Contacts of the helix formed by residues 411 - 424 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B TYR* 4.0 0.6 - - - -
382B ASP* 3.0 13.1 + - - -
410B ILE* 1.3 73.4 - - - +
412B TYR* 1.3 65.2 + - - +
413B THR 3.3 2.5 + - - -
414B LEU* 3.5 6.1 + - - -
415B ALA 3.8 1.2 + - - -
437B ALA* 3.3 24.8 - - - +
440B LEU* 4.3 1.6 - - - -
441B THR* 2.8 40.2 + - - +
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Residues in contact with TYR 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TYR* 3.4 37.9 - + + +
60B ASP* 2.7 42.0 + - + +
61B GLY 4.0 2.1 + - - -
64B ARG* 3.2 16.9 + - - -
382B ASP* 4.6 0.7 - - - +
402B ILE* 4.0 15.5 - - + +
404B GLN* 3.5 46.4 - - + +
409B SER 3.1 19.0 + - - +
410B ILE 3.2 3.2 + - - -
411B GLY* 1.3 79.3 - - - +
413B THR* 1.3 73.8 + - + +
415B ALA* 3.3 3.1 + - - +
416B ALA* 2.8 52.1 + - + +
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Residues in contact with THR 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LEU* 3.9 16.3 - - + +
381B ALA 3.4 10.5 - - - +
382B ASP* 3.1 56.3 + - - +
402B ILE 5.3 1.1 - - - +
403B VAL* 6.0 0.4 - - - -
404B GLN* 6.0 0.9 - - + +
412B TYR* 1.3 90.0 - - + +
414B LEU* 1.3 62.7 + - - +
416B ALA* 3.7 3.7 - - - +
417B ALA* 2.8 31.2 + - - +
431B VAL* 4.2 5.2 - - - +
432B LEU 4.0 2.1 + - - -
433B THR* 3.9 13.0 - - - -
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ASP* 4.4 0.4 + - - -
411B GLY 3.5 3.1 + - - +
412B TYR 3.4 1.2 - - - -
413B THR* 1.3 83.4 + - - +
415B ALA* 1.3 62.1 + - - +
417B ALA* 3.4 13.5 - - - +
418B PHE* 3.4 5.2 + - - +
431B VAL* 4.4 16.6 - - + -
433B THR* 5.1 8.0 + - + +
438B ALA* 4.0 19.5 - - + +
441B THR* 3.5 35.4 - - - +
442B ILE* 3.8 27.4 - - + +
444B GLU* 5.1 2.0 - - + +
445B LEU* 4.8 10.8 - - + +
448B MET* 3.7 26.1 - - + +
457B ILE* 4.6 17.9 - - + -
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Residues in contact with ALA 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ASN* 3.7 25.8 - - + +
57B TYR* 3.4 33.7 - - + -
58B ALA* 3.3 9.9 - - - +
411B GLY 3.8 2.6 + - - +
412B TYR 3.3 1.4 + - - -
413B THR 3.3 0.4 - - - -
414B LEU* 1.3 77.1 - - - +
416B ALA* 1.3 66.7 + - - +
418B PHE* 3.1 13.9 + - - +
419B GLY 3.2 8.1 + - - -
441B THR* 4.2 3.3 + - - -
444B GLU* 4.3 13.7 - - + -
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Residues in contact with ALA 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TYR* 3.6 15.8 - - - +
58B ALA* 4.2 0.2 - - - +
61B GLY* 3.8 9.6 - - - -
380B LEU* 3.8 11.9 - - + -
412B TYR* 2.8 52.5 + - + +
413B THR* 3.7 4.5 - - - +
415B ALA* 1.3 76.9 - - - +
417B ALA* 1.3 57.4 + - - +
419B GLY* 2.9 4.5 + - - -
420B ALA* 2.9 26.7 + - - +
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Residues in contact with ALA 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LEU* 3.5 19.0 - - + +
413B THR 2.8 17.5 + - - +
414B LEU 3.4 7.6 - - - +
415B ALA 3.1 0.2 - - - -
416B ALA* 1.3 74.8 - - - +
418B PHE* 1.3 67.1 + - - +
420B ALA* 3.1 2.8 + - - +
421B GLN* 2.8 27.2 + - - +
429B VAL* 4.3 3.2 - - + +
431B VAL* 3.5 31.0 - - + -
448B MET* 3.8 8.1 - - + -
