Contacts of the helix formed by residues 524 - 537 (chain B) in PDB entry 3UO8
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 LYS 524 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B LYS* 1.3 73.3 - - - +
525B ILE* 1.3 67.6 + - - +
526B THR* 3.4 20.9 - - - +
527B VAL* 3.0 25.1 + - + +
528B LEU 3.1 8.3 + - - -
554B LEU* 3.0 34.3 + - + -
556B GLU 3.2 18.8 + - - +
557B LYS* 3.9 14.8 - - + -
558B ARG 3.4 20.0 - - - +
559B ALA* 4.1 2.2 - - - +
530C ASP* 2.9 26.3 + - - +
534C GLU* 2.9 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B LEU* 4.8 10.5 - - + -
458B VAL* 4.6 11.4 - - + -
460B LEU* 5.6 2.9 - - + -
487B VAL* 3.8 18.2 - - + -
519B LEU* 5.4 1.6 - - + -
523B LYS 3.2 4.7 + - - -
524B LYS* 1.3 70.8 - - - +
526B THR* 1.3 64.9 + - - +
528B LEU* 3.3 18.3 + - + -
529B LEU* 3.0 47.1 + - + +
554B LEU* 3.7 26.2 - - + -
558B ARG 3.2 9.4 + - - +
559B ALA* 4.2 2.8 - - - +
560B LEU* 4.1 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B VAL* 3.9 18.6 - - + -
524B LYS* 3.4 23.4 - - - +
525B ILE* 1.3 77.0 - - + +
527B VAL* 1.3 58.2 + - - -
529B LEU* 3.4 6.5 + - - +
530B ASP* 2.9 28.2 + - - +
550B ILE* 4.3 10.3 - - + +
552B SER* 3.2 36.8 - - - +
554B LEU* 4.6 0.2 - - + -
530C ASP* 2.8 30.5 + - - +
550C ILE* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B LYS* 4.1 17.3 - - + -
524B LYS* 3.0 21.2 + - + +
526B THR* 1.3 77.9 + - - +
528B LEU* 1.3 66.8 + - - +
530B ASP* 3.2 9.8 + - + +
531B GLU* 3.0 39.2 + - + +
527C VAL* 5.7 15.3 - - + -
530C ASP* 3.9 17.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
515B LEU* 4.2 11.9 - - + -
518B ARG* 3.3 42.9 - - + +
519B LEU* 3.6 22.4 - - + +
521B GLU* 3.9 21.5 - - + +
523B LYS* 4.4 10.9 - - + +
524B LYS 3.1 10.8 + - - +
525B ILE* 3.4 26.5 - - + +
527B VAL* 1.3 77.5 - - - +
529B LEU* 1.3 62.6 + - + +
531B GLU* 3.0 15.9 + - - +
532B VAL* 3.0 29.4 + - + +
560B LEU* 5.2 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B LEU* 4.3 17.3 - - + -
487B VAL* 3.8 28.5 - - + -
488B PHE 4.4 1.8 - - - +
489B GLY* 4.0 24.0 - - - +
511B PHE* 4.7 2.5 - - + -
515B LEU* 4.0 26.9 - - + -
525B ILE* 3.0 31.3 + - + +
526B THR* 3.8 2.7 - - - +
528B LEU* 1.3 74.7 - - + +
530B ASP* 1.3 54.8 + - - +
532B VAL* 3.1 5.6 + - + +
533B ALA* 2.8 31.0 + - - +
548B LEU* 3.9 13.9 - - + +
550B ILE* 3.3 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B THR 2.9 14.8 + - - +
527B VAL* 3.2 14.6 + - + +
529B LEU* 1.3 75.1 - - - +
531B GLU* 1.3 61.7 + - + +
533B ALA* 3.4 3.6 + - - +
534B GLU* 3.2 25.9 + - - +
550B ILE* 3.3 14.3 - - + +
524C LYS* 2.8 34.1 + - - +
526C THR* 2.7 31.4 + - - +
527C VAL* 4.0 12.8 + - - +
