - -
540B PRO* 1.3 74.6 - - - +
542B LEU* 1.4 62.5 + - - +
544B ARG* 3.4 6.3 + - - +
545B LYS* 3.2 22.2 + - - +
714B LEU* 3.7 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B MET* 4.7 6.7 - - - -
538B LEU* 2.8 54.9 + - + +
539B MET* 4.0 9.6 - - + +
541B SER* 1.4 69.3 - - - +
543B ARG* 1.4 65.1 + - - +
545B LYS* 3.2 23.9 + - + +
546B TRP* 3.1 63.6 + - + +
603B ALA* 4.7 3.6 - - + +
604B THR* 4.0 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B MET* 2.8 54.8 + - + +
540B PRO* 3.7 30.5 - - - +
542B LEU* 1.4 71.1 - - - +
544B ARG* 1.4 64.1 + - + +
546B TRP* 3.3 21.9 + - + +
547B ALA* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B PRO* 2.9 35.0 + - - +
541B SER* 3.4 8.9 + - - +
542B LEU 3.3 0.6 - - - -
543B ARG* 1.4 76.2 - - + +
545B LYS* 1.3 59.5 + - - +
547B ALA* 3.5 7.7 + - - +
548B ALA* 3.0 29.1 + - - +
686B HIS 5.1 0.6 - - - -
687B HIS 3.0 29.1 + - - -
688B ASP* 3.4 26.3 + - - +
714B LEU* 3.4 52.0 + - - +
715B CYS* 5.5 0.4 - - - +
716B THR* 6.3 0.4 - - - -
719B GLU* 5.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B SER 3.2 13.0 + - - +
542B LEU* 3.2 25.3 + - + +
544B ARG* 1.3 73.9 - - - +
546B TRP* 1.4 66.7 + - + +
548B ALA* 3.2 8.4 + - - +
549B GLN* 3.0 55.6 + - + +
604B THR 3.1 27.6 + - - +
605B ILE* 3.8 3.6 + - - +
606B GLY 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B MET* 3.9 18.2 - - - -
539B MET* 4.0 18.2 - - + -
542B LEU* 3.1 40.4 + - + +
543B ARG* 3.3 26.4 + - + +
545B LYS* 1.4 75.8 - - + +
547B ALA* 1.4 60.7 + - - +
549B GLN* 3.1 23.3 + - - +
550B ILE* 3.1 28.1 + - - +
603B ALA 3.0 28.4 + - - -
606B GLY* 3.5 12.3 - - - -
607B TYR* 3.8 20.8 - + + -
639B LEU* 4.0 13.8 - - + +
640B PRO* 3.6 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B ARG 3.2 10.0 + - - +
544B ARG* 3.6 11.2 - - - +
546B TRP* 1.4 77.6 - - - +
548B ALA* 1.3 60.1 + - - +
549B GLN 3.1 1.6 + - - -
550B ILE* 3.3 12.7 + - + +
551B GLU* 3.2 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ARG 3.0 17.7 + - - +
545B LYS* 3.2 9.4 + - - +
547B ALA* 1.3 74.6 - - - +
549B GLN* 1.4 58.5 + - + +
551B GLU* 4.3 9.2 - - - +
552B GLN* 3.3 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B LYS* 3.0 30.5 + - + +
546B TRP* 3.3 23.8 - - - +
547B ALA 3.1 0.6 - - - -
548B ALA* 1.4 75.2 - - - +
550B ILE* 1.4 64.7 + - - +
551B GLU 3.2 1.6 - - - -
552B GLN* 3.1 23.3 + - - +
605B ILE 3.0 24.0 + - - -
606B GLY* 3.6 1.4 - - - -
607B TYR* 2.8 42.6 + - + +
608B SER* 3.4 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B TRP 3.1 14.6 + - - +
547B ALA* 3.4 19.7 - - + +
549B GLN* 1.4 74.4 - - - +
551B GLU* 1.4 62.8 + - + +
552B GLN 3.3 7.8 + - - +
607B TYR* 3.7 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B ALA* 3.2 25.2 + - - +
548B ALA* 4.6 7.0 - - - +
549B GLN 3.2 1.4 - - - -
550B ILE* 1.4 84.6 - - + +
552B GLN* 1.3 64.1 + - - +
647B ILE* 5.9 3.2 - - - +
----------------------------------------------------------
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