Contacts of the helix formed by residues 492 - 509 (chain A) in PDB entry 3OEE
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 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A GLU* 5.3 1.0 + - - -
488A LYS* 5.7 2.9 + - - +
490A GLU* 5.2 2.9 + - - +
491A LEU* 1.3 76.9 - - - +
493A LYS* 1.3 57.7 + - - +
494A GLU* 3.0 21.8 - - - -
495A LEU* 3.0 22.2 + - - +
496A LEU* 2.7 34.0 + - - +
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Residues in contact with LYS 493 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A SER* 1.3 76.2 - - - +
494A GLU* 1.3 64.1 + - - +
496A LEU* 3.8 14.2 - - + +
497A ALA* 3.0 30.1 + - - +
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Residues in contact with GLU 494 (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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492A SER* 3.4 19.5 - - - -
493A LYS* 1.3 82.4 + - - +
495A LEU* 1.3 59.9 + - - +
497A ALA* 3.5 4.9 + - - +
498A SER* 2.9 33.3 + - - -
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Residues in contact with LEU 495 (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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481A LEU* 4.0 12.2 - - + +
484A GLU* 3.3 55.2 - - + +
485A ILE* 3.8 25.6 - - + +
488A LYS* 5.1 2.9 - - + -
490A GLU 3.7 12.8 - - - +
491A LEU* 3.8 13.2 - - + -
492A SER* 3.0 36.8 + - - +
494A GLU* 1.3 79.4 - - + +
496A LEU* 1.3 52.3 + - - +
498A SER* 3.2 7.3 + - - -
499A LEU* 2.7 35.6 + - - +
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Residues in contact with LEU 496 (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 GLN* 4.9 12.6 - - + +
388A VAL* 4.9 3.4 - - + -
448A TYR* 3.9 27.8 + - + +
491A LEU* 3.7 34.1 - - + +
492A SER 2.7 22.0 + - - +
493A LYS* 3.8 14.4 - - + +
495A LEU* 1.3 70.9 - - - +
497A ALA* 1.3 53.5 + - - +
499A LEU* 3.1 6.9 + - + +
500A LYS* 2.8 35.0 + - - +
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Residues in contact with ALA 497 (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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493A LYS 3.0 20.2 + - - +
494A GLU* 3.8 5.8 - - - +
496A LEU* 1.3 75.3 - - - +
498A SER* 1.3 62.7 + - - +
500A LYS* 3.2 11.2 + - - +
501A SER* 3.0 24.3 + - - -
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Residues in contact with SER 498 (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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481A LEU* 3.7 29.0 - - - +
494A GLU 2.9 19.4 + - - -
495A LEU* 3.4 8.5 - - - -
497A ALA* 1.3 76.1 - - - +
499A LEU* 1.3 62.7 + - - +
501A SER* 3.4 5.0 + - - -
502A ALA* 3.0 26.2 + - - +
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Residues in contact with LEU 499 (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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444A VAL* 4.5 4.7 - - + -
445A PRO* 3.9 29.8 - - + -
448A TYR* 3.5 42.6 - - + -
470A PHE* 5.3 0.4 - - + -
474A LEU* 5.2 7.9 - - + -
481A LEU* 4.2 19.7 - - + +
482A LEU* 6.4 0.4 - - + -
485A ILE* 5.0 9.4 - - + -
491A LEU* 4.4 19.7 - - + -
495A LEU 2.7 15.6 + - - +
496A LEU* 3.3 9.9 - - + +
498A SER* 1.3 71.5 - - - +
500A LYS* 1.3 60.2 + - - +
502A ALA* 3.9 0.4 - - + -
503A THR* 2.6 38.5 + - - +
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Residues in contact with LYS 500 (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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448A TYR* 3.2 27.5 + - - +
454A HIS* 4.4 7.6 + - + -
496A LEU 2.8 13.4 + - - +
497A ALA* 3.2 13.2 + - - +
499A LEU* 1.3 74.6 - - - +
501A SER* 1.3 61.4 + - - +
503A THR* 3.2 2.5 + - - -
504A GLU* 2.8 63.9 + - - +
