Contacts of the helix formed by residues 465 - 479 (chain A) in PDB entry 1OYW
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 SER 465 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A ARG* 3.8 5.8 - - - +
464A LYS* 1.3 78.6 - - - +
466A HIS* 1.3 64.2 + - - +
467A GLU* 3.4 16.6 + - - +
468A HIS* 3.0 23.4 + - - +
469A TRP* 3.2 22.3 + - - -
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Residues in contact with HIS 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A MSE 6.1 0.4 - - + +
433A GLY* 5.3 7.9 - - - -
436A VAL* 3.5 25.6 - - + +
437A GLU* 4.1 16.3 + - - -
440A ARG* 3.7 18.2 - - - +
465A SER* 1.3 74.6 - - - +
467A GLU* 1.3 67.6 + - - +
469A TRP* 3.2 5.4 + - - +
470A VAL* 3.0 48.1 + - + +
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Residues in contact with GLU 467 (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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465A SER* 3.4 13.6 + - - +
466A HIS* 1.3 85.5 + - - +
468A HIS* 1.3 64.9 + - - +
470A VAL* 3.7 8.4 - - - +
471A SER* 2.9 25.1 + - - -
513A PRO* 4.4 1.9 - - + +
514A ARG 3.7 11.4 - - - +
515A ILE* 3.3 19.6 - - - +
516A VAL* 2.9 54.8 + - + +
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Residues in contact with HIS 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A TYR* 3.6 13.4 + - - -
415A ASP* 2.8 31.1 + - - -
464A LYS* 3.4 33.4 + - + +
465A SER* 3.0 31.2 + - - +
467A GLU* 1.3 77.6 - - - +
469A TRP* 1.3 67.1 + + - +
471A SER* 3.2 3.5 + - - -
472A VAL* 2.9 41.7 + - + +
513A PRO* 3.3 35.7 - - + +
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Residues in contact with TRP 469 (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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415A ASP* 3.4 54.3 - - + -
418A ILE* 4.2 21.8 - - + -
419A ALA* 4.7 3.6 - - + -
436A VAL* 3.9 21.5 - - + -
439A ILE* 3.5 24.2 - - + -
440A ARG* 3.8 16.6 - - + -
460A MSE 4.9 0.2 - - - -
461A GLY* 2.9 42.7 + - - -
463A ASP* 5.3 0.4 - - - -
464A LYS* 3.6 21.0 - - + +
465A SER 3.2 20.3 + - - -
466A HIS 3.2 7.1 + - - +
468A HIS* 1.3 80.3 - - - +
470A VAL* 1.3 65.4 + - - +
472A VAL* 3.2 15.2 + - + +
473A ILE* 2.9 29.3 + - - +
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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
----------------------------------------------------------
432A MSE 3.8 28.2 - - + +
436A VAL* 4.4 9.0 - - + -
466A HIS* 3.0 47.4 + - + +
467A GLU* 3.7 9.6 - - - +
469A TRP* 1.3 75.2 - - - +
471A SER* 1.3 59.3 + - - +
473A ILE 3.7 0.3 - - - -
474A ARG* 2.8 60.3 + - - +
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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
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378A GLN* 3.0 21.4 + - - -
467A GLU 2.9 11.1 + - - -
468A HIS 3.5 8.1 - - - -
470A VAL* 1.3 76.0 - - - +
472A VAL* 1.3 65.8 + - - +
474A ARG* 3.7 8.9 - - - +
475A GLN* 2.8 50.7 + - - +
513A PRO* 3.5 19.3 - - - +
514A ARG* 5.8 0.7 - - - -
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Residues in contact with VAL 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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410A TYR* 3.7 14.1 - - - +
415A ASP* 4.1 24.0 - - + +
416A ALA 4.5 0.2 - - - +
419A ALA* 4.3 14.8 - - + -
468A HIS* 2.9 43.5 + - + +
469A TRP* 3.2 15.2 + - + +
471A SER* 1.3 76.2 - - - +
473A ILE* 1.3 64.9 + - - +
475A GLN* 3.3 9.8 + - - +
476A LEU* 3.0 29.4 + - + +
510A LEU* 4.2 16.8 - - + +
513A PRO* 4.6 4.0 - - + -
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Residues in contact with ILE 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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419A ALA* 4.0 20.6 - - + -
