Contacts of the helix formed by residues 411 - 424 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D TYR* 4.0 1.2 - - - -
382D ASP* 2.9 13.3 + - - -
410D ILE* 1.3 73.4 - - - +
412D TYR* 1.3 63.9 + - - +
413D THR 3.4 2.8 + - - -
414D LEU* 3.6 5.7 + - - -
415D ALA 3.8 1.2 + - - -
437D ALA* 3.4 24.2 - - - +
438D ALA* 5.4 0.2 - - - -
440D LEU* 4.2 1.6 - - - -
441D THR* 2.8 41.1 + - - +
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Residues in contact with TYR 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D TYR* 3.3 40.2 - + + -
60D ASP* 2.8 39.4 + - + -
61D GLY 4.1 2.6 + - - -
64D ARG* 3.1 18.6 + - - -
380D LEU* 5.6 0.2 - - + -
382D ASP* 4.6 0.7 - - - +
402D ILE* 3.8 19.4 - - + +
403D VAL 5.1 0.7 - - - -
404D GLN* 3.5 43.3 - - + +
409D SER 3.1 18.6 + - - +
410D ILE 3.2 2.8 + - - -
411D GLY* 1.3 77.8 - - - +
413D THR* 1.3 73.6 + - + +
415D ALA* 3.2 5.4 + - - +
416D ALA* 2.8 51.4 + - + +
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Residues in contact with THR 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D LEU* 3.8 16.5 - - + +
381D ALA 3.3 11.4 - - - +
382D ASP* 3.0 56.3 + - - +
402D ILE 5.3 1.1 - - - +
403D VAL* 6.0 0.4 - - - -
404D GLN 6.1 0.4 - - - +
412D TYR* 1.3 92.7 - - + +
414D LEU* 1.3 59.9 + - - +
416D ALA* 3.6 3.9 - - - +
417D ALA* 2.7 32.6 + - - +
431D VAL* 4.2 4.6 - - - +
432D LEU 4.1 1.4 + - - -
433D THR* 3.9 13.2 - - - -
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Residues in contact with LEU 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382D ASP* 4.4 0.2 + - - -
411D GLY* 3.6 3.3 + - - +
412D TYR 3.4 0.8 - - - -
413D THR* 1.3 84.7 + - - +
415D ALA* 1.3 61.9 + - - +
417D ALA* 3.5 12.3 - - - +
418D PHE* 3.5 5.9 + - - +
431D VAL* 4.4 13.9 - - + -
433D THR* 5.2 7.4 - - + +
438D ALA* 4.0 19.7 - - + +
441D THR* 3.5 34.1 - - - +
442D ILE* 3.8 27.8 - - + +
444D GLU* 5.0 2.4 - - + +
445D LEU* 4.8 8.7 - - + +
448D MET* 3.8 15.2 - - + +
457D ILE* 4.1 30.5 - - + -
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Residues in contact with ALA 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ASN* 3.7 23.6 - - + +
57D TYR* 3.4 31.9 - - + -
58D ALA* 3.5 8.7 - - - +
411D GLY 3.8 3.2 + - - +
412D TYR 3.2 2.8 + - - +
414D LEU* 1.3 75.5 - - - +
416D ALA* 1.3 69.5 + - - +
417D ALA 3.1 1.8 - - - -
418D PHE* 3.0 15.2 + - - +
419D GLY 3.2 8.0 + - - -
441D THR* 4.1 5.8 + - - -
444D GLU* 4.3 13.2 - - + -
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Residues in contact with ALA 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D TYR* 3.6 14.3 - - - +
58D ALA* 4.2 0.4 - - - +
61D GLY* 3.8 10.5 - - - -
380D LEU* 3.7 11.7 - - + -
402D ILE* 5.2 0.2 - - + -
412D TYR* 2.8 57.6 + - + +
413D THR* 3.6 4.0 - - - +
415D ALA* 1.3 72.2 - - - +
417D ALA* 1.3 59.0 + - - +
419D GLY* 2.9 4.9 + - - -
420D ALA* 2.9 25.3 + - - +
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Residues in contact with ALA 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D LEU* 3.3 19.5 - - + +
413D THR 2.7 17.0 + - - +
414D LEU 3.5 7.6 - - - +
415D ALA 3.1 0.2 - - - -
416D ALA* 1.3 77.4 - - - +
418D PHE* 1.3 63.3 + - - +
420D ALA* 3.0 2.8 + - - +
421D GLN* 2.8 27.8 + - - +
429D VAL* 4.3 3.7 - - + +