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Residues in contact with SER 501 (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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478A HIS* 6.0 0.7 - - - -
497A ALA 3.0 16.3 + - - -
498A SER* 3.7 5.6 - - - -
500A LYS* 1.3 77.3 - - - +
502A ALA* 1.3 65.2 + - - +
503A THR 3.0 0.5 + - - -
504A GLU* 3.3 7.2 + - - +
505A SER* 2.9 27.5 + - - -
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Residues in contact with ALA 502 (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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470A PHE* 4.2 2.2 - - - -
473A TYR* 3.6 12.1 - - - -
474A LEU* 4.3 6.5 - - + -
478A HIS* 3.5 37.0 - - + +
481A LEU* 3.9 14.4 - - + -
498A SER 3.0 15.5 + - - +
499A LEU* 4.0 2.7 - - + +
501A SER* 1.3 80.5 + - - +
503A THR* 1.3 64.0 + - - +
505A SER* 3.3 8.8 - - - -
506A PHE* 3.2 13.9 + - - +
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Residues in contact with THR 503 (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 5.3 0.2 + - - -
448A TYR* 4.0 11.6 - - - -
449A ALA* 3.9 18.3 - - + +
454A HIS* 3.6 37.7 - - + +
466A PHE* 5.2 0.7 - - + -
470A PHE* 3.9 23.0 - - + -
499A LEU* 2.6 25.7 + - - +
500A LYS 3.5 4.7 - - - -
501A SER 3.1 0.2 - - - -
502A ALA* 1.3 72.8 - - - +
504A GLU* 1.3 54.5 + - - +
506A PHE* 2.7 25.3 + - - +
507A VAL* 2.8 22.1 + - + +
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Residues in contact with GLU 504 (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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454A HIS* 3.0 28.7 + - + +
500A LYS* 2.8 52.8 + - - +
501A SER* 3.9 5.5 - - - +
503A THR* 1.3 72.7 - - - +
505A SER* 1.3 63.8 + - - +
507A VAL* 3.1 5.5 + - - +
508A ALA* 2.8 30.1 + - - +
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Residues in contact with SER 505 (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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473A TYR* 3.4 17.3 + - - -
478A HIS* 5.5 0.4 - - - -
501A SER* 2.9 21.4 + - - -
502A ALA* 3.3 11.4 - - - -
504A GLU* 1.3 79.0 - - - +
506A PHE* 1.3 60.6 + - - -
508A ALA* 3.8 4.7 - - - +
509A THR* 3.2 21.4 + - - -
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Residues in contact with PHE 506 (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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466A PHE* 3.8 29.6 - + - -
469A SER* 3.5 17.7 - - - -
470A PHE* 3.4 47.8 - + + -
473A TYR* 3.4 51.8 + + + -
502A ALA 3.2 2.4 + - - +
503A THR 2.7 13.6 + - - +
505A SER* 1.3 74.8 - - - +
507A VAL* 1.3 65.1 + - - +
509A THR* 3.0 45.2 + - + +
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Residues in contact with VAL 507 (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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454A HIS* 3.4 43.1 - - + +
458A ILE* 4.4 12.7 - - + +
466A PHE* 3.8 26.9 - - + -
503A THR* 2.8 23.3 + - + +
504A GLU* 3.8 7.2 - - - +
506A PHE* 1.3 73.7 - - - +
508A ALA* 1.3 64.6 - - - +
509A THR 4.0 2.9 - - - -
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Residues in contact with ALA 508 (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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504A GLU 2.8 20.2 + - - +
505A SER* 3.8 5.4 - - - +
507A VAL* 1.3 75.5 - - - +
509A THR* 1.3 60.9 + - - +
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Residues in contact with THR 509 (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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473A TYR* 5.3 7.0 - - + -
505A SER 3.2 10.1 + - - +
506A PHE* 3.0 49.3 + - + +
507A VAL 4.0 2.9 - - - -
508A ALA* 1.3 83.8 - - - +
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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