Contacts of the strand formed by residues 469 - 480 (chain A) in PDB entry 2OMU
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 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450A ASP* 4.3 4.2 - - - +
467A THR* 3.3 16.7 + - - +
468A ASN* 1.3 102.5 + - - +
470A VAL* 1.3 70.7 + - - +
471A SER* 6.3 0.7 - - - -
492A THR* 3.3 23.9 - - + +
493A GLN 3.2 15.5 - - - +
494A PRO* 3.9 7.7 - - + +
495A LEU* 4.1 2.9 - - - +
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Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A VAL* 5.1 0.4 - - + -
449A SER* 3.6 4.5 - - - +
450A ASP* 3.7 15.5 - - - +
461A TRP* 3.6 55.9 - - + +
463A LEU* 4.0 21.5 - - + -
467A THR* 4.1 6.1 - - + -
469A GLU* 1.3 82.6 - - - +
471A SER* 1.3 62.9 + - - +
492A THR* 3.8 1.2 - - - +
493A GLN* 2.8 46.0 + - + +
495A LEU* 4.2 11.9 - - + -
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Residues in contact with SER 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A SER* 2.9 43.5 + - - -
461A TRP* 3.8 8.2 - - - -
469A GLU* 6.3 0.2 - - - -
470A VAL* 1.3 76.5 - - - +
472A TYR* 1.3 69.8 + - - +
473A THR* 6.1 0.2 - - - +
490A THR* 4.8 9.0 - - - +
491A VAL 3.2 17.9 - - - -
492A THR* 4.2 9.2 - - - -
493A GLN* 4.5 1.3 - - - +
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Residues in contact with TYR 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ASN* 4.9 1.3 + - - -
431A ILE* 4.0 18.6 - - + -
432A PRO 4.6 1.6 + - - -
433A ASN* 3.5 21.4 + - - -
434A THR* 3.7 17.3 + - - -
435A VAL* 3.8 14.4 - - + +
443A ILE 6.0 0.2 - - - -
445A PRO* 3.9 19.1 - - + -
447A THR* 3.3 13.9 - - - +
448A ILE* 4.1 15.7 - - + +
449A SER 4.6 0.2 - - - +
459A ILE* 3.5 26.9 - - + +
461A TRP* 4.5 5.8 - + + -
471A SER* 1.3 78.7 - - - +
473A THR* 1.3 69.9 + - - +
474A PHE* 4.9 2.7 - + + -
490A THR* 3.5 4.0 - - - +
491A VAL* 2.8 74.5 + - + +
493A GLN* 5.9 1.3 - - + -
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Residues in contact with THR 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A PRO* 3.3 9.4 - - - +
446A ALA* 2.7 33.3 + - - +
447A THR* 2.6 40.6 + - - +
471A SER* 6.1 0.4 - - - +
472A TYR* 1.3 80.1 - - - +
474A PHE* 1.3 60.4 + - - +
489A GLY 3.2 10.1 - - - -
490A THR* 3.7 23.3 - - + +
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Residues in contact with PHE 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ILE 4.4 0.2 - - - -
416A GLN* 4.4 0.4 - - + -
418A TRP* 3.7 30.1 - + - -
435A VAL* 3.5 34.8 - - + -
443A ILE* 4.2 19.3 - - + +
444A ALA 4.3 5.8 - - - +
445A PRO* 4.6 2.9 - - + -
446A ALA* 3.9 8.1 - - - +
472A TYR* 4.9 1.8 - + + -
473A THR* 1.3 77.3 - - - +
475A SER* 1.3 64.0 + - - +
487A PHE* 3.4 45.1 - + - -
488A SER* 3.1 22.4 - - - -
489A GLY* 3.0 55.8 + - - +
491A VAL* 4.1 7.2 - - + -
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Residues in contact with SER 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A ILE* 5.0 2.1 - - - +
444A ALA 5.3 0.8 + - - -
446A ALA* 4.0 16.6 - - - +
474A PHE* 1.3 78.0 - - - +
476A GLN* 1.3 63.8 + - - +
477A PRO* 4.1 6.3 - - - +
486A THR* 3.3 19.4 - - - +
487A PHE 3.6 4.3 - - - -
488A SER* 3.9 7.5 - - - -
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Residues in contact with GLN 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A ASN* 4.0 16.9 - - - +
443A ILE* 3.8 44.0 - - + +
475A SER* 1.3 76.6 + - - +
477A PRO* 1.4 100.5 + - - +
478A VAL* 3.6 0.9 + - + +
486A THR* 4.0 1.5 - - - +
487A PHE* 2.8 40.6 + - + +
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Residues in contact with PRO 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A ASN* 4.9 1.4 + - - -
475A SER* 4.1 6.1 - - - +
476A GLN* 1.4 114.1 + - - +
478A VAL* 1.3 60.3 + - - +
484A THR* 5.8 3.8 - - + -
485A THR 3.4 11.4 - - - +
486A THR* 4.1 14.6 - - + +
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Residues in contact with VAL 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A LEU* 4.0 11.0 - - + -
411A LEU* 4.5 2.1 - - + +
413A LEU* 4.4 2.7 - - + -
437A ASN* 3.4 27.1 - - - +
438A VAL* 4.1 14.6 - - + -
476A GLN 4.1 1.1 - - - +
477A PRO* 1.3 76.9 - - - +
479A THR* 1.3 77.1 + - - +
480A ILE* 4.3 6.5 - - + -
483A GLY 3.8 1.0 - - - +
484A THR* 3.5 3.8 - - - +
485A THR* 2.9 53.6 + - + +
487A PHE* 3.9 22.9 - - + -
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Residues in contact with THR 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A VAL* 4.7 5.0 - - - +
478A VAL* 1.3 79.7 - - - +
480A ILE* 1.3 68.2 + - - +
481A GLY 3.5 22.4 - - - +
482A LYS* 4.2 3.1 - - - -
483A GLY 3.2 14.6 - - - +
484A THR* 2.8 29.5 + - - +
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Residues in contact with ILE 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A LEU* 4.9 4.7 - - + +
402A LEU* 3.5 44.2 - - + +
403A ALA* 4.3 10.5 - - - +
405A LEU 3.4 22.9 - - - +
406A THR* 5.1 0.7 - - + -
408A ILE* 3.5 19.8 - - + +
411A LEU* 3.8 25.6 - - + -
413A LEU* 4.8 5.2 - - + -
438A VAL* 3.8 27.4 - - + -
478A VAL* 4.4 5.8 - - + -
479A THR* 1.3 77.6 - - - +
481A GLY* 1.3 62.2 + - - +
482A LYS 3.1 0.2 + - - -
483A GLY 2.9 23.5 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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