Contacts of the helix formed by residues 537 - 562 (chain B) in PDB entry 3TVX
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 537 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B TRP* 4.8 11.0 - - + +
315B GLY* 4.6 15.7 - - - +
535B THR 4.5 2.0 - - - +
536B LYS* 1.4 89.4 - - + +
538B LEU* 1.3 55.9 + - - +
539B GLU* 3.0 20.9 - - - +
540B LEU* 2.7 47.2 + - + +
541B TYR 3.1 5.0 + - - -
610B THR* 4.5 11.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
536B LYS 3.1 5.7 + - - -
537B PRO* 1.3 70.2 - - - +
539B GLU* 1.3 73.3 + - - +
541B TYR* 3.7 13.2 - - + -
542B ARG* 3.0 47.7 + - + +
610B THR* 5.2 0.8 - - - +
614B ASN* 3.8 26.6 + - + +
617B TRP* 3.5 62.6 - - + +
618B TYR* 4.5 2.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
317B ASN* 6.2 0.2 - - - +
537B PRO* 2.9 19.8 + - - +
538B LEU* 1.3 91.2 + - - +
540B LEU* 1.3 59.3 - - + +
542B ARG* 4.2 5.8 + - - +
543B GLN* 2.7 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B TRP 5.1 0.2 - - - +
315B GLY 4.6 2.7 - - - +
316B LEU 3.6 22.4 - - - +
317B ASN* 3.5 37.9 - - - +
318B ILE* 5.5 1.1 - - + +
319B PHE* 3.7 20.4 - - + -
536B LYS* 4.1 27.1 - - + -
537B PRO* 2.7 32.6 + - + +
539B GLU* 1.3 75.0 - - + +
541B TYR* 1.3 64.7 + - - +
542B ARG 3.2 2.0 - - - -
543B GLN* 2.9 21.9 + - - +
544B TRP* 3.0 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B ASN* 3.5 23.3 + - + +
534B PRO* 3.5 34.7 - - + +
536B LYS* 4.0 5.6 - - - +
537B PRO 3.1 8.4 + - - +
538B LEU* 3.7 10.8 - - + +
540B LEU* 1.3 79.0 - - - +
542B ARG* 1.3 53.9 + - - +
544B TRP* 3.4 5.9 + - - +
545B THR* 2.7 50.3 + - - -
581B GLN* 2.6 32.9 + - - +
585B ILE* 3.3 19.4 - - + +
614B ASN* 3.6 31.9 - - + -
618B TYR* 3.5 26.0 - + - -
902B PNX 4.4 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B LEU* 3.0 38.7 + - + +
539B GLU* 4.5 4.9 - - - +
541B TYR* 1.3 74.4 - - - +
543B GLN* 1.3 60.0 + - + +
545B THR* 3.7 0.9 - - - -
546B ASP* 3.0 37.7 + - - +
617B TRP* 3.5 38.4 - - + -
618B TYR* 3.6 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ASN* 5.5 1.2 - - - +
319B PHE* 3.6 48.7 - - + +
539B GLU* 2.7 29.4 + - - +
540B LEU* 2.9 10.8 + - - +
542B ARG* 1.3 76.4 - - + +
544B TRP* 1.3 64.7 + - - +
546B ASP* 3.4 8.2 + - - +
547B ARG* 3.2 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ILE* 3.6 18.8 - - + -
319B PHE* 3.4 35.1 - + - -
371B TYR* 3.7 21.0 - + + -
375B LEU* 3.8 13.2 - - + -
376B HIS* 4.3 18.6 - - + -
379B ASP* 3.4 40.1 + - + -
533B ASN* 3.3 46.9 - - + +
536B LYS* 4.8 5.2 - - + +
540B LEU* 3.0 35.8 + - + +
541B TYR* 3.6 7.6 - - - +
543B GLN* 1.3 75.8 - - - +
545B THR* 1.3 56.9 + - - +
547B ARG* 3.3 15.6 + - - +
548B ILE* 2.9 29.3 + - - +
902B PNX 4.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B TYR* 2.7 43.5 + - - -
542B ARG 3.7 4.3 - - - -
543B GLN 3.3 0.2 - - - -
544B TRP* 1.3 77.0 - - - +
546B ASP* 1.3 63.0 + - - +
548B ILE* 3.2 8.2 - - - +
549B MET* 3.2 23.6 + - + +
577B VAL* 3.7 26.9 - - + -
581B GLN* 3.6 24.2 - - + +
618B TYR* 3.4 19.2 + - - +