423A ILE* 4.8 7.6 - - + -
432A MSE 3.6 32.8 - - + -
435A VAL* 3.9 28.7 - - + -
436A VAL* 3.9 10.8 - - + -
439A ILE* 4.3 9.9 - - + -
469A TRP* 2.9 20.3 + - + +
472A VAL* 1.3 74.6 - - + +
474A ARG* 1.3 65.0 + - - +
476A LEU* 3.1 9.3 + - + +
477A ILE* 2.9 24.6 + - + +
482A VAL* 4.8 2.0 - - + -
492A LEU* 3.8 25.6 - - + -
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Residues in contact with ARG 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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373A ALA* 3.5 29.3 - - + +
376A GLU* 3.9 37.6 + - - +
377A ALA* 5.0 1.6 - - - +
378A GLN 5.8 0.7 - - - +
432A MSE 4.0 7.3 - - + +
470A VAL* 2.8 44.4 + - - +
471A SER* 3.7 8.4 - - - +
473A ILE* 1.3 72.4 - - - +
475A GLN* 1.3 58.8 + - + +
477A ILE* 3.2 14.4 + - + +
478A HIS* 2.8 64.0 + - + +
514A ARG* 6.0 1.4 - - - +
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Residues in contact with GLN 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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378A GLN* 4.4 9.6 - - + +
379A THR* 3.7 22.9 + - - +
471A SER* 2.8 44.5 + - - +
472A VAL* 3.6 7.4 - - - +
474A ARG* 1.3 74.4 - - + +
476A LEU* 1.3 58.4 + - - +
478A HIS* 3.2 2.3 + - + +
479A LEU* 2.9 39.5 + - + +
510A LEU* 3.5 25.0 - - + +
511A ALA* 2.8 55.4 + - - +
513A PRO* 4.6 1.0 - - - +
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Residues in contact with LEU 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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416A ALA* 4.1 10.8 - - + -
419A ALA* 4.0 27.6 - - + -
420A LEU* 4.0 21.1 - - + -
472A VAL* 3.0 25.2 + - + +
473A ILE* 3.5 11.2 - - + +
475A GLN* 1.3 77.3 - - - +
477A ILE* 1.3 58.7 + - - +
479A LEU* 3.5 4.3 + - + -
480A GLY 3.3 2.9 + - - -
481A LEU* 2.9 47.5 + - + +
482A VAL* 3.3 17.7 + - + -
508A LEU* 3.8 29.6 - - + -
510A LEU* 5.0 3.6 - - + -
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Residues in contact with ILE 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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387A ASN* 3.8 8.5 - - - +
432A MSE 4.4 5.4 - - + -
473A ILE* 2.9 23.5 + - + +
474A ARG* 3.5 14.4 - - + +
476A LEU* 1.3 76.9 - - - +
478A HIS* 1.3 73.3 + - + +
480A GLY* 3.1 14.9 + - - -
482A VAL* 3.3 35.3 - - + +
483A THR* 5.2 2.0 - - - -
484A GLN* 3.6 44.6 - - + +
492A LEU* 3.9 12.1 - - + -
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Residues in contact with HIS 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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370A ALA 5.3 1.1 - - - -
373A ALA* 3.3 29.9 + - + -
374A PHE 4.5 0.2 - - - -
377A ALA* 3.9 11.7 - - + -
378A GLN 5.0 0.7 - - - -
379A THR* 3.8 19.5 - - - +
383A LEU* 3.4 17.3 - - - +
384A VAL* 3.4 49.7 + - + +
387A ASN* 2.9 17.5 + - - -
474A ARG* 2.8 44.7 + - + +
475A GLN* 3.2 5.1 + - + +
477A ILE* 1.3 86.1 - - + +
479A LEU* 1.3 56.9 + - - +
480A GLY 3.4 0.2 - - - -
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Residues in contact with LEU 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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379A THR* 3.9 21.1 - - + +
383A LEU* 3.9 17.0 - - + -
387A ASN* 3.4 8.3 - - - +
393A ARG 3.4 2.1 - - - +
394A GLN* 2.8 45.5 + - + +
475A GLN* 2.9 23.5 + - + +
476A LEU* 4.0 4.0 - - + +
477A ILE 3.2 0.4 - - - -
478A HIS* 1.3 74.8 - - - +
480A GLY* 1.3 59.4 + - - +
481A LEU* 3.6 14.4 - - + +
508A LEU* 4.4 20.0 - - + -
509A GLN 5.1 2.7 - - - +
510A LEU* 4.0 25.1 - - + -
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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