552C SER* 5.0 1.4 + - - -
554C LEU 4.2 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B ARG* 3.5 24.5 + - - +
521B GLU* 2.5 31.5 - - - +
523B LYS* 2.8 31.7 + - - +
527B VAL* 3.0 25.7 + - + +
528B LEU* 3.0 9.3 + - - +
530B ASP* 1.3 75.4 - - + +
532B VAL* 1.3 65.9 + - - +
534B GLU* 3.1 13.7 + - - +
535B ASP* 2.9 27.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
511B PHE* 4.6 6.1 - - + +
514B PHE* 3.9 21.1 - - + +
515B LEU* 4.0 29.8 - - + +
518B ARG* 3.8 26.0 - - + -
528B LEU* 3.0 16.0 + - + +
529B LEU* 3.1 9.2 + - - +
531B GLU* 1.3 74.5 - - - +
533B ALA* 1.3 62.7 - - - +
535B ASP* 3.1 9.4 + - - +
536B MET* 2.8 27.2 + - + +
548B LEU* 3.5 20.0 - - + -
----------------------------------------------------------
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 LEU 2.8 13.3 + - - +
530B ASP* 3.5 14.4 - - - +
532B VAL* 1.3 76.6 - - - +
534B GLU* 1.3 57.4 + - - +
536B MET* 3.3 5.2 + - - +
537B GLY 3.0 21.3 + - - -
548B LEU* 3.8 31.1 + - + +
550B ILE* 4.4 7.2 - - + -
552C SER 6.1 0.7 - - - +
553C SER 5.7 2.0 - - - +
554C LEU 4.4 15.7 - - - +
555C SER* 3.7 12.7 - - - -
----------------------------------------------------------
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 ASP* 3.2 15.6 + - - +
531B GLU* 3.1 13.8 + - - +
533B ALA* 1.3 76.5 - - - +
535B ASP* 1.3 67.6 + - - +
537B GLY* 3.1 10.4 + - - -
538B LYS* 3.5 21.9 - - - +
524C LYS* 2.7 42.2 + - - +
555C SER 3.5 21.5 - - - +
556C GLU* 4.5 1.3 - - - +
557C LYS* 2.8 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B PHE* 3.7 34.0 - - + +
517B ASP* 5.7 1.7 - - - +
518B ARG* 2.9 49.5 + - - +
531B GLU 2.9 15.5 + - - +
532B VAL* 3.4 8.1 - - - +
534B GLU* 1.3 77.1 - - - +
536B MET* 1.3 61.1 + - - +
538B LYS* 3.0 30.2 + - - +
539B CYS 3.6 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B ALA 3.8 3.6 - - - +
510B ILE* 4.4 6.3 - - + -
511B PHE* 4.3 20.9 - - - -
514B PHE* 3.5 32.5 - - + -
532B VAL* 2.8 17.5 + - + +
533B ALA* 3.6 5.4 - - - +
535B ASP* 1.3 70.8 - - - +
537B GLY* 1.3 57.4 + - - +
538B LYS 2.9 5.6 - - - -
539B CYS* 3.0 25.8 + - + +
542B THR* 4.4 4.9 + - - +
543B LYS* 5.0 1.4 + - - +
546B GLN* 3.8 41.5 - - + +
547B ALA* 3.9 1.3 - - - -
548B LEU* 3.6 47.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B ALA 3.0 13.1 + - - -
534B GLU 3.1 5.6 + - - -
535B ASP 3.1 1.0 - - - -
536B MET* 1.3 76.1 - - - +
538B LYS* 1.3 62.7 + - - +
539B CYS 3.5 0.2 - - - -
543B LYS* 3.8 24.6 + - - -
555C SER* 4.0 21.9 + - - -
556C GLU* 4.3 11.5 - - - +
----------------------------------------------------------
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