902B PNX 4.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B ARG* 3.0 24.8 + - - +
543B GLN* 3.8 8.7 - - - +
544B TRP 3.3 0.2 - - - -
545B THR* 1.3 77.9 - - - +
547B ARG* 1.3 59.2 + - + +
549B MET* 3.7 4.8 + - - +
550B ALA* 3.1 27.7 + - - +
577B VAL* 5.5 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B PHE* 3.8 16.9 - - - -
370B ALA* 3.4 42.4 + - + +
371B TYR* 4.0 9.0 - - + +
373B ASN* 4.1 11.5 + - - +
375B LEU* 3.7 31.5 - - - +
543B GLN* 3.2 19.0 + - - +
544B TRP* 3.5 26.6 - - - +
545B THR 3.2 0.2 - - - -
546B ASP* 1.3 77.6 - - + +
548B ILE* 1.3 64.9 + - - +
550B ALA* 3.3 4.7 + - - -
551B GLU* 3.0 20.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
371B TYR* 3.6 32.7 - - + -
372B HIS* 4.3 9.4 - - + -
544B TRP 2.9 15.5 + - - +
545B THR* 3.2 13.9 - - - +
547B ARG* 1.3 75.2 - - - +
549B MET* 1.3 68.5 + - - +
551B GLU* 3.2 4.4 + - + +
552B PHE* 2.7 68.7 + - + +
581B GLN* 4.2 2.7 - - - +
902B PNX 3.5 48.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B THR* 3.2 17.6 + - + +
546B ASP* 4.1 4.3 - - - +
548B ILE* 1.3 83.9 - - + +
550B ALA* 1.3 57.2 + - - +
552B PHE* 4.2 13.2 - - - -
553B PHE* 2.7 80.6 + - + -
569B MET* 4.0 13.5 - - + +
575B ALA* 4.6 8.1 - - + -
577B VAL* 3.7 43.1 - - + +
580B SER* 4.8 12.3 - - - +
581B GLN* 5.0 6.5 - - - -
902B PNX 5.5 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ALA* 3.7 14.8 - - + -
546B ASP 3.1 19.2 + - - +
547B ARG* 3.5 7.6 - - - +
549B MET* 1.3 76.4 - - - +
551B GLU* 1.3 60.0 + - - +
553B PHE* 4.1 6.5 - - - +
554B GLN* 3.2 30.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
369B VAL* 3.1 13.1 - - + +
370B ALA* 3.9 8.9 - - + +
371B TYR* 2.9 29.3 + - + +
372B HIS* 2.8 37.6 + - - -
416B HIS* 3.8 2.1 - - - -
418B GLY* 3.2 35.0 - - - +
547B ARG 3.0 12.7 + - - +
548B ILE* 3.6 8.7 - - + +
550B ALA* 1.3 74.3 - - - +
552B PHE* 1.3 71.5 + - + +
554B GLN* 3.3 7.5 + - - +
555B GLN* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B HIS* 5.7 4.3 - + - -
420B SER* 6.4 1.8 - - - -
548B ILE* 2.7 51.9 + - + +
549B MET* 3.8 17.5 - - - +
551B GLU* 1.3 77.9 - - + +
553B PHE* 1.3 62.7 + - - +
555B GLN* 3.1 10.2 + - - -
556B GLY 3.0 17.5 + - - -
568B PRO 4.7 1.8 - - - -
569B MET* 3.7 54.1 - - + +
570B CYS* 3.3 25.8 - - - +
902B PNX 3.9 26.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B MET* 2.7 67.1 + - + +
550B ALA* 4.1 6.7 - - - +
552B PHE* 1.3 72.3 - - - +
554B GLN* 1.3 55.7 + - - +
556B GLY* 3.3 1.4 + - - -
557B ASP* 2.9 35.5 + - - +
569B MET 3.6 12.1 - - - -
570B CYS 3.4 17.5 - - - +
572B LYS* 3.9 41.7 - - + +
575B ALA* 4.2 12.8 - - + -
577B VAL* 4.3 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ASP 5.3 8.9 + - - +
370B ALA* 5.4 6.5 - - - +
418B GLY 6.1 0.2 - - - +
550B ALA* 3.2 21.2 + - - +
551B GLU* 3.6 7.4 - - - +
552B PHE 3.2 0.6 - - - -
553B PHE* 1.3 76.9 - - - +
555B GLN* 1.3 63.7 + - - +
557B ASP* 3.5 10.8 + - + +
558B ARG* 3.2 37.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
418B GLY 4.2 4.4 + - - +
