Contacts of the helix formed by residues 506 - 518 (chain C) in PDB entry 1OVM
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 506 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358C GLY* 3.5 5.0 - - - -
359C SER* 3.0 29.8 + - - -
360C LEU* 3.8 3.8 - - - -
504C VAL* 3.4 1.9 - - - +
505C SER* 1.3 101.1 + - - +
507C ALA* 1.3 65.7 + - - +
508C GLU* 3.2 18.8 - - - +
509C GLN* 2.8 41.6 + - + +
510C LEU* 3.1 10.2 + - - +
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Residues in contact with ALA 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C PRO* 4.1 22.4 - - + +
357C ASP 3.5 15.7 - - - +
358C GLY 2.9 23.1 + - - +
360C LEU* 4.0 14.2 - - - +
364C ASN* 4.6 12.1 - - + +
368C THR* 4.6 7.4 + - - +
506C GLU* 1.3 71.3 - - - +
508C GLU* 1.3 58.4 + - - +
510C LEU* 3.5 3.3 + - - +
511C ALA* 3.1 27.6 + - - +
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Residues in contact with GLU 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C PRO 5.5 1.6 - - - +
357C ASP* 2.5 31.3 - - - +
358C GLY* 4.1 2.1 - - - +
506C GLU* 3.2 29.1 - - - +
507C ALA* 1.3 71.4 + - - +
509C GLN* 1.3 66.3 + - - +
511C ALA* 3.8 7.0 - - - +
512C ASP* 3.0 37.1 + - - +
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Residues in contact with GLN 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503C ARG 4.7 2.8 + - - +
504C VAL* 3.2 19.4 - - + +
505C SER* 3.0 30.9 + - - -
506C GLU* 2.8 28.2 + - + +
508C GLU* 1.3 78.9 - - - +
510C LEU* 1.3 67.7 + - - +
512C ASP* 3.0 8.0 + - - +
513C VAL* 2.9 27.4 + - + +
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Residues in contact with LEU 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C LEU* 4.4 12.8 - - + -
365C PHE* 4.5 20.9 - - + +
368C THR* 3.0 41.3 - - + +
369C LEU* 4.9 0.9 - - + +
458C LEU* 4.6 6.1 - - + -
504C VAL* 3.1 21.2 - - + +
506C GLU 3.1 2.8 + - - +
507C ALA 3.7 6.3 - - - +
509C GLN* 1.3 78.6 - - - +
511C ALA* 1.3 62.4 + - - +
512C ASP 3.0 0.5 + - - -
513C VAL* 3.1 2.8 + - + +
514C LEU* 3.0 48.6 + - + +
526C ILE* 4.3 24.9 - - + -
528C VAL* 4.5 10.5 - - + -
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Residues in contact with ALA 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C THR* 4.0 20.4 - - + +
507C ALA 3.1 15.3 + - - +
508C GLU* 3.9 8.1 - - - +
510C LEU* 1.3 80.1 - - - +
512C ASP* 1.3 54.3 + - - +
514C LEU* 4.0 4.8 - - - +
515C GLU* 2.6 40.0 + - - +
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Residues in contact with ASP 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508C GLU* 3.0 23.1 + - - +
509C GLN* 3.0 9.3 + - - +
511C ALA* 1.3 80.8 - - - +
513C VAL* 1.3 65.7 + - + +
515C GLU* 3.2 11.6 - - - +
516C LYS* 3.1 35.6 + - - +
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Residues in contact with VAL 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502C TRP* 3.5 53.4 - - + +
504C VAL* 3.5 23.6 - - + -
509C GLN* 2.9 16.5 + - + +
510C LEU* 3.7 4.3 - - - +
512C ASP* 1.3 74.9 - - + +
514C LEU* 1.3 69.5 + - - +
516C LYS* 2.7 23.4 + - - +
517C VAL* 2.8 14.3 + - + +
526C ILE* 3.8 22.9 - - + -
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Residues in contact with LEU 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C THR* 3.6 17.7 - - + +
369C LEU* 4.6 4.0 - - + -
371C THR* 5.9 0.2 - - - +
372C PHE* 3.6 53.6 - - + -
456C ILE* 4.9 1.3 - - + -
458C LEU* 4.6 11.2 - - + -
510C LEU* 3.0 47.8 + - + +
511C ALA* 4.0 5.6 - - - +
513C VAL* 1.3 77.1 - - - +
515C GLU* 1.3 66.9 + - - +
517C VAL* 3.1 7.2 + - + +
518C ALA* 2.8 25.8 + - - +
526C ILE* 4.2 19.3 - - + -
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Residues in contact with GLU 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C PHE* 5.4 3.1 - - - -
511C ALA* 2.6 28.7 - - - +
512C ASP* 3.2 15.7 - - - +
514C LEU* 1.3 83.1 - - - +
516C LYS* 1.3 63.5 + - + +
518C ALA* 3.6 16.6 + - - +
519C HIS* 5.1 3.6 + - - -
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Residues in contact with LYS 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502C TRP* 4.1 33.7 - - + +
512C ASP* 3.1 26.5 + - - +
513C VAL* 2.7 17.0 + - - +
515C GLU* 1.3 74.6 - - + +
517C VAL* 1.3 62.9 + - + +
518C ALA 3.6 0.7 + - - -
519C HIS* 4.8 2.8 + - - -
521C GLU* 4.6 9.5 - - - +
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Residues in contact with VAL 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C PHE* 4.5 7.2 - - + -
456C ILE* 4.2 25.1 - - + +
502C TRP* 3.4 40.6 - - + -
513C VAL* 2.8 19.3 + - + +
514C LEU* 3.5 17.3 - - - +
516C LYS* 1.3 72.1 - - - +
518C ALA* 1.3 63.3 + - - +
519C HIS 3.0 5.5 + - - -
520C HIS* 3.0 18.1 + - - +
521C GLU* 5.8 0.9 - - - -
524C SER* 3.7 25.4 - - - +
526C ILE* 4.4 3.1 - - + -
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Residues in contact with ALA 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C PHE* 3.9 11.0 - - + -
428C ARG* 2.9 36.0 + - - +
514C LEU 2.8 14.1 + - - +
515C GLU* 3.6 14.8 - - - +
516C LYS 3.4 2.2 + - - -
517C VAL* 1.3 76.7 - - - +
519C HIS* 1.3 73.1 + - + +
520C HIS* 3.5 0.6 + - - -
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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