Contacts of the helix formed by residues 544 - 560 (chain B) in PDB entry 3U11
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 544 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B LYS 3.6 3.8 - - - +
543B LEU* 1.3 92.0 - - + +
545B PRO* 1.4 73.0 - - + +
546B ASP* 3.4 15.9 - - - +
547B THR* 3.2 19.1 + - + +
548B ARG* 3.2 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B LEU 3.6 2.6 - - - +
544B PRO* 1.4 84.0 - - + +
546B ASP* 1.3 67.9 + - - +
548B ARG* 3.3 12.2 + - + +
549B GLN* 3.1 22.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
544B PRO* 3.6 18.5 - - - +
545B PRO* 1.3 76.2 - - - +
547B THR* 1.3 70.2 + - - +
549B GLN* 3.4 6.2 + - - +
550B ARG* 3.0 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B LEU* 4.3 15.9 - - + -
544B PRO* 3.2 30.5 + - + +
546B ASP* 1.3 81.6 + - - +
548B ARG* 1.3 59.1 + - - +
550B ARG* 3.3 8.8 + - + +
551B ILE* 2.9 51.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B GLU 5.2 0.8 + - - -
538B MET* 3.5 59.8 + - + +
539B SER* 3.9 20.4 + - - +
542B LYS* 3.6 14.8 - - - +
543B LEU* 2.8 29.8 + - + +
544B PRO 3.2 13.5 + - - +
545B PRO* 3.7 11.1 - - + +
546B ASP 3.2 0.4 - - - -
547B THR* 1.3 74.7 - - - +
549B GLN* 1.3 59.3 + - - +
551B ILE* 3.3 2.4 + - - +
552B HIS* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B PRO 3.1 15.8 + - - +
546B ASP* 3.9 6.3 - - - +
548B ARG* 1.3 75.2 - - - +
550B ARG* 1.3 58.3 + - - +
552B HIS* 3.3 18.8 + - - +
553B ASP* 2.9 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ASP* 3.0 16.4 + - + +
547B THR* 3.4 12.6 - - - +
549B GLN* 1.3 73.8 - - - +
551B ILE* 1.3 56.7 + - + +
553B ASP* 3.3 2.9 + - - +
554B TYR* 2.7 32.6 + - - +
617B GLN* 3.0 44.7 + - - +
618B PRO 2.9 27.9 + - - -
619B GLY 4.4 1.8 - - - -
620B ASP* 2.5 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B TYR* 4.8 0.4 - - + -
534B VAL* 3.8 27.6 - - + -
537B TYR* 6.2 0.9 - - + -
538B MET* 3.6 23.6 - - + -
543B LEU* 4.0 12.1 - - + -
547B THR* 2.9 37.1 + - + +
548B ARG 3.7 4.0 - - - +
550B ARG* 1.3 73.4 - - + +
552B HIS* 1.3 68.0 + - - +
554B TYR* 3.4 7.0 + - + +
555B TYR* 3.0 37.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B TYR* 3.1 43.8 + + - +
535B GLU* 5.8 0.4 - - - -
548B ARG 2.8 14.0 + - - +
549B GLN* 3.4 21.9 + - - +
551B ILE* 1.3 79.4 - - - +
553B ASP* 1.3 83.4 + - - +
555B TYR* 3.3 3.3 + - - +
556B GLU* 3.2 56.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B GLN* 2.9 37.9 + - - +
550B ARG* 3.8 5.0 - - - +
552B HIS* 1.3 97.6 + - - +
554B TYR* 1.3 62.7 - - - +
556B GLU* 3.1 8.4 + - - +
557B HIS* 3.1 33.0 + - + +
617B GLN* 3.9 3.4 - - - +
678B TYR* 3.4 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B ARG 2.7 21.6 + - - +
551B ILE* 3.6 8.1 - - + +
553B ASP* 1.3 71.9 - - - +
555B TYR* 1.3 73.7 + + - +
557B HIS* 3.9 3.5 - - - +
558B ARG* 2.8 76.4 + - + +
559B TYR* 4.6 8.5 - + - -
615B VAL* 3.4 44.0 + - + -
617B GLN* 3.2 24.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B TYR* 3.5 22.1 - + - +
530B LYS* 4.6 16.1 - - + +
531B TYR* 3.9 22.9 - + + -
534B VAL* 3.4 30.4 - - + +
551B ILE* 3.0 44.0 + - + +
552B HIS 3.8 6.7 - - - +
554B TYR* 1.3 86.3 - + - +
556B GLU* 1.3 56.6 + - - +
559B TYR* 2.9 63.6 + + - +
563B MET* 5.0 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A ASN* 3.5 17.2 - - - +
527B TYR* 3.4 17.6 + - + +
552B HIS* 3.2 42.0 + - + +
553B ASP* 3.1 11.6 + - - +
555B TYR* 1.3 77.9 - - - +
557B HIS* 1.3 59.2 + - - +
560B GLN* 2.7 33.4 + - - +
561B GLY 5.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A LYS* 5.5 0.2 - - - +
647A ASN* 3.8 39.0 + - + +
648A LYS 5.7 2.2 + - - -
553B ASP* 3.1 29.4 + - + +
554B TYR 4.1 1.8 - - - +
556B GLU* 1.3 80.1 - - + +
558B ARG* 1.3 64.3 + - - +
560B GLN* 3.9 8.3 - - - +
615B VAL* 4.8 6.5 - - + +
678B TYR* 3.4 64.1 - + + -
680B ARG* 3.8 17.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
554B TYR* 2.8 52.7 + - + +
557B HIS* 1.3 80.1 - - - +
559B TYR* 1.3 113.6 + - + +
560B GLN* 5.0 1.9 - - - +
613B PHE* 4.2 42.2 + - - +
614B GLU* 5.4 0.6 - - - +
615B VAL* 3.9 28.2 - - + +
680B ARG* 4.8 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B TYR* 3.6 13.7 - - + -
554B TYR* 4.6 7.7 + + - -
555B TYR* 2.9 52.3 + + - +
558B ARG* 1.3 130.6 + - + +
560B GLN* 1.3 72.5 + - - +
561B GLY 3.2 0.2 - - - -
562B LYS* 3.0 36.9 + - - +
563B MET* 4.3 22.4 - - + -
564B PHE 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A LYS* 2.9 48.9 + - - +
646A GLY* 5.0 0.9 - - - -
647A ASN* 4.3 2.7 - - - +
524B ARG* 5.3 3.5 + - - -
555B TYR 3.8 0.2 + - - -
556B GLU 2.7 28.4 + - - +
557B HIS 3.9 9.1 - - - +
558B ARG 5.0 1.6 - - - +
559B TYR* 1.3 74.9 - - - +
561B GLY* 1.3 58.5 + - - +
562B LYS* 3.6 13.6 + - + +
680B ARG* 3.1 26.0 + - - -
----------------------------------------------------------
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