Contacts of the strand formed by residues 468 - 479 (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 GLU 468 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A SER* 6.0 0.2 - - - -
449A ASP* 4.1 5.7 - - - +
466A THR* 3.3 17.5 + - - +
467A ASN* 1.3 84.7 - - + +
469A VAL* 1.3 88.1 + - - +
470A SER* 4.1 6.9 + - - -
491A THR* 4.0 19.0 - - + +
492A GLN 3.3 20.0 - - - +
493A PRO* 4.1 3.1 - - + -
494A LEU* 4.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A SER* 3.5 6.5 - - - +
449A ASP* 3.7 19.5 - - + +
460A TRP* 3.4 58.3 - - + -
462A LEU* 4.2 3.6 - - + -
466A THR* 4.2 6.3 - - + -
468A GLU* 1.3 87.8 - - - +
470A SER* 1.3 63.1 + - - +
492A GLN* 2.9 40.7 + - + +
494A LEU* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A SER* 2.9 41.6 + - - -
460A TRP* 3.8 7.9 - - - -
468A GLU* 4.1 9.1 + - - -
469A VAL* 1.3 78.7 - - - +
471A TYR* 1.3 69.6 + - - +
489A THR* 5.1 7.5 - - - +
490A VAL 3.2 16.2 - - - -
491A THR* 4.2 8.3 - - - -
492A GLN* 4.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ASN* 4.7 1.8 + - - -
430A ILE* 4.0 19.1 - - + -
431A PRO 4.8 1.6 + - - -
432A ASN* 3.6 15.3 + - - -
433A THR* 3.7 19.9 + - - -
434A VAL* 3.8 17.9 - - + +
442A ILE 5.9 0.2 - - - -
444A PRO* 3.9 13.2 - - + -
446A THR* 3.3 15.5 - - - +
447A ILE* 4.1 15.5 - - + +
458A ILE* 3.5 28.1 - - + +
460A TRP* 4.5 4.9 - + - -
470A SER* 1.3 79.9 - - - +
472A THR* 1.3 76.0 + - - +
473A PHE* 4.9 1.8 - + + -
489A THR* 3.6 3.5 - - - +
490A VAL* 2.9 71.0 + - + +
492A GLN* 5.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A PRO* 3.3 10.9 - - - +
445A ALA* 2.9 24.3 + - - +
446A THR* 2.6 42.4 + - - +
471A TYR* 1.3 79.6 - - - +
473A PHE* 1.3 66.0 + - - +
488A GLY 3.2 11.0 - - - -
489A THR* 4.0 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A GLN* 4.4 0.9 - - + -
417A TRP* 3.7 32.3 - + - -
434A VAL* 3.6 37.5 - - + -
442A ILE* 4.1 20.0 - - + +
443A ALA 4.4 4.3 - - - +
444A PRO* 4.7 2.0 - - + -
445A ALA* 3.9 9.4 - - - +
471A TYR* 4.9 2.2 - + + -
472A THR* 1.3 77.8 - - - +
474A SER* 1.3 62.8 + - - +
486A PHE* 3.5 37.2 - + - -
487A SER* 3.2 24.7 - - - -
488A GLY* 3.1 50.5 + - - +
490A VAL* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ILE* 4.9 2.6 - - - +
443A ALA 5.2 0.6 + - - -
445A ALA* 4.1 16.7 - - - +
473A PHE* 1.3 78.4 - - - +
475A GLN* 1.3 61.9 + - - +
476A PRO* 4.1 5.5 - - - +
485A THR* 3.3 19.4 - - - +
486A PHE 3.6 5.2 - - - -
487A SER* 3.8 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ASN* 3.9 16.9 - - - +
442A ILE* 3.7 46.4 - - + +
474A SER* 1.3 75.4 + - - +
476A PRO* 1.3 106.5 + - - +
477A VAL* 3.5 1.1 + - + +
485A THR* 3.9 1.9 - - - +
486A PHE* 2.9 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ASN* 4.8 1.7 + - - -
474A SER* 4.1 5.8 - - - +
475A GLN* 1.3 114.5 + - - +
477A VAL* 1.3 60.7 + - - +
483A THR* 5.7 4.7 - - + -
484A THR 3.3 11.7 - - - +
485A THR* 4.1 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LEU* 4.1 12.1 - - + -
410A LEU* 4.4 2.6 - - + +
412A LEU* 4.4 2.2 - - + -
436A ASN* 3.4 26.0 - - - +
437A VAL* 3.8 20.4 - - + -
475A GLN 4.0 1.6 - - - +
476A PRO* 1.3 76.7 - - - +
478A THR* 1.3 71.0 + - - +
479A ILE* 4.5 3.6 - - + -
482A GLY 3.9 0.7 - - - +
483A THR* 3.4 4.2 - - - +
484A THR* 3.0 54.1 + - + +
486A PHE* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A VAL* 4.6 5.5 - - - +
477A VAL* 1.3 78.9 - - - +
479A ILE* 1.3 67.9 + - - +
480A GLY 3.5 24.2 + - - +
481A LYS* 4.1 5.4 - - - -
482A GLY 3.2 12.1 - - - +
483A THR* 2.8 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LEU* 5.1 4.0 - - + -
401A LEU* 3.5 42.2 - - + +
402A ALA* 4.3 10.1 - - - +
404A LEU 3.5 22.9 - - - +
405A THR* 4.9 0.7 - - + -
407A ILE* 3.6 19.5 - - + +
410A LEU* 3.9 25.1 - - + -
412A LEU* 4.9 5.8 - - + -
437A VAL* 3.9 29.4 - - + -
477A VAL* 4.5 4.3 - - + -
478A THR* 1.3 76.3 - - - +
480A GLY* 1.3 62.2 + - - +
481A LYS 3.2 0.3 + - - -
482A GLY 3.0 23.6 + - - +
----------------------------------------------------------
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