Contacts of the helix formed by residues 539 - 553 (chain B) in PDB entry 6V3O
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 539 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B GLU* 3.2 34.3 - - + +
537B ALA* 5.7 0.5 - - - +
538B THR* 1.3 87.0 - - - +
540B PRO* 1.3 76.5 - - + +
541B SER* 3.0 3.1 - - - +
542B ASP* 2.9 23.1 + - - +
543B VAL* 4.1 3.1 + - - +
565B PHE* 5.0 1.5 - - - -
577B SER* 3.9 4.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
483B GLU* 3.8 7.2 - - + +
487B GLN* 3.9 20.9 - - + +
539B ALA* 1.3 87.1 - - + +
541B SER* 1.3 60.8 + - - +
542B ASP 3.2 0.2 - - - -
543B VAL* 3.2 7.2 + - + +
544B LEU* 3.2 28.5 + - + +
577B SER* 3.3 37.7 - - - +
580B ARG* 4.3 10.8 - - + -
581B LEU* 3.7 30.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
478B TYR* 3.9 17.7 + - - -
483B GLU* 2.4 39.0 + - - -
486B ARG* 4.1 20.0 + - - -
487B GLN* 4.6 4.9 - - - +
490B LEU* 4.2 9.3 - - - +
539B ALA* 3.7 4.9 - - - +
540B PRO* 1.3 75.5 - - - +
542B ASP* 1.3 63.4 + - - +
544B LEU* 4.1 1.7 - - - +
545B ALA* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B SER* 3.6 30.0 + - - +
460B GLU* 5.2 2.3 - - - +
462B HIS* 5.0 1.9 + - - +
463B THR* 4.8 8.0 + - - -
486B ARG* 5.0 6.1 + - - -
534B ILE* 3.1 25.0 - - + +
537B ALA* 4.6 3.8 - - + -
538B THR* 2.8 37.9 + - - +
539B ALA* 2.9 18.4 + - - +
541B SER* 1.3 82.4 + - - +
543B VAL* 1.3 62.5 + - + +
545B ALA* 3.8 12.5 + - - +
546B VAL* 3.8 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ILE* 3.7 15.0 - - + -
537B ALA* 5.9 0.2 - - + -
539B ALA 5.0 4.3 - - - +
540B PRO* 3.2 8.1 + - + +
541B SER 3.2 0.4 - - - -
542B ASP* 1.3 76.1 - - + +
544B LEU* 1.3 65.5 + - - +
545B ALA 3.1 1.6 - - - -
546B VAL* 3.1 13.9 + - - +
547B GLU* 3.2 12.3 + - + +
561B VAL* 3.5 20.8 - - + +
563B PRO* 4.2 28.0 - - + -
581B LEU* 4.2 19.3 - - + -
587B TYR* 3.8 36.6 - - + +
595B GLN* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B GLN* 4.8 17.9 - - + -
490B LEU* 4.4 13.3 - - + +
491B LEU* 3.8 33.2 - - + -
494B LEU* 4.1 23.0 - - + +
540B PRO* 3.2 19.3 + - + +
541B SER* 4.1 2.7 - - - +
543B VAL* 1.3 78.6 - - - +
545B ALA* 1.3 62.8 + - - +
547B GLU* 3.4 6.3 + - + +
548B LEU* 3.1 23.4 + - - +
581B LEU* 4.0 12.6 - - + -
584B VAL* 5.5 4.5 - - + -
586B TRP* 4.7 4.9 - - + -
587B TYR* 4.0 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B HIS* 4.8 12.6 - - + -
463B THR* 5.9 0.9 - - - +
466B ILE* 3.6 26.1 - - + +
478B TYR* 4.1 9.9 - - + +
490B LEU* 4.3 7.1 - - - +
541B SER 2.8 19.3 + - - +
542B ASP* 3.8 8.5 - - - +
543B VAL 3.1 0.2 - - - -
544B LEU* 1.3 78.4 - - - +
546B VAL* 1.3 56.3 + - - +
548B LEU* 3.4 4.0 + - - +
549B LEU* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B HIS* 3.4 48.7 - - + +
518B PHE* 3.8 22.0 - - + -
532B TYR* 3.9 21.5 - - + -
534B ILE* 4.3 7.4 - - + -
542B ASP 3.8 9.1 + - - +
543B VAL 3.1 7.9 + - - +
545B ALA* 1.3 74.1 - - - +
547B GLU* 1.3 58.4 + - - +
