Contacts of the helix formed by residues 537 - 561 (chain B) in PDB entry 3VF1
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 ASN 537 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B ASP* 3.5 28.0 - - - +
502B VAL* 3.9 15.8 - - - +
535B PHE* 3.5 1.3 - - - +
536B GLU* 1.3 86.5 + - - +
538B ARG* 1.3 62.6 + - - +
539B GLU* 3.1 18.7 + - - +
540B GLU* 2.9 58.3 + - - +
541B LEU* 3.5 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B ILE* 4.6 11.2 - - + +
493B GLN* 3.6 39.4 + - + +
496B TYR* 2.9 37.6 + - + -
497B ASN* 3.4 19.3 + - - +
498B ASP* 3.8 11.3 - - - +
499B ASP* 3.3 15.9 + - - +
502B VAL* 3.5 22.2 - - + -
537B ASN* 1.3 73.7 - - - +
539B GLU* 1.3 73.3 + - - +
541B LEU* 3.2 5.3 + - - +
542B VAL* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B HIS* 5.6 0.7 + - - -
489B GLN* 5.7 7.3 + - - +
493B GLN* 5.2 5.4 + - - -
499B ASP* 3.9 6.8 - - - +
537B ASN* 3.1 17.7 + - - +
538B ARG* 1.3 96.1 + - - +
540B GLU* 1.3 65.7 + - - +
542B VAL* 3.3 7.7 + - - +
543B HIS* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B PRO* 4.7 9.8 - - + +
534B SER 3.6 12.3 - - - +
535B PHE* 3.9 13.5 - - + -
536B GLU* 3.5 24.2 + - - +
537B ASN* 2.9 39.1 + - - +
538B ARG 3.4 0.2 - - - -
539B GLU* 1.3 75.7 - - - +
541B LEU* 1.3 61.8 + - - +
543B HIS* 3.8 4.6 - - - +
544B PHE* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B VAL* 5.0 0.7 - - + -
492B ILE* 3.9 27.6 - - + -
496B TYR* 4.0 25.1 - - + +
502B VAL* 4.3 15.7 - - + -
508B ILE* 4.1 14.4 - - + -
535B PHE* 3.6 39.4 - - + -
537B ASN 3.5 10.1 + - - +
538B ARG 3.2 8.7 + - - +
539B GLU 3.2 0.4 - - - -
540B GLU* 1.3 80.1 - - - +
542B VAL* 1.3 62.4 + - - +
544B PHE* 3.5 1.2 + - - +
545B LEU* 3.2 49.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B HIS* 3.6 40.4 - - + +
488B VAL* 3.7 19.3 - - + +
489B GLN* 3.9 28.7 - - + +
492B ILE* 4.0 20.2 - - + -
493B GLN* 6.0 1.1 - - + -
538B ARG* 2.9 24.3 + - + +
539B GLU* 3.8 7.4 - - - +
541B LEU* 1.3 76.8 - - - +
543B HIS* 1.3 57.4 - - - +
545B LEU* 3.3 1.6 + - - -
546B THR* 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B PHE 5.4 3.2 + - - -
455B ASP* 3.6 38.4 + - + +
481B TRP* 4.1 20.8 - + - -
485B HIS* 4.8 10.6 + - - +
539B GLU 3.0 17.0 + - - +
540B GLU* 3.8 6.3 - - - +
542B VAL* 1.3 78.0 - - - +
544B PHE* 1.3 68.1 + + + +
546B THR* 3.0 8.6 + - - -
547B VAL* 3.0 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B THR* 4.7 3.6 - - + -
451B PHE* 4.1 35.7 - + + -
511B TRP* 3.7 35.7 - + - -
512B ILE* 4.0 5.2 - - + -
515B LEU* 3.9 20.6 - - + -
520B TYR* 5.0 2.9 - + - -
531B VAL* 4.0 22.7 - - + -
532B PRO* 4.2 17.5 - - + -
535B PHE* 4.0 13.7 - + + -
540B GLU 3.2 14.0 + - - +
541B LEU 4.0 3.4 - - - +
543B HIS* 1.3 85.9 - + + +
545B LEU* 1.3 61.8 + - + +
547B VAL* 3.4 7.9 + - + +
548B VAL* 3.3 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B VAL* 4.2 11.9 - - + -
401B LEU* 4.1 16.6 - - + -
402B LEU* 3.9 24.0 - - + +
488B VAL* 3.9 9.9 - - + -
492B ILE* 3.8 26.2 - - + -
511B TRP* 3.7 33.4 - - + -
541B LEU* 3.2 35.3 + - + +
542B VAL 3.8 2.9 - - - +
544B PHE* 1.3 75.6 - - + +
