Contacts of the strand formed by residues 534 - 540 (chain C) in PDB entry 1UER
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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493C LEU* 4.1 4.7 - - + -
496C ALA* 3.7 26.9 - - + +
497C ILE* 3.6 35.4 - - + +
500C GLN* 3.7 28.6 + - + +
501C PHE* 4.1 13.5 - - + -
526C LEU* 4.2 10.8 - - + -
527C ALA 3.3 5.2 - - - +
528C SER* 4.1 2.0 - - - -
532C GLY 4.1 4.5 - - - +
533C LYS* 1.3 82.6 + - - +
535C SER* 1.3 63.4 + - - +
553C LEU* 3.8 21.8 - - + -
591C TYR* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 535 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C PHE* 5.0 3.6 - - - -
525C TRP 3.5 0.3 - - - +
526C LEU* 3.5 6.1 - - - +
527C ALA* 2.8 40.8 + - - +
528C SER 5.9 0.2 - - - -
533C LYS* 5.2 2.3 + - - -
534C LEU* 1.3 76.3 - - - +
536C ILE* 1.3 64.2 + - - +
537C GLU* 2.7 30.3 + - - +
550C LEU* 4.3 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 536 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C PHE* 3.7 31.5 - - + -
507C PHE* 4.1 6.5 - - + -
510C GLU* 4.1 13.2 - - + +
511C PHE* 3.9 39.3 - - + +
514C ALA* 3.9 15.7 - - + -
524C VAL* 3.9 26.0 - - + -
525C TRP 3.4 3.1 - - - -
526C LEU* 4.8 0.7 - - + -
535C SER* 1.3 74.4 - - - +
537C GLU* 1.3 66.9 + - - +
538C LYS* 4.0 6.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 537 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C TRP 3.7 0.2 - - - +
524C VAL* 3.6 2.9 - - - -
525C TRP* 2.8 47.3 + - + +
527C ALA* 4.0 18.6 - - + -
535C SER* 2.7 32.4 + - - +
536C ILE* 1.3 74.6 - - - +
538C LYS* 1.3 62.4 + - - +
539C GLU* 3.7 16.0 + - + +
545C PRO* 4.8 4.3 - - + -
548C LYS* 2.9 31.3 + - + -
550C LEU* 3.8 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 538 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C ALA* 3.0 42.9 + - + +
517C THR* 3.4 21.5 + - - -
518C LEU* 3.5 29.2 - - + +
523C TRP 3.7 4.7 - - - -
524C VAL* 4.7 2.2 - - + +
536C ILE* 4.0 7.7 + - + +
537C GLU* 1.3 72.5 + - - +
539C GLU* 1.3 62.2 + - - +
540C PRO* 3.8 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 539 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C LEU* 4.0 3.4 - - - +
522C GLY* 3.1 1.0 - - - -
523C TRP* 2.8 44.9 + - + +
525C TRP* 4.0 14.8 - - + -
537C GLU* 4.4 15.1 - - + +
538C LYS* 1.3 77.1 - - - +
540C PRO* 1.3 75.5 - - - +
541C ASN 4.3 0.7 - - - +
543C GLY* 3.4 35.3 - - - +
544C ASN* 3.8 23.5 - - - +
545C PRO* 4.1 5.9 - - - +
547C ARG* 5.8 0.7 - - - +
548C LYS* 4.7 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 540 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C LEU* 4.9 6.7 - - + -
519C PHE 5.8 2.0 - - - +
521C SER 3.7 8.5 - - - +
522C GLY* 4.1 0.4 - - - -
538C LYS 3.8 8.1 - - - +
539C GLU* 1.3 90.0 - - - +
541C ASN* 1.3 74.6 + - - +
542C ALA 3.1 3.8 + - - -
543C GLY* 3.1 10.9 + - - -
741D ASN* 6.2 2.7 - - - +
----------------------------------------------------------
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