Contacts of the helix formed by residues 521 - 545 (chain B) in PDB entry 6T8G
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 MET 521 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B PRO* 3.8 19.3 - - + -
520B ASP* 1.3 76.8 - - - +
522B LYS* 1.3 64.3 + - - +
523B GLU 3.3 0.9 - - - -
524B ALA* 3.1 6.6 + - + +
525B ALA* 2.9 25.6 + - - +
599B ASP* 3.5 46.4 - - + +
600B MET* 3.6 17.0 - - + +
603B ILE* 4.0 17.3 - - + -
604B VAL* 3.7 35.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B ASP* 4.6 1.9 - - + +
521B MET* 1.3 76.6 - - - +
523B GLU* 1.3 58.2 + - - +
525B ALA* 3.2 14.2 + - + +
526B ASN* 2.9 38.3 + - - +
604B VAL* 4.0 22.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B PRO* 4.6 15.9 - - - +
518B VAL* 4.2 19.5 - - + +
519B THR 5.5 1.2 + - - -
520B ASP* 4.6 21.6 + - + +
521B MET 3.3 1.0 - - - +
522B LYS* 1.3 77.2 - - - +
524B ALA* 1.3 58.7 + - - +
526B ASN* 3.2 10.1 + - - +
527B ALA* 2.8 22.3 + - - +
720B ILE* 3.3 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B ILE* 3.7 31.2 - - + -
518B VAL* 3.7 17.4 - - + +
520B ASP 3.8 6.3 - - - +
521B MET* 3.1 14.9 + - + +
523B GLU* 1.3 76.4 - - - +
525B ALA* 1.3 59.0 + - - +
527B ALA* 3.0 6.0 + - - +
528B LEU* 2.9 36.6 + - - +
600B MET* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B MET 2.9 13.3 + - - +
522B LYS* 3.2 20.2 + - + +
524B ALA* 1.3 76.5 - - - +
526B ASN* 1.3 61.7 + - - +
528B LEU* 4.0 4.6 + - - +
529B ARG* 3.6 12.1 + - - +
600B MET* 5.0 3.9 - - + +
604B VAL* 5.1 11.2 - - + -
607B LYS* 3.4 33.9 + - + +
608B VAL* 5.7 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B LYS* 2.9 29.5 + - - +
523B GLU* 3.4 14.7 - - - +
525B ALA* 1.3 77.6 - - - +
527B ALA* 1.3 59.4 + - - +
529B ARG* 3.8 7.9 - - - +
530B TRP* 3.6 11.8 + - - +
719B ASP 4.7 2.5 - - - +
720B ILE* 3.3 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ILE* 4.5 12.9 - - + +
497B ILE* 4.6 9.2 - - + -
518B VAL* 4.5 11.2 - - + -
523B GLU 2.8 12.5 + - - +
524B ALA* 3.0 13.2 + - - +
526B ASN* 1.3 76.0 - - - +
528B LEU* 1.3 55.8 + - - +
529B ARG 3.2 1.6 - - - -
530B TRP* 3.3 5.7 + - - +
531B SER* 2.7 34.9 + - - -
720B ILE* 3.7 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B ILE* 4.2 23.3 - - + -
524B ALA 2.9 25.0 + - - +
525B ALA* 4.0 4.9 + - - +
527B ALA* 1.3 74.4 - - - +
529B ARG* 1.3 60.4 + - - +
531B SER* 3.2 15.7 - - - +
532B VAL* 3.0 30.3 + - - +
592B VAL* 5.6 6.7 - - + -
594B VAL* 6.0 3.1 - - + -
600B MET* 4.0 22.2 - - + -
607B LYS* 5.4 0.2 - - - +
608B VAL* 6.0 1.3 - - + +
611B LEU* 3.5 38.1 - - + +
612B ILE* 3.8 23.8 - - + -
615B ILE* 4.3 5.8 - - + -
626B LEU* 5.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B ALA 3.6 12.7 + - - +
526B ASN* 3.8 12.3 - - - +
527B ALA 3.2 0.2 - - - -
528B LEU* 1.3 78.6 - - - +
530B TRP* 1.3 58.7 + - - +
532B VAL* 3.3 14.2 - - - +
533B ALA* 2.9 32.7 + - + +
607B LYS* 3.8 28.6 - - - +
611B LEU* 4.1 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ILE* 4.7 14.1 - - + -
514B LEU* 3.9 33.7 - - + -
526B ASN 3.6 2.9 + - - +
527B ALA 3.3 6.5 + - - +
529B ARG* 1.3 76.5 - - - +
531B SER* 1.3 62.9 + - - +
533B ALA* 4.0 10.5 - - + -
534B GLU* 2.9 57.2 + - + +
717B ILE* 3.7 33.8 - - + +
719B ASP* 3.7 31.9 + - + +
720B ILE* 3.6 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ILE* 4.7 10.6 - - - +
527B ALA 2.7 20.9 + - - -
528B LEU* 3.2 28.0 - - - +
529B ARG 3.2 0.2 - - - -
530B TRP* 1.3 80.6 - - - +
532B VAL* 1.3 58.8 + - - +
534B GLU* 3.8 3.8 - - - +
535B MET* 2.9 26.7 + - - +
592B VAL* 5.3 12.1 - - - +
615B ILE* 4.2 13.3 - - - +
624B ILE* 5.0 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B LEU 3.0 14.6 + - - +
529B ARG* 3.3 19.5 - - - +
531B SER* 1.3 74.9 - - - +
533B ALA* 1.3 57.6 + - - +
535B MET* 3.4 9.7 - - - +
536B GLU* 2.9 39.0 + - + +
611B LEU* 3.6 33.2 - - + +
614B ARG* 4.7 6.7 - - + +