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Residues in contact with PHE 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 4.2 7.9 - + - -
47B VAL* 3.7 24.7 - - + -
49B CYS* 4.2 7.0 - - - -
58B ALA* 4.1 13.9 - - + -
414B LEU 3.4 6.4 + - - +
415B ALA 3.1 11.5 + - - +
417B ALA* 1.3 77.6 - - - +
419B GLY* 1.3 64.2 + - - +
421B GLN 3.4 0.5 + - - -
422B THR* 3.0 28.9 + - - -
444B GLU* 4.0 24.2 - - + -
447B SER* 3.5 31.0 - - - -
448B MET* 3.8 19.4 - - + +
450B ARG* 4.0 1.8 - - - -
451B ASP* 3.2 27.4 - - - -
453B GLN* 3.1 37.3 + - - -
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Residues in contact with GLY 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 4.0 10.1 - - - -
58B ALA* 3.3 30.9 - - - +
62B TYR* 3.6 16.3 - - - -
415B ALA 3.2 4.4 + - - -
416B ALA 2.9 5.3 + - - -
418B PHE* 1.3 80.5 - - - +
420B ALA* 1.3 60.7 + - - +
422B THR* 3.3 5.2 + - - -
423B ALA* 3.1 17.2 + - - +
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Residues in contact with ALA 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLY 4.4 4.5 - - - +
62B TYR 4.2 1.2 - - - +
65B CYS* 3.8 25.4 - - - -
378B ILE* 4.2 21.1 - - + -
380B LEU* 4.6 2.0 - - + -
402B ILE* 4.6 6.5 - - + -
416B ALA 2.9 11.8 + - - +
417B ALA* 3.1 12.3 + - - +
419B GLY* 1.3 73.6 - - - +
421B GLN* 1.3 60.1 + - - +
423B ALA* 3.1 4.6 + - - +
424B CYS* 2.8 32.4 + - - +
429B VAL* 4.8 4.0 - - + -
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Residues in contact with GLN 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B ALA 2.8 14.2 + - - +
420B ALA* 1.3 75.8 - - - +
422B THR* 1.3 63.6 + - - +
424B CYS 3.2 17.8 + - - +
425B PRO* 3.1 35.8 + - - +
427B ARG 3.7 8.6 + - - +
428B ARG* 5.3 0.2 - - - +
429B VAL* 3.3 32.4 - - + +
453B GLN* 3.2 35.4 - - + +
454B HIS* 3.7 13.9 + - - +
455B PRO* 3.3 32.5 - - + +
520B HIS* 5.7 2.2 - - - -
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Residues in contact with THR 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B HIS* 3.4 48.2 + - + +
24B PHE* 4.0 20.4 - - + -
47B VAL* 4.4 5.9 - - + +
62B TYR* 4.0 5.4 - - + -
418B PHE* 3.0 24.3 + - - -
419B GLY 3.4 9.6 - - - -
420B ALA 3.2 0.2 - - - -
421B GLN* 1.3 79.1 - - - +
423B ALA* 1.3 59.2 + - - +
425B PRO* 3.9 11.9 - - - +
451B ASP* 5.2 0.5 + - - -
453B GLN* 3.4 12.0 + - - +
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Residues in contact with ALA 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B HIS* 5.4 0.7 - - - -
62B TYR* 3.6 26.7 - - + +
65B CYS* 3.9 16.2 - - + -
66B LYS* 3.7 33.9 + - + +
419B GLY 3.1 7.1 + - - +
420B ALA 3.1 8.7 + - - +
422B THR* 1.3 78.8 - - - +
424B CYS* 1.3 61.6 + - - +
425B PRO* 3.5 7.2 - - - +
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Residues in contact with CYS 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B CYS* 4.0 22.7 - - - -
66B LYS* 5.8 0.9 - - - -
378B ILE* 3.7 27.6 - - + -
420B ALA 2.8 10.6 + - - +
421B GLN* 3.2 16.6 - - - +
423B ALA* 1.3 85.5 - - - +
425B PRO* 1.3 66.8 - - - +
426B ASN 3.1 4.4 + - - +
427B ARG* 3.1 35.5 + - + +
429B VAL* 5.0 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