546B THR* 1.3 66.5 + - - +
548B VAL* 3.2 5.0 + - + +
549B VAL* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B TRP* 3.9 34.5 - - + +
484B ILE* 4.3 6.6 - - + +
485B HIS* 3.4 48.4 - - + +
488B VAL* 4.0 11.0 - - - +
542B VAL* 2.8 22.4 + - - +
543B HIS* 3.0 9.6 + - - -
545B LEU* 1.3 77.8 - - - +
547B VAL* 1.3 61.7 + - - +
549B VAL* 4.0 0.5 - - - +
550B PHE* 2.9 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B MET* 4.8 3.6 - - + -
451B PHE* 4.1 23.1 - - + +
454B TYR* 3.9 40.2 - - + +
481B TRP* 3.7 25.1 - - + -
543B HIS* 3.0 34.0 + - + +
544B PHE* 3.4 11.4 - - + +
546B THR* 1.3 76.7 - - - +
548B VAL* 1.3 58.7 + - + +
550B PHE* 3.9 0.7 - - - +
551B THR* 2.9 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B MET* 4.0 12.8 - - + -
384B THR* 4.0 38.6 - - + +
402B LEU* 4.2 19.1 - - + -
405B HIS* 5.7 1.1 - - + -
406B THR* 4.6 5.6 - - + -
451B PHE* 6.0 0.9 - - + -
511B TRP* 5.1 4.0 - - + -
544B PHE* 3.3 29.2 - - + +
545B LEU* 3.2 10.0 + - + +
547B VAL* 1.3 79.5 - - + +
549B VAL* 1.3 64.0 + - - +
551B THR* 3.3 0.9 + - - -
552B CYS* 3.0 43.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LEU* 5.1 5.4 - - + -
402B LEU* 4.1 16.6 - - + -
405B HIS* 3.7 47.4 + - + +
484B ILE* 3.6 31.9 - - + -
487B PHE* 5.8 3.1 - - + -
488B VAL* 4.4 14.1 - - + -
545B LEU 3.0 17.0 + - - +
548B VAL* 1.3 75.9 - - - +
550B PHE* 1.3 54.7 + - - +
552B CYS* 3.7 1.2 + - - +
553B SER* 2.6 36.1 + - - +
623B LEU* 5.1 1.3 - - + -
626B TYR* 5.3 0.4 - - - +
643B PHE* 5.6 2.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
454B TYR 5.8 0.2 - - - -
456B LEU* 3.7 26.0 - - + -
473B TYR* 5.7 0.4 - + - -
477B ALA* 3.5 33.7 - - + -
481B TRP* 3.5 43.7 - + + -
484B ILE* 4.0 12.6 - - + -
546B THR* 2.9 20.9 + - + +
547B VAL 3.9 1.6 - - - +
549B VAL* 1.3 78.0 - - - +
551B THR* 1.3 66.5 + - - +
553B SER* 3.9 3.8 - - - -
554B CYS* 2.9 47.4 + - + -
555B GLN* 3.1 35.9 + - + -
668B LEU* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ARG 3.8 19.3 - - - +
377B CYS* 4.2 11.6 - - - -
381B MET* 3.5 32.8 - - + -
454B TYR* 3.7 20.8 - - + -
481B TRP* 6.0 0.2 - - - -
547B VAL* 2.9 22.8 + - - +
550B PHE* 1.3 79.3 - - - +
552B CYS* 1.3 64.5 + - - +
555B GLN* 3.8 12.3 - - + +
556B HIS* 3.3 24.8 + - - +
677B ILE* 4.2 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B MET* 3.8 26.7 - - - -
384B THR* 5.3 0.4 - - - -
405B HIS* 3.2 32.5 - - + +
406B THR* 4.7 6.5 - - - -
409B ILE* 5.1 3.8 - - - -
548B VAL* 3.0 37.9 + - - +
549B VAL 4.2 2.7 - - - +
551B THR* 1.3 76.6 - - - +
553B SER* 1.3 59.7 + - - +
556B HIS* 4.1 2.5 - - - +
675B ASN 4.0 3.1 - - - +
676B SER 3.1 27.2 - - - +
677B ILE* 3.4 17.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B HIS* 4.6 1.1 - - - -
484B ILE* 4.2 1.6 - - - +
549B VAL 2.6 24.0 + - - -
550B PHE* 3.6 1.9 + - - -
552B CYS* 1.3 79.6 - - - +
554B CYS* 1.3 79.2 + - - +
555B GLN 3.7 0.9 - - - -
556B HIS* 4.2 0.9 + - - +
557B ALA* 3.2 16.9 + - - +
623B LEU* 3.8 23.4 - - - +
673B VAL* 3.2 15.6 - - - +
674B PRO* 3.3 21.6 - - - +
675B ASN 3.6 9.6 - - - -
676B SER 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 3.7 35.4 - - + -
