Contacts of the strand formed by residues 507 - 517 (chain A) 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 ALA 507 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ALA* 5.0 0.7 - - - -
489A CYS* 3.5 18.2 - - - +
506A VAL* 1.3 77.0 - - - +
508A GLY* 1.3 59.1 + - - +
548A ALA* 3.3 4.6 - - - -
549A GLY 2.9 30.7 + - - +
582A LYS* 3.7 12.9 - - + +
585A ILE* 3.8 22.2 - - + -
586A LEU* 3.8 22.3 - - + +
589A MET* 3.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ARG* 4.7 3.1 + - - -
485A MET* 3.5 22.0 + - - +
488A ALA* 4.8 1.2 - - - +
489A CYS* 3.6 11.5 - - - -
507A ALA* 1.3 75.4 - - - +
509A VAL* 1.3 66.2 + - - +
547A ILE 3.1 13.7 - - - -
548A ALA* 3.6 9.8 - - - +
582A LYS* 5.3 2.0 - - - -
585A ILE* 3.3 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 4.4 0.9 - - + -
388A ARG* 5.3 3.8 - - - +
482A SER* 4.5 0.2 - - - -
485A MET* 3.4 12.5 - - - +
508A GLY* 1.3 75.8 - - - +
510A ALA* 1.3 65.1 + - - +
511A ILE* 4.5 3.6 - - + -
531A THR* 4.6 0.2 - - + -
532A ASP* 3.8 35.9 - - + +
545A PHE 3.7 1.2 - - - +
546A LYS* 3.6 0.3 - - - -
547A ILE* 2.9 32.0 + - + +
578A ALA* 3.9 38.6 - - + +
581A ALA* 4.2 16.2 - - + -
582A LYS* 4.5 4.3 - - + +
585A ILE* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A SER* 3.3 29.4 + - - +
509A VAL* 1.3 76.9 - - - +
511A ILE* 1.3 63.5 + - - +
532A ASP* 2.8 31.7 + - - +
533A ILE* 3.5 14.9 + - + +
544A ASP* 3.3 25.8 - - - +
545A PHE 3.4 4.0 - - - -
546A LYS* 4.0 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A VAL* 4.5 5.8 - - + -
510A ALA* 1.3 80.8 - - - +
512A GLY* 1.3 73.7 + - - +
529A LEU* 3.9 14.8 - - + -
530A LEU 3.3 8.3 - - - +
531A THR* 3.9 25.1 - - + +
532A ASP 4.4 0.9 - - - +
533A ILE* 4.3 2.0 - - - -
543A MET* 3.7 15.6 - - + +
544A ASP* 3.9 0.7 - - - -
545A PHE* 2.8 50.9 + - + +
574A ALA* 3.8 13.7 - - + +
577A GLN* 4.5 3.8 - - + +
578A ALA* 3.7 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A ILE* 1.3 80.0 - - - +
513A LEU* 1.3 62.2 + - - +
529A LEU* 3.4 6.1 - - - +
530A LEU* 2.8 35.2 + - - -
533A ILE* 3.5 21.6 - - - +
537A GLU 5.6 0.9 - - - -
543A MET* 3.6 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A GLY* 1.3 75.9 - - - +
514A VAL* 1.3 72.5 + - - +
515A THR* 3.9 16.8 - - + -
527A TYR* 4.1 21.1 - - + -
528A ARG 3.5 12.6 - - - +
529A LEU* 3.7 18.2 - - + -
530A LEU* 4.4 3.2 - - - +
537A GLU 5.5 0.4 + - - -
541A GLY* 3.6 3.1 - - - -
542A ASP* 2.8 45.7 + - + +
543A MET* 3.8 30.9 + - + -
566A ILE* 4.1 23.8 - - + -
570A ILE* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A PHE* 5.4 5.4 - - + -
349A ARG* 3.7 46.7 - - + +
352A VAL* 4.3 20.9 - - + -
353A LEU* 3.9 22.0 - - + +
513A LEU* 1.3 80.7 - - - +
515A THR* 1.3 63.9 + - - +
527A TYR* 3.2 4.5 - - - +
528A ARG* 2.8 34.6 + - + +
530A LEU* 4.0 20.9 - - + -
537A GLU 5.6 0.7 - - - +
541A GLY* 4.8 7.9 - - - -
542A ASP* 3.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ARG* 2.7 29.1 + - - +
353A LEU* 4.0 9.7 - - - +
513A LEU* 3.9 11.2 - - + -
514A VAL* 1.3 78.4 - - - +
516A LYS* 1.3 60.4 + - - +
517A THR* 4.2 11.0 + - - +
524A ILE* 3.9 20.6 - - + -
526A ASP 3.4 6.1 - - - -
527A TYR* 3.8 15.3 - - + +
542A ASP* 2.7 25.3 + - - +
563A LEU* 3.7 25.7 - - + +
570A ILE* 5.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A GLU* 6.0 0.2 + - - -
353A LEU* 3.8 21.7 - - + +
515A THR* 1.3 72.8 - - - +
517A THR* 1.3 66.9 + - - +
524A ILE* 3.7 0.2 - - - -
525A GLU* 2.8 55.7 + - + +
526A ASP* 2.9 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A THR* 4.1 12.8 + - - +
516A LYS* 1.3 78.3 + - - +
518A ASP* 1.3 67.8 + - - +
519A PRO* 3.7 2.8 - - - +
522A GLY* 3.3 29.2 - - - +
523A GLU 3.2 6.7 - - - -
524A ILE* 3.4 29.6 - - + -
525A GLU* 4.1 5.5 - - - -
563A LEU* 5.6 6.9 - - + +
----------------------------------------------------------
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