548B LEU 3.2 0.4 - - - -
549B LEU* 4.1 4.7 - - - +
550B GLN* 2.7 37.3 + - + +
561B VAL* 4.4 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B LEU* 4.4 4.4 - - + +
543B VAL 3.2 15.5 + - - +
544B LEU* 3.5 14.4 - - - +
546B VAL* 1.3 78.8 - - - +
548B LEU* 1.3 62.1 + - - +
550B GLN* 3.4 17.7 + - - +
551B ARG* 3.2 22.7 + - - +
559B LEU 4.4 2.5 - - - +
560B PRO* 5.9 0.3 - - - +
561B VAL* 3.5 19.3 + - + +
586B TRP* 4.1 21.3 - - + -
587B TYR* 3.6 25.4 + - + -
590B ARG* 2.9 47.2 + - - +
591B ILE* 4.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B ILE* 4.9 7.9 - - + -
489B TRP* 4.1 15.9 - - + -
490B LEU* 4.0 24.7 - - + -
493B GLU* 4.0 21.5 - - + -
494B LEU* 3.6 27.1 - - + +
500B LEU* 4.2 15.5 - - + -
544B LEU 3.1 13.5 + - - +
545B ALA 3.5 7.6 - - - +
546B VAL 3.2 0.2 - - - -
547B GLU* 1.3 77.2 - - - +
549B LEU* 1.3 60.3 + - + +
551B ARG* 3.2 15.2 + - - +
552B GLU* 2.8 51.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B HIS* 4.1 45.5 - - + +
465B VAL* 3.6 29.2 - - + -
466B ILE* 4.2 14.6 - - + -
469B ILE* 4.4 10.3 - - + -
501B LEU* 6.1 1.6 - - + -
514B VAL* 4.9 0.2 - - + -
515B ILE* 6.1 0.7 - - + -
518B PHE* 3.9 22.1 - - + -
545B ALA 3.0 20.7 + - - +
546B VAL* 3.2 5.6 + - - +
548B LEU* 1.3 78.9 - - + +
550B GLN* 1.3 62.7 + - - +
552B GLU* 4.4 7.0 - - + +
553B CYS* 3.0 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B PHE* 3.8 24.6 - - + -
521B LEU* 4.9 1.5 - - + +
532B TYR* 5.3 4.3 - - - -
546B VAL* 2.7 22.6 + - + +
547B GLU* 3.4 21.9 + - - +
549B LEU* 1.3 74.6 - - - +
551B ARG* 1.3 62.2 + - - +
553B CYS 3.5 0.2 + - - -
554B GLY 3.4 3.6 + - - -
555B VAL* 3.1 40.4 + - + +
558B PRO* 3.5 16.4 - - + +
559B LEU* 2.6 60.7 + - - +
561B VAL* 4.0 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B GLU* 3.0 25.7 + - - +
494B LEU* 2.9 40.8 + - + +
496B GLY 3.8 8.9 + - - -
497B LYS* 5.6 0.8 - - - +
498B ARG 4.9 7.5 + - - +
547B GLU 3.2 10.7 + - - +
548B LEU* 3.7 12.3 - - - +
550B GLN* 1.3 78.2 - - - +
552B GLU* 1.3 80.1 + - - +
554B GLY* 3.0 19.8 + - - -
555B VAL 4.8 8.1 - - - +
558B PRO* 6.0 0.2 - - - +
586B TRP* 4.4 8.5 - - - +
590B ARG* 4.8 15.9 - - - +
503D PRO* 5.7 12.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
498B ARG 4.8 0.4 - - - +
499B PRO* 3.4 14.4 - - - +
500B LEU* 2.8 40.1 + - + -
501B LEU* 3.7 30.6 + - + +
548B LEU* 2.8 41.2 + - + +
549B LEU* 4.1 9.2 - - + +
550B GLN 3.3 0.2 - - - -
551B ARG* 1.3 104.8 + - - +
553B CYS* 1.3 59.6 + - - +
554B GLY 3.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B LEU* 3.9 19.3 - - - -
515B ILE* 4.4 16.2 - - - -
518B PHE* 3.7 31.0 - - + +
519B HIS* 3.3 34.8 - - + -
522B ALA* 4.1 7.3 - - - +
549B LEU* 3.0 29.7 + - - +
550B GLN 3.8 0.9 - - - +
552B GLU* 1.3 79.0 - - - +
554B GLY* 1.3 61.5 + - - +
555B VAL* 3.6 2.2 - - - -
----------------------------------------------------------
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