Contacts of the helix formed by residues 411 - 424 (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 GLY 411 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C TYR* 4.0 1.3 - - - -
382C ASP* 2.9 12.3 + - - -
410C ILE* 1.3 74.9 - - - +
412C TYR* 1.3 64.9 + - - +
413C THR 3.4 3.0 + - - -
414C LEU* 3.5 6.2 + - - -
415C ALA 3.8 0.9 + - - -
437C ALA* 3.4 23.7 + - - +
438C ALA* 5.4 0.2 - - - -
440C LEU* 4.3 1.3 - - - -
441C THR* 2.8 40.5 + - - +
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Residues in contact with TYR 412 (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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57C TYR* 3.4 37.5 - + + -
60C ASP* 2.7 44.4 + - + +
61C GLY* 4.1 2.3 + - - -
64C ARG* 3.2 15.4 + - - -
382C ASP* 3.4 0.6 + - - +
402C ILE* 3.8 19.2 - - + +
403C VAL 5.1 0.4 - - - -
404C GLN* 3.6 42.0 - - + +
409C SER 3.1 19.0 + - - +
410C ILE 3.2 2.8 + - - -
411C GLY* 1.3 77.4 - - - +
413C THR* 1.3 73.3 + - + +
415C ALA* 3.3 5.0 + - - +
416C ALA* 2.8 48.3 + - + +
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Residues in contact with THR 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C LEU* 3.8 17.1 - - + +
381C ALA* 3.3 11.4 - - - +
382C ASP* 3.0 55.1 + - - +
402C ILE 5.3 1.3 - - - +
403C VAL* 6.0 0.2 - - - -
404C GLN 6.1 0.4 - - - +
412C TYR* 1.3 89.3 - - + +
414C LEU* 1.3 68.6 + - - +
416C ALA* 4.0 3.4 - - - -
417C ALA* 2.9 24.3 + - - +
431C VAL* 4.2 4.9 - - - +
432C LEU 4.1 1.7 + - - -
433C THR* 3.9 13.7 - - - -
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Residues in contact with LEU 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C ASP* 4.5 0.4 + - - -
411C GLY* 3.5 2.9 + - - +
412C TYR 3.4 1.0 - - - -
413C THR* 1.3 83.3 + - - +
415C ALA* 1.3 62.1 + - - +
417C ALA* 3.3 13.5 - - - +
418C PHE* 3.4 5.5 + - - +
431C VAL* 4.4 14.4 - - + -
433C THR* 5.2 6.3 - - + +
438C ALA* 4.0 21.5 - - + +
441C THR* 3.4 35.0 - - - +
442C ILE* 3.9 26.7 - - + +
444C GLU* 5.1 2.8 - - + +
445C LEU* 4.9 9.0 - - + +
448C MET* 3.7 15.2 - - + +
457C ILE* 4.3 28.7 - - + -
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Residues in contact with ALA 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASN* 3.7 27.1 - - + +
57C TYR* 3.4 33.0 - - + -
58C ALA* 3.4 8.7 - - - +
411C GLY 3.8 3.4 + - - +
412C TYR 3.3 1.4 + - - -
414C LEU* 1.3 75.3 - - - +
416C ALA* 1.3 67.9 + - - +
417C ALA 3.1 1.3 - - - -
418C PHE* 3.0 14.6 + - - +
419C GLY 3.2 8.0 + - - -
441C THR* 4.0 2.9 + - - -
444C GLU* 4.3 13.5 - - + -
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Residues in contact with ALA 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TYR 3.5 16.7 + - - +
58C ALA* 4.2 0.2 - - - +
61C GLY* 3.8 9.2 - - - -
380C LEU* 3.8 11.7 - - + -
412C TYR* 2.8 52.7 + - + +
413C THR 3.8 4.7 - - - +
415C ALA* 1.3 77.0 - - - +
417C ALA* 1.3 57.7 + - - +
419C GLY* 3.0 4.3 + - - -
420C ALA* 2.8 27.2 + - - +
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Residues in contact with ALA 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C LEU* 3.5 18.2 - - + -
413C THR 2.9 19.2 + - - +
414C LEU 3.3 8.3 - - - +
416C ALA* 1.3 74.6 - - - +
418C PHE* 1.3 66.9 + - - +
420C ALA* 3.1 3.8 + - - +
421C GLN* 2.8 27.4 + - - +
429C VAL* 4.4 2.8 - - + +
431C VAL* 3.5 30.5 - - + -
448C MET* 3.8 8.7 - - + -
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Residues in contact with PHE 418 (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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24C PHE* 4.2 6.5 - + - -
