Contacts of the helix formed by residues 522 - 541 (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 SER 522 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B ASP* 1.3 77.4 - - - +
523B SER* 1.3 60.1 + - - +
525B ARG* 3.3 24.5 + - - +
526B GLN* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B ASP 5.0 2.3 + - - -
522B SER* 1.3 79.6 + - - +
524B ARG* 1.3 66.5 + - - +
525B ARG 3.2 0.4 - - - -
526B GLN* 3.6 2.3 + - - +
527B TYR 3.3 8.8 + - - -
562B LYS* 4.2 10.4 - - - +
563B MET 3.0 45.0 + - - +
564B PHE* 3.5 31.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B ASP* 3.0 26.0 + - - +
523B SER* 1.3 81.7 + - - +
525B ARG* 1.3 58.0 + - - +
527B TYR* 3.3 4.3 + - - +
528B GLN* 3.0 44.5 + - - +
560B GLN 5.3 5.3 + - - -
561B GLY* 3.5 23.1 + - - +
562B LYS* 3.6 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B ASP* 2.6 34.3 + - - +
522B SER* 3.3 41.0 + - - +
524B ARG* 1.3 72.4 - - - +
526B GLN* 1.3 59.6 + - - +
528B GLN* 3.3 14.9 + - + +
529B GLU* 3.0 57.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B SER 3.0 18.1 + - - +
523B SER* 3.9 5.7 - - - +
524B ARG 3.3 0.2 - - - -
525B ARG* 1.3 73.2 - - - +
527B TYR* 1.3 60.0 + - - +
529B GLU* 3.5 10.7 + - + +
530B LYS* 2.9 33.7 + - + +
563B MET* 3.4 49.0 - - + +
564B PHE 4.7 4.9 + - - +
565B ASP* 4.7 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B SER 3.3 4.0 + - - -
524B ARG 3.3 8.0 + - - +
526B GLN* 1.3 78.7 - - - +
528B GLN* 1.3 69.6 + - + +
530B LYS* 3.3 2.3 + - - +
531B TYR* 2.9 40.5 + + + +
555B TYR* 3.5 35.4 - + + +
556B GLU* 3.4 35.3 + - + +
559B TYR* 3.6 17.0 - + + -
561B GLY* 3.4 35.7 - - - +
562B LYS* 3.5 18.6 - - - +
563B MET* 3.5 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B ARG* 3.0 31.7 + - - +
525B ARG* 3.3 16.2 + - + +
527B TYR* 1.3 88.0 - - + +
529B GLU* 1.3 59.0 + - + +
531B TYR* 3.2 4.7 + - - +
532B LYS* 2.9 47.1 + - - +
561B GLY 5.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B ARG* 3.0 46.4 + - + +
526B GLN* 3.9 9.2 - - + +
528B GLN* 1.3 77.5 - - + +
530B LYS* 1.3 61.9 + - - +
532B LYS* 3.4 17.2 + - + +
533B GLN* 3.3 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B GLN* 2.9 21.2 + - - +
527B TYR 3.9 2.0 - - - +
529B GLU* 1.3 74.3 - - - +
531B TYR* 1.3 65.8 + - - +
532B LYS 3.1 1.8 - - - -
533B GLN* 3.1 25.7 + - + +
534B VAL* 3.0 35.8 + - + +
555B TYR* 4.6 10.1 - - + +
563B MET* 3.4 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B TYR* 2.9 35.7 + + + +
528B GLN* 3.8 4.5 - - - +
530B LYS* 1.3 77.6 - - - +
532B LYS* 1.3 59.6 + - + +
534B VAL* 3.2 21.7 + - + -
535B GLU* 3.0 56.4 + - + +
538B MET* 3.9 13.0 - - + +
551B ILE 4.6 0.4 - - - -
552B HIS* 3.1 56.7 - + - +
555B TYR* 3.9 30.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B GLN* 2.9 34.6 + - - +
529B GLU* 3.6 14.8 - - + +
530B LYS 3.1 0.4 - - - -
531B TYR* 1.3 76.7 - - + +
533B GLN* 1.3 64.3 + - - +
535B GLU* 3.3 18.5 + - - +
536B GLN* 3.0 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B GLU 3.3 10.8 + - - +
530B LYS* 3.1 30.7 + - + +
532B LYS* 1.3 78.4 - - - +
534B VAL* 1.3 58.0 + - + +
536B GLN* 3.4 14.2 + - - +
537B TYR* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B LYS* 3.0 26.9 + - + +
531B TYR* 3.4 18.2 - - + +
532B LYS 3.1 0.4 - - - -
533B GLN* 1.3 76.7 - - - +
535B GLU* 1.3 58.2 + - - +
537B TYR* 3.0 12.4 + - + +
538B MET* 2.9 35.5 + - + +
551B ILE* 3.8 29.4 - - + -
555B TYR* 3.4 36.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B TYR* 3.0 50.0 + - + +
532B LYS* 3.3 23.7 + - - +
534B VAL* 1.3 75.2 - - - +
536B GLN* 1.3 58.4 + - + +
538B MET* 3.4 14.7 + - + +
539B SER* 2.9 29.9 + - - -
548B ARG* 5.2 1.2 + - - -
552B HIS* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B LYS* 3.0 31.6 + - - +
533B GLN* 3.8 13.5 - - - +
535B GLU* 1.3 76.0 - - + +
537B TYR* 1.3 61.2 + - - +
539B SER* 3.8 6.3 - - - -
540B PHE* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B GLN 2.9 14.6 + - - +
534B VAL* 3.2 16.4 - - + +
536B GLN* 1.3 78.4 - - - +
538B MET* 1.3 66.2 + - + +
540B PHE* 3.4 3.9 + + - +
541B HIS* 3.0 73.0 + + + -
543B LEU* 4.4 15.4 - - + +
551B ILE* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B TYR* 3.9 21.1 - - - +
534B VAL* 2.9 22.8 + - + +
535B GLU* 3.8 24.2 - - + +
537B TYR* 1.3 76.8 - - + +
539B SER* 1.3 60.2 + - - +
542B LYS* 2.9 23.0 + - - -
543B LEU* 3.1 36.3 + - + -
548B ARG* 3.5 47.5 + - + +
551B ILE* 3.6 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B GLU 2.9 18.8 + - - -
536B GLN* 3.8 7.4 - - - -
538B MET* 1.3 75.2 - - - +
540B PHE* 1.3 68.0 + - - +
542B LYS* 3.0 20.4 + - - +
548B ARG* 3.9 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B GLN 2.8 22.1 + - - +
537B TYR* 3.4 5.1 + + - +
539B SER* 1.3 77.1 + - - +
541B HIS* 1.3 89.4 + + - +
542B LYS* 3.3 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B TYR* 3.0 64.4 + + + +
540B PHE* 1.3 100.4 - + - +
542B LYS* 1.3 71.7 + - - +
543B LEU* 3.3 23.9 + - + +
----------------------------------------------------------
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