Contacts of the strand formed by residues 500 - 506 (chain A) in PDB entry 3U0Z
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 500 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A GLU* 3.2 30.6 + - - +
485A PHE* 6.0 0.4 - - - -
498A GLY 3.8 0.6 - - - -
499A LYS* 1.3 83.3 - - + +
501A MET* 1.4 60.7 + - - +
502A TYR* 3.1 34.9 + - + +
528A GLY 3.6 1.6 - - - +
532A LEU* 3.7 7.0 - - - +
538A ARG* 2.8 32.3 + - - +
552A SER* 4.4 7.9 - - - +
553A LEU 3.6 9.0 - - - +
554A SER* 4.9 5.8 - - - -
555A VAL 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A LYS* 1.4 70.8 - - - +
502A TYR* 1.3 74.0 + - - +
503A PHE* 4.1 19.9 - - + -
526A TYR* 3.9 29.4 - - + -
527A PHE 3.6 18.2 - - - +
528A GLY 3.4 17.9 - - - +
529A GLU* 3.9 11.9 - - + -
532A LEU* 3.6 8.5 - - + +
552A SER* 3.1 6.4 - - - -
553A LEU* 2.8 53.5 + - + +
558A PHE* 3.8 29.2 - - - -
572A PHE* 4.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A GLU* 4.0 8.7 - - - -
485A PHE* 4.2 15.6 - + - -
491A ILE* 3.6 28.5 + - + +
492A ILE* 3.9 17.0 - - + -
500A LYS* 3.1 38.3 + - + +
501A MET* 1.3 77.7 - - - +
503A PHE* 1.3 64.9 + - - +
504A ILE 4.2 0.2 + - - -
526A TYR* 3.3 8.3 - - - +
527A PHE* 2.8 71.0 + + + -
538A ARG* 4.5 1.2 + - - -
550A LEU* 3.8 22.2 - - + -
551A TYR 3.3 3.1 - - - -
552A SER* 3.6 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A LEU* 4.7 11.9 - - + -
462A MET* 3.2 29.6 - - + -
464A LEU* 5.1 2.7 - - + -
465A PHE* 3.8 32.3 - + - -
476A MET* 4.2 11.2 - - + -
480A LEU* 4.0 27.4 - - + -
501A MET* 4.1 27.8 - - + -
502A TYR* 1.3 72.1 - - - +
504A ILE* 1.3 64.1 + - - +
505A GLN 3.4 1.0 + - - -
525A SER 3.7 1.6 - - - -
526A TYR* 3.6 22.9 - + + -
550A LEU* 3.4 5.8 - - - -
551A TYR* 2.5 54.6 + - + +
553A LEU* 4.4 11.2 - - + -
572A PHE* 4.9 2.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A LEU* 3.8 6.9 - - - +
503A PHE* 1.3 68.8 - - - +
505A GLN* 1.3 61.5 + - - +
506A HIS 4.1 2.0 - - - -
507A GLY* 3.8 34.8 - - - +
509A ALA* 4.7 5.6 - - + -
521A LEU* 3.8 23.1 - - + +
522A THR 3.8 12.8 - - - +
523A ASP* 4.0 2.5 - - - +
524A GLY* 2.9 25.5 + - - -
525A SER* 2.9 35.9 + - - +
527A PHE* 3.6 34.1 - - + -
548A CYS* 5.7 1.6 - - - -
550A LEU* 3.6 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ASN 5.8 2.2 + - - -
457A LYS* 5.5 4.7 + - - -
458A LEU* 4.6 17.6 - - + +
482A PHE* 4.5 1.2 - - - -
503A PHE 3.4 3.6 + - - -
504A ILE* 1.3 73.2 - - - +
506A HIS* 1.3 63.0 + - - +
523A ASP* 3.4 22.9 - - - +
524A GLY 4.6 0.5 + - - -
549A ARG* 2.4 57.1 + - - +
551A TYR* 4.3 31.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LYS* 5.8 1.0 + - - -
504A ILE* 4.1 3.5 - - - +
505A GLN* 1.3 85.7 + - - +
507A GLY* 1.3 64.4 + - - +
523A ASP* 3.0 23.7 + - - -
547A TYR 4.0 5.2 - - - +
548A CYS* 3.6 0.9 - - - -
549A ARG* 2.7 56.9 + - + +
----------------------------------------------------------
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