484B ILE* 3.9 14.8 - - - -
550B PHE* 2.9 26.7 + - + +
553B SER* 1.3 85.3 + - - +
555B GLN* 1.3 66.4 + - - +
557B ALA* 3.0 5.2 + - - +
558B ALA* 2.9 19.4 + - - +
623B LEU* 4.0 12.8 - - - -
668B LEU* 3.5 19.5 - - + +
673B VAL* 3.7 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B PRO* 5.6 0.8 - - - +
249B GLU* 3.3 30.3 + - - +
372B THR* 4.9 1.0 + - - +
376B ARG 5.7 0.4 - - - +
377B CYS* 3.8 17.0 - - - -
454B TYR* 6.4 1.3 - - + -
456B LEU* 6.0 0.4 - - - -
473B TYR* 2.8 33.8 + - - -
550B PHE* 3.1 20.8 + - + +
551B THR* 3.8 25.1 - - + +
554B CYS* 1.3 77.8 - - - +
556B HIS* 1.3 63.8 + - - +
558B ALA* 3.1 11.7 + - - +
559B VAL* 3.1 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B HIS* 3.8 10.5 - + - -
377B CYS* 3.9 13.0 - - + -
378B HIS* 3.3 15.6 + + - -
551B THR 3.3 16.3 + - - +
552B CYS 4.1 5.4 + - - +
553B SER 4.2 1.0 + - - +
554B CYS 3.3 0.6 - - - -
555B GLN* 1.3 78.5 - - - +
557B ALA* 1.3 59.2 + - - +
559B VAL* 3.7 1.5 - - - +
560B ASN* 2.8 53.3 + - + +
561B PHE* 4.2 13.8 - + - -
674B PRO* 5.8 0.4 - - - +
676B SER 4.3 5.3 + - - -
677B ILE* 3.7 33.3 - - + +
679B ILE* 3.0 17.7 + - + -
701B FE2 2.2 31.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B SER 3.2 17.9 + - - +
554B CYS 3.0 5.7 + - - +
556B HIS* 1.3 78.1 + - - +
558B ALA* 1.3 63.1 + - - +
561B PHE* 3.2 39.0 + - + +
562B SER 4.0 1.7 + - - -
667B TRP* 4.0 18.2 - - - +
672B HIS 4.9 1.1 - - - +
673B VAL* 3.7 18.6 - - + -
674B PRO* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B GLY 4.1 7.4 - - - +
246B SER* 4.2 0.9 - - - -
248B PRO* 6.3 0.2 - - - -
473B TYR* 4.0 20.9 - - + -
554B CYS 2.9 11.9 + - - +
555B GLN* 3.1 8.7 + - - +
557B ALA* 1.3 76.6 - - - +
559B VAL* 1.3 56.4 + - + +
562B SER* 2.6 28.8 + - - -
665B TYR* 3.8 19.3 + - - +
667B TRP* 4.4 12.1 + - - +
668B LEU* 3.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B SER 3.3 24.5 - - - +
248B PRO* 4.5 8.3 - - + -
368B HIS* 2.8 31.1 + - - +
372B THR* 3.7 31.4 - - + +
373B HIS* 4.1 22.0 - - + -
377B CYS* 4.2 7.2 - - - -
473B TYR* 5.7 0.2 - - + -
555B GLN* 3.1 32.7 + - - +
556B HIS 3.7 4.9 - - - +
558B ALA* 1.3 80.7 - - + +
560B ASN* 1.3 59.5 + - - +
562B SER* 4.0 3.8 - - - -
563B GLN* 3.7 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B HIS* 2.5 14.3 + - - +
556B HIS* 2.8 35.8 + - + +
558B ALA 3.4 0.4 - - - -
559B VAL* 1.3 79.4 - - - +
561B PHE* 1.3 74.6 + - + +
562B SER 3.1 3.6 - - - -
563B GLN* 3.0 38.3 + - - +
613B LEU* 2.8 29.2 + - - +
614B THR* 3.6 2.1 - - - +
679B ILE* 3.7 0.7 - - - +
701B FE2 2.2 32.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B HIS* 4.2 15.0 - + - -
557B ALA* 3.2 27.8 + - + +
560B ASN* 1.3 79.6 - - - +
562B SER* 1.3 57.1 + - - +
563B GLN 3.2 4.2 + - - -
564B MET* 4.6 3.5 + - - +
614B THR* 3.8 33.1 - - - +
615B THR 4.0 0.7 - - - -
616B ILE* 3.4 35.7 - - + -
620B GLU* 6.3 0.7 - - + -
667B TRP* 3.1 28.3 - - + -
672B HIS 5.0 3.8 - - - +
674B PRO* 3.4 36.6 - - + -
679B ILE* 3.6 31.2 - - + -
----------------------------------------------------------
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