615B ILE* 3.7 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ARG* 2.9 23.0 + - + +
530B TRP* 3.8 13.2 - - + +
531B SER 3.2 0.2 - - - -
532B VAL* 1.3 75.1 - - - +
534B GLU* 1.3 61.6 + - - +
536B GLU* 4.1 2.2 - - - +
537B ARG* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B TRP* 2.9 47.1 + - + +
531B SER* 3.8 4.5 - - - +
533B ALA* 1.3 75.0 - - - +
535B MET* 1.3 62.2 + - - +
537B ARG* 3.6 11.9 - - - +
538B ARG* 3.0 71.3 + - - +
587B LEU* 6.2 0.3 - - - +
590B ILE* 6.1 0.9 - - + -
624B ILE* 5.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B SER 2.9 19.6 + - - +
532B VAL* 3.4 11.0 - - - +
533B ALA 3.2 0.2 - - - -
534B GLU* 1.3 76.6 - - - +
536B GLU* 1.3 67.6 + - + +
538B ARG* 3.5 7.4 - - - +
539B TYR* 2.7 55.7 + - + +
614B ARG 4.0 11.4 - - - +
615B ILE* 3.6 24.7 - - + -
618B LYS* 3.3 41.1 - - + +
619B ALA* 3.8 10.8 - - - +
622B ALA* 4.4 11.2 - - + +
624B ILE* 4.3 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B VAL* 2.9 26.4 + - + +
533B ALA* 4.4 2.0 - - - +
535B MET* 1.3 83.8 - - + +
537B ARG* 1.3 59.5 + - - +
539B TYR* 3.7 11.4 - - + -
540B ARG* 2.9 56.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B ALA 2.9 19.5 + - - +
534B GLU* 3.6 16.4 - - - +
536B GLU* 1.3 76.8 - - - +
538B ARG* 1.3 59.7 + - - +
540B ARG* 3.6 12.8 - - - +
541B LEU* 3.0 41.4 + - - +
570B PRO* 3.4 40.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
534B GLU* 3.0 51.6 + - - +
535B MET* 3.5 6.3 - - - +
537B ARG* 1.3 80.7 - - - +
539B TYR* 1.3 60.0 + - + +
541B LEU* 3.7 9.0 - - + +
542B MET* 2.8 30.1 + - - +
550B LEU* 4.1 28.0 - - + +
553B PHE* 4.7 17.1 - - + -
554B ASN* 5.6 0.6 - - - +
587B LEU* 5.3 15.0 + - - +
588B PRO* 3.6 25.5 + - - +
589B THR* 5.3 0.4 - - - +
590B ILE* 3.7 25.9 - - - +
622B ALA* 4.1 16.5 + - + +
624B ILE* 4.5 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B MET* 2.7 38.8 + - + +
536B GLU* 3.7 13.5 - - + -
537B ARG 3.1 0.4 - - - -
538B ARG* 1.3 80.1 - - + +
540B ARG* 1.3 61.5 + - + +
542B MET* 3.7 32.6 - - + +
543B ALA* 3.6 16.5 + - - +
548B ARG 5.4 0.9 - - - -
550B LEU* 5.8 0.9 - - + -
618B LYS* 4.3 19.3 + - + +
621B ALA* 4.5 8.3 - - + -
622B ALA* 4.4 10.1 - - + -
501C MET* 2.9 54.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B GLU* 2.9 45.0 + - - +
537B ARG* 3.6 14.1 - - - +
539B TYR* 1.3 76.4 - - + +
541B LEU* 1.3 63.9 + - - +
542B MET 3.2 0.4 - - - -
543B ALA* 3.3 8.2 + - + +
544B ALA* 2.9 26.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
537B ARG* 3.0 32.5 + - - +
538B ARG* 3.4 8.7 + - + +
540B ARG* 1.3 77.7 - - - +
542B MET* 1.3 57.8 + - - +
544B ALA* 3.2 9.6 + - + +
545B MET* 2.9 60.2 + - + +
553B PHE* 3.8 24.0 - - + -
569B ASP* 5.2 1.6 - - + -
570B PRO* 4.3 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B ARG 2.8 17.7 + - - +
539B TYR* 3.7 40.8 - - + +
540B ARG 3.2 0.2 - - - -
541B LEU* 1.3 74.7 - - - +
543B ALA* 1.3 60.8 + - + +
545B MET* 3.1 3.8 + - - +
546B GLY 2.9 22.9 + - - -
547B VAL* 3.5 27.6 + - + +
548B ARG 3.3 20.2 - - - +
549B ASN 3.5 28.3 - - - +
550B LEU* 3.7 18.2 - - + -
553B PHE* 3.6 20.8 - - + -
621B ALA 3.9 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B TYR 3.6 10.2 + - - +
540B ARG* 3.3 10.2 + - - +
542B MET* 1.3 76.8 - - + +
544B ALA* 1.3 64.1 + - - +
546B GLY* 3.3 12.2 + - - +
547B VAL 4.5 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B ARG 2.9 15.1 + - - +
541B LEU* 3.3 18.4 - - + +
542B MET 3.2 0.4 - - - -
543B ALA* 1.3 78.9 - - - +
545B MET* 1.3 74.8 + - + +
546B GLY* 3.2 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B LEU* 2.9 52.5 + - + +
542B MET 3.1 5.8 + - - +
544B ALA* 1.3 88.2 - - + +
546B GLY* 1.3 62.1 + - - +
547B VAL* 3.7 6.9 - - + +
553B PHE* 4.6 13.7 - - + -
556B LYS* 5.8 4.1 - - + +
567B LEU* 5.0 10.3 - - + -
569B ASP* 3.3 33.0 - - + +
----------------------------------------------------------
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