47C VAL* 3.7 26.7 - - + -
49C CYS* 4.2 7.6 - - - -
58C ALA* 4.0 14.1 - - + -
414C LEU 3.4 5.3 + - - +
415C ALA 3.0 11.7 + - - +
417C ALA* 1.3 78.2 - - - +
419C GLY* 1.3 59.3 + - - +
422C THR* 3.0 35.2 + - - -
444C GLU* 4.0 29.2 - - + -
447C SER* 3.6 24.5 - - - -
448C MET* 3.7 20.5 - - + +
450C ARG* 4.0 2.0 - - - -
451C ASP* 3.3 26.9 - - - -
453C GLN* 3.3 35.0 + - - -
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Residues in contact with GLY 419 (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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24C PHE* 4.0 9.9 - - - -
58C ALA* 3.3 30.7 - - - +
62C TYR* 3.6 15.9 - - - -
415C ALA 3.2 4.4 + - - -
416C ALA 3.0 5.1 + - - -
418C PHE* 1.3 81.2 - - - +
420C ALA* 1.3 60.1 + - - +
422C THR* 3.3 4.3 + - - -
423C ALA* 3.0 17.7 + - - +
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Residues in contact with ALA 420 (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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61C GLY 4.4 4.7 - - - +
62C TYR 4.2 0.8 - - - +
65C CYS* 3.9 25.6 - - - -
378C ILE* 4.1 21.8 - - + -
380C LEU* 4.7 6.1 - - + -
402C ILE* 4.7 1.6 - - + -
416C ALA 2.8 12.7 + - - +
417C ALA* 3.1 11.9 + - - +
419C GLY* 1.3 74.1 - - - +
421C GLN* 1.3 60.9 + - - +
423C ALA* 3.0 4.6 + - - +
424C CYS* 2.8 32.0 + - - +
429C VAL* 4.8 3.1 - - + -
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Residues in contact with GLN 421 (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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417C ALA 2.8 17.1 + - - +
420C ALA* 1.3 72.0 - - - +
422C THR* 1.3 62.3 + - - +
424C CYS 3.2 17.7 - - - +
425C PRO* 3.2 34.7 + - - +
427C ARG 3.6 8.3 + - - +
428C ARG* 5.4 0.2 - - - +
429C VAL* 3.3 34.2 - - + +
448C MET* 5.6 0.2 - - + -
453C GLN* 3.1 39.3 - - + +
454C HIS* 3.7 11.3 + - - +
455C PRO* 3.6 31.8 - - + +
520C HIS* 5.7 2.2 - - - -
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Residues in contact with THR 422 (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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22C HIS* 3.5 47.7 + - + +
24C PHE* 3.9 24.9 - - + -
47C VAL* 4.4 5.7 - - + +
62C TYR* 4.0 1.1 - - + -
418C PHE* 3.0 24.9 + - - -
419C GLY 3.4 9.0 - - - -
421C GLN* 1.3 77.0 - - - +
423C ALA* 1.3 61.4 + - - +
425C PRO* 3.8 12.0 - - - +
451C ASP* 5.2 0.9 + - - -
453C GLN* 3.4 11.6 + - - +
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Residues in contact with ALA 423 (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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22C HIS* 5.2 1.1 - - - -
62C TYR* 3.6 27.8 - - + -
65C CYS* 3.9 15.9 - - + -
66C LYS* 3.7 34.7 + - + +
419C GLY 3.0 7.1 + - - +
420C ALA 3.0 7.9 + - - +
422C THR* 1.3 79.1 - - - +
424C CYS* 1.3 62.0 + - - +
425C PRO* 3.5 6.9 - - - +
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Residues in contact with CYS 424 (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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65C CYS* 3.9 22.9 - - - -
66C LYS* 5.7 0.9 - - - -
378C ILE* 3.7 28.3 - - + -
420C ALA 2.8 13.5 + - - +
421C GLN* 3.2 17.1 - - - +
423C ALA* 1.3 82.0 - - - +
425C PRO* 1.3 66.2 - - - +
426C ASN 3.2 3.1 + - - -
427C ARG* 3.2 36.2 + - + +
429C VAL* 4.9 0.3 - - - +
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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