419B VAL* 3.3 20.8 - - + -
420B SER* 2.8 51.1 + - - +
423B PHE* 3.5 18.1 - - + +
551B GLU 3.1 10.9 + - - +
552B PHE* 3.1 16.5 + - - +
554B GLN* 1.3 75.3 - - - +
556B GLY* 1.3 58.1 + - - +
558B ARG* 3.1 7.4 + - - +
559B GLU* 2.8 54.6 + - - +
567B SER* 3.6 5.1 + - - -
570B CYS* 4.3 11.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B PHE 3.0 10.3 + - - -
553B PHE 3.3 0.6 + - - -
555B GLN* 1.3 77.2 - - - +
557B ASP* 1.3 57.2 + - - +
559B GLU* 3.2 16.7 + - - +
560B ARG* 2.8 34.5 + - - +
566B ILE* 4.3 7.6 - - - +
570B CYS* 3.4 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B PHE* 2.9 23.9 + - - +
554B GLN* 3.8 11.7 - - + +
555B GLN 3.3 0.2 - - - -
556B GLY* 1.3 74.8 - - - +
558B ARG* 1.3 59.3 + - + +
560B ARG* 2.8 30.7 + - - +
561B GLU* 3.0 36.7 + - + +
572B LYS* 3.4 32.1 + - - +
904B SO4 4.8 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ARG* 3.8 11.7 - - - +
363A ASP* 3.0 50.6 + - - +
364A HIS* 6.0 1.4 - - - -
417B PRO* 3.9 16.2 + - - +
418B GLY 4.9 1.4 + - - -
419B VAL* 3.4 31.9 - - - +
423B PHE* 4.3 19.4 - - + -
554B GLN* 3.2 22.6 + - + +
555B GLN 3.1 7.9 + - - +
557B ASP* 1.3 74.6 - - + +
559B GLU* 1.3 65.8 + - - +
561B GLU* 3.5 10.6 + - - +
562B ARG* 3.1 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B PHE* 3.5 21.1 - - + +
426B ASN* 5.9 1.0 + - - -
555B GLN* 2.8 31.4 + - - +
556B GLY* 3.4 22.2 + - - +
558B ARG* 1.3 77.6 - - - +
560B ARG* 1.3 60.1 + - - +
562B ARG 3.3 1.4 + - - -
563B GLY 3.2 3.6 + - - -
564B MET* 2.8 50.0 + - + +
565B GLU 3.9 12.4 - - - +
566B ILE* 3.6 6.0 - - + +
567B SER* 2.6 47.8 + - - -
570B CYS* 4.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A MET* 5.3 1.4 - - - +
556B GLY 2.8 19.4 + - - +
557B ASP* 2.8 34.3 + - - +
559B GLU* 1.3 74.5 - - - +
561B GLU* 1.3 65.9 + - - +
563B GLY* 3.1 13.7 + - - -
564B MET 4.9 1.8 - - - -
566B ILE* 3.8 22.9 - - + +
570B CYS 4.6 0.4 + - - -
571B ASP* 3.1 31.3 + - - +
572B LYS* 4.0 18.4 - - - +
573B HIS* 4.1 6.4 - - - -
904B SO4 3.0 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A MET* 3.2 26.2 - - - +
297A LYS* 6.2 4.5 - - + -
328A ARG* 2.5 53.4 + - - +
355A VAL* 5.4 0.5 - - - +
359A LEU* 3.6 22.3 - - + +
363A ASP* 5.2 0.5 - - - +
557B ASP* 3.0 19.0 + - - +
558B ARG* 3.5 19.2 - - - +
560B ARG* 1.3 76.8 - - - +
562B ARG* 1.3 57.4 + - + +
563B GLY 3.3 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 562 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A MET* 3.7 18.3 - - + +
356A THR* 4.6 18.6 + - + +
359A LEU* 4.1 16.6 - - + +
360A THR* 3.0 46.7 + - - +
363A ASP* 2.6 32.5 + - - +
364A HIS* 5.6 1.8 - - - -
455A GLU* 4.4 3.2 + - - -
458A CYS* 5.5 1.0 - - - -
423B PHE* 3.9 17.4 - - - -
427B THR* 3.9 17.4 - - - +
558B ARG* 3.1 25.7 + - - +
559B GLU 3.3 0.4 + - - +
560B ARG 3.2 0.2 - - - -
561B GLU* 1.3 77.0 + - - +
563B GLY* 1.3 65.6 + - - +
564B MET* 3.2 32.5 + - + +
----------------------------------------------------------
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