Contacts of the helix formed by residues 534 - 540 (chain B) in PDB entry 3U1K
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 LEU 534 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ARG* 4.4 8.7 - - - +
359B CYS* 3.7 30.1 - - - -
360B ASP* 3.9 23.8 - - + +
362B ARG* 3.4 19.1 - - - +
368B ARG* 3.4 24.5 - - - +
480B ASN* 3.5 20.9 - - - +
481B GLY* 4.7 0.7 - - - -
532B ASP 3.8 0.2 + - - -
533B ILE* 1.3 78.2 - - - +
535B GLY* 1.3 65.3 + - - +
536B ILE* 3.8 16.8 - - + +
537B GLU* 3.0 32.8 + - - +
538B ASP* 3.1 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B CIT 6.5 0.9 - - - -
306B LYS* 6.2 1.6 - - - -
480B ASN* 3.2 28.3 + - - -
481B GLY* 4.7 4.3 - - - -
534B LEU* 1.3 71.5 - - - +
536B ILE* 1.3 56.3 + - - +
538B ASP* 2.8 25.0 + - - +
539B TYR* 2.9 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PHE* 3.8 22.2 - - + -
309B ARG* 4.2 17.9 - - + +
310B ASP* 5.0 5.8 - - - +
313B VAL* 5.4 3.1 - - + -
348B PHE* 3.6 29.3 - - + -
359B CYS* 4.0 11.0 - - - -
480B ASN* 4.9 1.2 + - - -
534B LEU* 3.8 17.9 - - + +
535B GLY* 1.3 74.4 - - - +
537B GLU* 1.3 60.6 + - - +
539B TYR* 3.5 30.3 - - + +
540B ASN* 2.9 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B PHE* 3.6 26.5 - - + -
352B VAL* 5.4 1.4 - - - +
358B ARG* 2.8 62.7 + - - +
359B CYS 4.8 1.0 + - - -
362B ARG* 4.0 1.2 + - - -
513B LEU 5.1 3.6 + - - +
514B VAL* 5.7 0.2 - - - +
530B LEU* 4.2 14.2 - - + +
533B ILE* 3.3 19.9 - - + +
534B LEU* 3.0 40.5 + - + +
536B ILE* 1.3 75.5 - - - +
538B ASP* 1.3 61.3 + - - +
540B ASN 4.7 0.2 - - - +
541B GLY* 3.3 20.9 + - - +
543B MET 4.9 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B CIT 4.0 14.7 - - - +
533B ILE* 4.0 10.9 - - + +
534B LEU 3.1 8.7 + - - +
535B GLY* 2.8 15.0 + - - +
537B GLU* 1.3 78.6 - - - +
539B TYR* 1.3 63.8 + - - +
541B GLY* 3.2 11.4 + - - +
543B MET 4.1 3.4 - - - +
544B ASP* 3.3 24.1 - - - +
562B LYS* 3.3 35.1 + - - -
670B CIT 3.1 20.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
310B ASP* 3.8 15.2 + - - -
345B LYS* 4.9 6.8 + - - +
535B GLY* 2.9 25.2 + - - -
536B ILE* 3.5 46.6 - - + +
538B ASP* 1.3 80.9 - - + +
540B ASN* 1.3 75.1 + - - +
541B GLY 4.4 2.6 - - - +
562B LYS* 5.1 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PHE* 5.1 1.8 - - - -
341B ASN 5.2 0.7 - - - +
344B ALA* 4.7 4.5 + - - +
345B LYS* 3.4 35.1 - - + +
348B PHE* 3.6 33.4 - - + +
349B ARG* 2.8 31.8 + - - +
514B VAL* 5.6 0.2 - - - -
536B ILE* 2.9 41.5 + - - +
537B GLU 4.3 0.4 - - - -
539B TYR* 1.3 91.5 - - - +
541B GLY* 1.3 57.9 + - - +
----------------------------------------------------------
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