Contacts of the helix formed by residues 485 - 501 (chain A) in PDB entry 1ONV
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 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A GLY 4.2 0.8 + - - -
484A LEU* 1.3 72.2 - - - +
486A SER* 1.3 60.4 + - - +
487A GLU* 3.8 8.8 + - - +
488A GLN* 2.9 36.9 + - - +
489A THR* 2.6 37.2 + - - -
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Residues in contact with SER 486 (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 GLN 5.5 0.2 - - - -
479A THR* 5.4 5.8 - - - +
484A LEU 3.7 1.4 + - - -
485A SER* 1.3 75.0 + - - +
487A GLU* 1.3 58.6 + - - +
489A THR 3.6 0.2 + - - -
490A VAL* 3.0 32.9 + - - +
949B MET* 3.4 38.8 - - - +
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Residues in contact with GLU 487 (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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485A SER* 3.2 8.5 + - - +
486A SER* 1.3 75.5 - - - +
488A GLN* 1.3 62.6 + - + +
490A VAL* 3.4 5.4 + - - +
491A ASN* 2.8 35.7 + - + +
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Residues in contact with GLN 488 (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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484A LEU* 4.7 18.4 - - + +
485A SER* 2.9 41.7 + - - +
487A GLU* 1.3 78.1 - - + +
489A THR* 1.3 63.8 + - - +
491A ASN* 3.6 5.3 - - - +
492A VAL* 2.8 36.5 + - + +
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Residues in contact with THR 489 (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 VAL* 6.3 0.9 - - + -
474A LEU* 4.8 9.1 - - + +
477A PHE* 3.1 36.6 + - + +
478A GLN* 4.4 8.2 + - - -
482A THR* 5.3 1.1 + - - +
484A LEU* 3.4 22.2 + - + +
485A SER 2.6 26.8 + - - -
486A SER* 3.8 5.9 - - - -
488A GLN* 1.3 73.0 - - - +
490A VAL* 1.3 62.2 + - - +
492A VAL* 4.6 2.9 - - - -
493A LEU* 3.3 38.6 + - + +
949B MET* 4.3 7.0 - - + -
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Residues in contact with VAL 490 (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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474A LEU* 3.6 17.0 - - + -
486A SER 3.0 19.9 + - - +
487A GLU* 3.9 4.7 - - - +
488A GLN 3.3 0.2 - - - -
489A THR* 1.3 73.7 - - - +
491A ASN* 1.3 55.8 + - - +
493A LEU* 3.6 3.1 - - - -
494A ALA* 2.6 45.1 + - + +
949B MET* 3.3 25.4 - - + +
952B ALA* 3.7 14.6 - - + -
953B LEU* 3.6 38.5 - - + +
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Residues in contact with ASN 491 (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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487A GLU* 2.8 23.5 + - + +
488A GLN* 3.3 8.5 + - - +
490A VAL* 1.3 77.4 - - - +
492A VAL* 1.3 64.9 + - - +
494A ALA* 3.6 5.4 - - - +
495A GLN* 3.0 59.8 + - - +
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Residues in contact with VAL 492 (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 VAL* 4.8 18.2 - - + +
484A LEU* 6.2 4.7 - - + -
488A GLN* 2.8 29.5 + - + +
489A THR* 3.9 5.8 - - - +
491A ASN* 1.3 83.1 - - + +
493A LEU* 1.3 71.0 + - + +
495A GLN* 3.5 9.7 + - - +
496A ILE* 3.3 27.8 + - + +
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Residues in contact with LEU 493 (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 VAL* 3.5 32.5 - - + -
459A VAL* 3.4 33.7 - - + -
473A LEU* 5.7 10.1 - - + +
474A LEU* 5.9 7.0 - - + -
477A PHE* 5.9 6.3 - - + -
489A THR* 3.3 28.5 + - + +
490A VAL* 4.1 1.1 - - - +
492A VAL* 1.3 80.9 - - + +
494A ALA* 1.3 55.8 + - - +
496A ILE* 3.9 6.5 - - + +
497A LEU* 2.6 51.3 + - + +
953B LEU* 3.6 17.5 - - + -
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Residues in contact with ALA 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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490A VAL* 2.6 30.7 + - + +
491A ASN* 3.6 8.3 - - - +
493A LEU* 1.3 71.5 - - - +
495A GLN* 1.3 55.2 + - + +
498A LYS* 2.6 42.9 + - - +
953B LEU* 3.5 13.2 - - + -
956B GLU* 3.8 26.0 - - + +
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Residues in contact with GLN 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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491A ASN* 3.0 46.6 + - - +
492A VAL* 3.8 8.2 - - - +
493A LEU 3.4 0.2 - - - -
494A ALA* 1.3 77.8 - - + +
496A ILE* 1.3 62.0 + - + +
498A LYS* 4.3 3.3 - - - +
499A ARG* 3.3 35.5 + - - +
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Residues in contact with ILE 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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454A VAL* 5.2 4.7 - - + +
455A THR* 3.8 7.2 - - - -
456A GLU* 3.1 67.4 - - + +
459A VAL* 4.6 11.9 - - + -
492A VAL* 3.3 19.5 + - + +
493A LEU* 4.0 7.2 - - + +
494A ALA 3.2 0.2 - - - -
495A GLN* 1.3 78.4 - - + +
497A LEU* 1.3 76.1 + - + +
499A ARG* 3.4 7.2 + - - +
500A LEU* 3.2 18.2 + - + +
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Residues in contact with LEU 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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459A VAL* 3.6 28.9 - - + -
463A LEU* 4.9 1.1 - - + -
473A LEU* 4.2 17.0 - - + -
493A LEU* 2.6 34.5 + - + +
494A ALA 4.2 0.4 - - - +
496A ILE* 1.3 76.6 - - + +
498A LYS* 1.3 52.7 + - - +
500A LEU* 2.6 46.5 + - + +
513A PHE* 6.3 0.7 - - + -
953B LEU* 3.3 46.0 - - + +
957B LEU* 2.6 39.6 - - + +
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Residues in contact with LYS 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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494A ALA* 2.6 26.6 + - - +
495A GLN* 4.3 4.3 - - - +
497A LEU* 1.3 72.5 - - - +
499A ARG* 1.3 59.3 + - + +
956B GLU* 2.7 55.1 + - + +
957B LEU* 3.6 9.5 - - - +
959B ASP* 3.1 37.4 + - - +
960B LEU* 2.6 35.1 - - - +
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Residues in contact with ARG 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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456A GLU* 5.6 2.5 - - - +
495A GLN* 3.3 24.2 + - - +
496A ILE* 3.4 5.7 + - - +
497A LEU 3.1 0.6 - - - -
498A LYS* 1.3 79.7 - - + +
500A LEU* 1.3 54.0 + - - +
501A ASN* 2.6 30.2 + - - +
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Residues in contact with LEU 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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456A GLU* 4.3 11.4 - - + +
459A VAL* 5.6 0.2 - - + -
460A ARG* 3.7 39.0 - - + +
463A LEU* 3.6 24.7 - - + -
496A ILE* 3.2 7.7 + - + +
497A LEU* 2.6 45.1 + - + +
499A ARG* 1.3 65.8 - - - +
501A ASN* 1.3 81.2 + - - +
502A PRO* 3.1 33.6 - - + +
515A LEU* 3.8 12.4 - - + +
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Residues in contact with ASN 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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499A ARG 2.6 26.3 + - - +
500A LEU* 1.3 83.2 + - - +
502A PRO* 1.3 73.6 - - - +
503A GLU* 4.6 4.9 - - - +
960B LEU* 3.2 35.8 - - + +
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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