Contacts of the helix formed by residues 534 - 551 (chain B) in PDB entry 6FEQ
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 VAL 534 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B VAL* 4.2 14.2 - - + +
446B GLU* 5.5 7.9 - - + +
449B VAL* 4.0 19.1 - - + -
450B VAL* 5.2 10.8 - - + -
532B SER 5.2 0.7 - - - +
533B VAL* 1.3 77.8 - - - +
535B SER* 1.3 61.9 + - - +
536B VAL 3.4 0.7 - - - -
537B ALA* 3.4 5.7 + - - +
538B THR* 2.7 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B VAL* 3.6 3.2 - - - +
534B VAL* 1.3 78.7 - - - +
536B VAL* 1.3 63.8 + - - +
538B THR* 3.8 6.3 - - - -
539B LEU* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B GLN* 4.7 11.9 - - - +
533B VAL* 3.8 24.6 - - + +
534B VAL 3.4 0.8 - - - -
535B SER* 1.3 79.3 - - - +
537B ALA* 1.3 63.4 + - - +
539B LEU* 3.5 7.6 + - - +
540B LEU* 3.1 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B VAL* 4.0 19.7 - - + -
449B VAL* 6.0 0.2 - - + -
527B ILE* 4.2 16.4 - - + +
528B ALA* 4.4 8.1 - - - -
531B GLN* 3.6 19.1 + - + +
533B VAL 4.6 5.8 + - - +
534B VAL 3.4 7.4 + - - +
535B SER 3.4 0.2 - - - -
536B VAL* 1.3 76.9 - - - +
538B THR* 1.3 60.6 + - - +
540B LEU* 3.2 8.0 + - - +
541B MET* 2.8 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B VAL* 3.7 23.3 + - + +
445B VAL* 4.1 9.2 - - - +
534B VAL* 2.7 37.7 + - + +
535B SER* 3.8 8.1 - - - -
536B VAL 3.3 0.2 - - - -
537B ALA* 1.3 73.1 - - - +
539B LEU* 1.3 63.7 + - - +
541B MET* 3.4 8.1 + - - +
542B THR* 2.8 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002A D6T 3.7 61.0 - - - +
535B SER 3.0 17.9 + - - +
536B VAL* 3.8 7.6 - - - +
538B THR* 1.3 77.2 - - - +
540B LEU* 1.3 56.3 + - - +
542B THR* 3.1 14.5 + - + -
543B ILE* 3.0 37.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
527B ILE* 4.1 25.4 - - + -
531B GLN* 5.6 6.3 - - - +
536B VAL* 3.1 21.5 + - + +
537B ALA* 3.2 6.9 + - - +
539B LEU* 1.3 74.7 - - - +
541B MET* 1.3 66.3 + - - +
543B ILE* 3.5 12.5 + - + +
544B CYS* 3.2 41.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B SER 5.4 0.7 - - - +
442B VAL* 4.3 18.2 - - + -
445B VAL* 4.1 20.6 - - + -
520B ALA 4.3 2.0 - - - +
523B MET* 4.2 9.4 - - + +
524B ALA* 3.8 35.0 - - + +
527B ILE* 3.6 31.4 - - + -
537B ALA 2.8 20.8 + - - +
538B THR 3.7 5.8 - - - +
540B LEU* 1.3 76.2 - - - +
542B THR* 1.3 61.5 + - - +
544B CYS* 3.5 3.1 + - + +
545B PHE* 3.3 63.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002A D6T 4.1 30.3 - - + +
439B PHE* 4.8 7.8 - - + -
442B VAL* 5.2 5.5 - - - +
538B THR* 2.8 22.2 + - - +
539B LEU* 3.1 20.1 + - + +
541B MET* 1.3 75.6 - - - +
543B ILE* 1.3 67.1 + - + +
545B PHE* 3.5 5.7 + - - +
546B VAL* 3.4 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A VAL* 5.7 8.5 - - + -
1002A D6T 4.8 34.1 - - - +
539B LEU* 3.0 27.7 + - + +
540B LEU* 3.5 15.0 + - + +
542B THR* 1.3 79.9 - - + +
544B CYS* 1.3 64.1 + - - +
545B PHE 3.3 0.5 + - - -
546B VAL* 3.4 9.8 - - + +
547B PHE* 3.2 45.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B MET* 3.7 31.6 - - + -
527B ILE* 4.5 9.6 - - - -
540B LEU* 3.2 35.9 + - - +
541B MET* 3.9 6.5 - - - +
542B THR 3.3 0.2 - - - -