431D VAL* 3.5 32.1 - - + -
448D MET* 3.8 8.1 - - + -
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Residues in contact with PHE 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D PHE* 4.1 4.3 - + - -
47D VAL* 3.7 24.9 - - + -
49D CYS* 4.1 9.6 - - - -
58D ALA* 4.1 14.1 - - + -
414D LEU 3.5 6.4 + - - +
415D ALA 3.0 11.3 + - - +
417D ALA* 1.3 78.1 - - - +
419D GLY* 1.3 63.0 + - - +
422D THR* 3.0 30.1 + - - -
444D GLU* 4.1 23.3 - - + -
447D SER* 3.5 30.5 - - - -
448D MET* 3.9 19.0 - - + +
450D ARG* 4.0 2.0 - - - -
451D ASP* 3.2 28.5 - - - -
453D GLN* 3.1 40.4 + - - -
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Residues in contact with GLY 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D PHE* 4.0 12.6 - - - -
58D ALA* 3.3 26.9 - - - -
62D TYR* 3.6 16.1 - - - -
415D ALA 3.2 4.4 + - - -
416D ALA 2.9 5.7 + - - -
418D PHE* 1.3 78.7 - - - +
420D ALA* 1.3 64.8 + - - +
422D THR* 3.3 4.9 + - - -
423D ALA* 3.1 17.3 + - - +
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Residues in contact with ALA 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D GLY 4.5 2.5 - - - +
62D TYR 4.1 1.6 - - - +
65D CYS* 3.8 26.7 - - - -
378D ILE* 4.2 21.3 - - + -
380D LEU* 4.7 1.8 - - + -
402D ILE* 4.6 8.7 - - + -
416D ALA 2.9 12.2 + - - +
417D ALA* 3.5 10.3 - - - +
419D GLY* 1.3 72.2 - - - +
421D GLN* 1.3 62.7 + - - +
423D ALA* 2.8 5.2 + - - +
424D CYS* 2.7 30.6 + - - +
429D VAL* 4.9 3.8 - - + -
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Residues in contact with GLN 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417D ALA 2.8 17.4 + - - +
420D ALA* 1.3 72.5 - - - +
422D THR* 1.3 63.3 + - - +
424D CYS 3.1 18.7 + - - +
425D PRO* 3.1 35.8 + - - +
427D ARG 3.6 9.0 + - - +
429D VAL* 3.2 31.8 - - + +
448D MET* 5.6 0.2 - - + -
453D GLN* 3.2 36.3 - - + +
454D HIS* 3.6 13.3 + - - +
455D PRO* 3.5 34.7 - - + +
520D HIS* 5.7 1.6 - - - -
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Residues in contact with THR 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D HIS* 3.5 47.4 + - + +
24D PHE* 4.1 16.8 - - + -
47D VAL* 4.4 7.0 - - + +
62D TYR* 4.0 5.2 - - + -
418D PHE* 3.0 25.8 + - - -
419D GLY 3.5 8.7 - - - -
420D ALA 3.1 0.2 - - - -
421D GLN* 1.3 76.6 - - - +
423D ALA* 1.3 60.6 + - - +
425D PRO* 3.9 11.6 - - - +
451D ASP* 5.0 1.2 + - - -
453D GLN* 3.4 11.8 + - - +
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Residues in contact with ALA 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D HIS* 5.2 0.9 - - - -
62D TYR* 3.7 27.3 - - + -
65D CYS* 3.8 17.0 - - + -
66D LYS* 3.7 33.9 + - + +
419D GLY 3.1 6.3 + - - +
420D ALA 2.8 8.3 + - - +
422D THR* 1.3 78.3 - - - +
424D CYS* 1.3 62.7 + - - +
425D PRO* 3.4 7.4 - - - +
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Residues in contact with CYS 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D CYS* 4.0 25.8 - - - -
66D LYS* 5.6 1.1 - - - -
378D ILE* 3.9 16.2 - - + -
420D ALA 2.7 12.8 + - - +
421D GLN* 3.1 18.5 - - - +
423D ALA* 1.3 81.1 - - - +
425D PRO* 1.3 65.5 - - - +
426D ASN 3.2 3.3 + - - -
427D ARG* 3.2 42.4 + - + +
429D VAL* 4.9 0.5 - - - +
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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