Contacts of the strand formed by residues 482 - 495 (chain A) in PDB entry 2OMZ
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 GLY 482 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ILE* 3.4 9.9 + - - -
408A THR 3.5 21.3 - - - -
409A GLN 3.8 3.1 - - - -
410A LEU* 3.5 14.3 - - - +
478A THR* 3.2 2.5 - - - -
479A ILE 3.0 31.8 + - - +
481A LYS* 1.3 78.0 - - - +
483A THR* 1.3 59.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A THR 4.9 0.2 + - - -
409A GLN* 5.3 0.2 - - - +
410A LEU* 3.3 14.7 + - - +
476A PRO* 5.7 3.6 - - + -
477A VAL 3.4 8.3 - - - +
478A THR* 2.8 26.4 + - - +
481A LYS 3.8 6.3 + - - -
482A GLY* 1.3 73.5 - - - -
484A THR* 1.3 68.6 + - - +
-3B GLY* 3.5 15.5 - - - -
-2B PRO* 3.7 21.7 - - + +
-1B LEU 4.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LEU* 3.3 23.9 + - + -
411A GLY* 3.4 5.0 - - - -
412A LEU* 3.1 48.4 + - + +
413A ASN* 4.2 4.9 + - - -
476A PRO* 3.3 5.4 - - - +
477A VAL* 3.0 47.4 + - + -
483A THR* 1.3 77.7 - - - +
485A THR* 1.3 69.6 + - - +
-3B GLY* 3.7 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU 3.4 0.7 - - - -
413A ASN* 3.2 34.6 + - - +
474A SER* 3.3 26.5 - - - +
475A GLN 3.8 16.2 - - - +
476A PRO* 4.1 13.5 - - + +
484A THR* 1.3 77.4 + - - +
486A PHE* 1.3 60.1 + - - +
487A SER* 3.4 11.4 + - - +
-3B GLY* 4.0 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ILE* 3.3 29.8 - - + -
396A SER 3.8 15.5 - - - -
398A LEU* 3.5 41.7 - - + -
412A LEU* 3.6 21.8 - - + -
415A GLN* 3.8 7.6 - - + -
434A VAL* 3.8 14.8 - - + -
435A LYS 3.7 13.7 - - - -
436A ASN* 5.0 0.2 - - - -
442A ILE* 3.5 19.7 - - + -
473A PHE* 3.5 23.2 - + - -
475A GLN* 2.9 36.7 + - + +
477A VAL* 4.0 15.5 - - + -
484A THR* 3.9 2.4 - - - +
485A THR* 1.3 68.5 - - - +
487A SER* 1.3 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU 3.6 2.6 + - - -
413A ASN* 3.6 9.7 - - - +
414A ASP* 3.0 28.1 + - - -
415A GLN* 2.9 28.9 + - - +
473A PHE* 3.2 22.8 - - - -
474A SER* 3.8 15.0 - - - -
485A THR* 3.4 8.7 + - - +
486A PHE* 1.3 75.2 - - - +
488A GLY* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ASP* 4.5 3.1 - - - -
415A GLN 3.0 15.0 - - - -
472A THR* 3.2 8.7 - - - -
473A PHE* 3.1 44.8 + - - +
487A SER* 1.3 78.9 - - - +
489A THR* 1.3 62.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A GLN 3.1 8.2 + - - -
416A ALA* 3.3 11.3 - - - +
417A TRP* 3.3 23.0 + - - +
470A SER* 5.1 7.6 - - - +
471A TYR 3.6 8.7 - - - +
472A THR* 4.0 14.4 - - + +
473A PHE* 4.4 0.6 - - - -
488A GLY* 1.3 76.6 + - - -
490A VAL* 1.3 67.5 + - - +
491A THR* 4.8 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TRP* 3.4 49.4 - - + +
419A ASN* 3.5 29.4 - - - +
433A THR* 5.4 0.2 - - - +
470A SER* 3.2 7.0 - - - -
471A TYR* 2.9 72.3 + - + +
473A PHE* 4.1 8.3 - - + -
489A THR* 1.3 76.3 - - - +
491A THR* 1.3 61.4 + - - +
492A GLN 4.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TRP 3.0 7.3 + - - -
418A THR* 3.3 26.7 + - + +
419A ASN* 3.0 26.5 + - - +
468A GLU* 4.0 29.2 - - + +
469A VAL 3.9 2.7 - - - -
470A SER* 4.2 5.2 - - - -
489A THR* 4.8 8.3 + - - +
490A VAL* 1.3 74.5 - - - +
492A GLN* 1.3 62.0 + - - +
493A PRO* 3.6 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ASN* 2.9 31.5 + - - +
420A ALA 3.0 23.5 + - - +
422A VAL* 3.6 17.3 - - - +
430A ILE* 3.6 34.4 - - + +
460A TRP* 4.9 1.1 - - + -
468A GLU* 3.3 4.0 - - - -
469A VAL* 2.9 53.0 + - + +
470A SER* 5.2 1.3 - - - -
471A TYR* 5.9 1.1 - - + -
490A VAL* 4.0 1.3 + - + +
491A THR* 1.3 72.5 - - - +
493A PRO* 1.3 87.9 + - - +
494A LEU* 3.6 6.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A THR* 3.7 15.3 - - + -
419A ASN 3.2 27.4 - - - +
421A PRO* 4.0 22.2 - - + -
422A VAL 3.3 10.2 + - - -
467A ASN 3.6 9.4 - - - +
468A GLU* 4.1 4.5 - - + -
491A THR* 3.6 8.7 - - + +
492A GLN* 1.3 107.3 + - - +
494A LEU* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A VAL* 3.3 32.8 - - + +
423A ASN 4.9 1.3 - - - +
424A TYR* 4.1 16.6 - - + -
428A VAL* 4.1 15.7 - - + -
430A ILE* 5.7 0.4 - - + -
460A TRP* 6.0 0.2 - - + -
462A LEU* 3.8 28.5 - - + -
465A TYR* 2.6 28.8 + - - -
466A THR* 3.5 23.3 - - + +
467A ASN 3.0 10.3 + - - +
468A GLU* 4.4 1.6 - - - -
469A VAL* 4.1 21.1 - - + +
492A GLN* 4.0 16.6 - - + +
493A PRO* 1.3 77.2 - - - +
495A LYS* 1.3 56.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A PRO* 3.7 30.3 - - + +
422A VAL 3.1 12.6 + - - +
423A ASN* 4.0 17.4 - - - +
424A TYR* 3.1 23.7 + - - +
465A TYR* 3.9 1.6 - - - -
493A PRO 4.2 0.2 - - - -
494A LEU* 1.3 71.3 - - - +
496A GLY* 1.3 62.2 + - - +
497A GLY 3.4 4.7 + - - +
----------------------------------------------------------
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