543B ILE* 1.3 78.5 - - - +
545B PHE* 1.3 64.2 + - + +
547B PHE* 3.9 4.4 + - - +
548B MET* 3.2 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B CYS* 3.3 40.6 - - + -
439B PHE* 3.5 41.7 - + + -
442B VAL* 3.9 13.7 - - + -
520B ALA* 4.0 18.4 - - + -
523B MET* 4.3 20.0 - - - -
541B MET* 3.3 42.6 + - + +
542B THR* 3.5 1.3 + - - +
543B ILE 3.2 0.6 - - - -
544B CYS* 1.3 79.0 - - - +
546B VAL* 1.3 53.4 + - - +
547B PHE 3.1 1.8 - - - -
548B MET* 2.9 18.1 + - + +
549B MET* 2.7 36.6 + - - +
573B ILE* 5.0 2.2 - - + -
574B PRO* 5.3 4.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
405A LEU* 5.8 1.8 - - + -
432A PHE* 4.5 8.2 - - + -
1002A D6T 3.6 69.8 - - + -
439B PHE* 4.3 9.9 - - + -
542B THR* 3.4 15.5 - - + +
543B ILE* 3.4 16.8 - - + +
545B PHE* 1.3 76.1 - - - +
547B PHE* 1.3 70.3 + - + +
549B MET* 3.9 10.3 - - + +
550B ILE* 3.3 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A VAL* 5.5 7.0 - - + -
405A LEU* 3.7 34.1 - - + -
408A VAL* 4.0 31.2 - - + -
412A ILE* 6.1 0.2 - - + -
1002A D6T 6.4 0.4 - - - -
543B ILE* 3.2 44.7 + - + +
544B CYS* 4.4 4.9 - - - +
545B PHE 3.1 0.6 - - - -
546B VAL* 1.3 84.3 - - + +
548B MET* 1.3 63.2 + - + +
549B MET 3.2 1.7 + - - -
550B ILE* 3.6 14.7 + - + +
551B PHE* 3.1 32.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B MET* 3.7 32.3 - - + -
544B CYS* 3.2 14.4 + - + +
545B PHE* 2.9 23.4 + - - +
547B PHE* 1.3 78.6 - - - +
549B MET* 1.3 62.3 + - - +
551B PHE* 3.4 9.5 + - - -
552B SER* 3.7 6.9 + - - -
571B PHE* 3.3 20.9 - - + +
572B SER* 3.7 28.4 - - - -
573B ILE* 3.8 25.4 - - + -
574B PRO* 3.6 22.7 - - + +
636B MET* 5.7 0.9 - - + -
640B PHE* 6.0 0.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
431A PHE* 5.9 4.5 - - + -
432A PHE* 4.7 7.9 - - + -
1002A D6T 3.3 57.0 - - + -
431B PHE* 3.5 30.0 - - + -
435B THR* 4.4 9.2 - - + -
439B PHE* 4.2 11.4 - - + -
545B PHE 2.7 20.0 + - - +
546B VAL* 4.0 9.0 - - - +
547B PHE 3.2 0.6 - - - -
548B MET* 1.3 72.1 - - - +
550B ILE* 1.3 63.6 + - - +
552B SER* 3.1 23.5 + - - -
555B LEU* 3.9 27.0 - - + +
574B PRO* 4.9 6.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
405A LEU* 5.2 0.4 - - + -
408A VAL* 5.5 0.2 - - + -
409A ILE* 3.9 23.3 - - + -
412A ILE* 4.0 24.5 - - + -
413A TYR* 4.0 23.6 - - + +
432A PHE* 4.2 22.2 - - + -
546B VAL 3.3 20.2 - - - +
547B PHE* 4.0 24.9 - - + +
548B MET 3.3 0.8 - - - -
549B MET* 1.3 76.7 - - + +
551B PHE* 1.3 62.2 + - + +
552B SER 3.2 4.9 + - - -
553B GLY 4.1 3.3 + - - -
555B LEU* 4.4 12.1 - - + +
556B VAL* 3.4 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A VAL* 6.1 0.7 - - + -
412A ILE* 3.8 31.4 - - + -
547B PHE* 3.1 33.7 - + + -
548B MET* 3.4 9.3 + - - +
549B MET 3.2 1.0 - - - -
550B ILE* 1.3 77.2 - - + +
552B SER* 1.3 63.0 + - - +
553B GLY 3.3 1.3 - - - -
556B VAL* 4.7 1.1 - - + -
558B LEU* 3.3 18.2 - - + +
561B ILE* 3.9 31.0 - - + -
565B LEU* 4.4 9.0 - - + -
568B LEU* 4.0 40.2 - - + -
569B GLN* 4.3 21.5 - - + +
572B SER* 4.1 13.0 - - - +
575B ARG* 3.8 13.6 - - - +
----------------------------------------------------------
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