Contacts of the helix formed by residues 461 - 472 (chain D) in PDB entry 3MY0
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 LEU 461 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296D PRO* 4.2 34.3 - - + +
299D ALA* 4.7 4.0 - - + -
300D LEU* 5.7 1.6 - - + +
409D ALA* 6.6 0.2 - - - -
412D THR* 4.1 23.3 - - + -
414D VAL* 4.8 12.1 - - + -
455D LEU* 3.9 39.2 - - + +
458D ASP* 3.0 27.4 + - + +
460D VAL* 1.3 82.9 - - + +
462D SER* 1.3 68.9 + - - +
463D GLY 3.4 1.8 - - - -
464D LEU* 3.0 41.7 + - + +
465D ALA 3.9 0.7 + - - -
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Residues in contact with SER 462 (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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455D LEU 4.2 9.2 - - - -
456D ALA* 4.3 19.6 + - - +
458D ASP 2.7 20.9 + - - -
459D PRO* 4.2 7.4 - - - -
460D VAL 3.8 0.6 - - - -
461D LEU* 1.3 70.4 - - - +
463D GLY* 1.3 68.0 + - - +
465D ALA* 2.8 26.7 + - - +
466D GLN* 3.9 1.4 + - - +
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Residues in contact with GLY 463 (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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459D PRO 5.2 2.6 + - - -
460D VAL 5.4 1.0 + - - -
461D LEU 3.4 0.6 - - - -
462D SER* 1.3 77.0 + - - +
464D LEU* 1.3 52.6 + - - +
466D GLN* 2.6 35.2 + - - +
467D MET* 3.0 13.2 + - - +
488D THR* 6.3 4.0 - - - -
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Residues in contact with LEU 464 (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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299D ALA* 5.6 7.0 - - + +
300D LEU* 4.7 12.6 - - + -
303D ALA* 5.3 11.7 - - + -
405D LEU* 4.5 10.7 - - + +
408D ILE* 6.2 3.1 - - + -
409D ALA* 5.6 6.7 - - + -
455D LEU* 4.5 6.1 - - + -
460D VAL 4.6 4.5 - - - +
461D LEU* 3.0 41.5 + - + +
462D SER 2.9 2.6 + - - -
463D GLY* 1.3 71.8 - - - +
465D ALA* 1.3 56.9 + - - +
467D MET* 3.7 13.4 - - + +
468D MET* 2.9 45.1 + - + +
489D LEU* 3.4 34.8 - - + -
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Residues in contact with ALA 465 (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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451D ILE* 3.4 26.7 - - + +
455D LEU* 4.5 10.7 - - + +
456D ALA* 6.1 1.8 - - - +
461D LEU 3.9 0.6 + - - -
462D SER* 2.8 14.4 + - - +
464D LEU* 1.3 79.2 - - - +
466D GLN* 1.3 62.7 + - - +
468D MET* 3.4 15.0 - - - +
469D ARG* 3.2 35.2 + - - +
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Residues in contact with GLN 466 (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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462D SER 3.9 0.6 + - - +
463D GLY* 2.6 19.7 + - - +
465D ALA* 1.3 73.0 - - - +
467D MET* 1.3 65.1 + - - +
469D ARG* 3.2 32.0 + - - +
470D GLU* 3.1 62.8 + - - +
473D TYR* 5.0 4.8 + - - -
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Residues in contact with MET 467 (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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401D PHE* 4.9 0.2 - - + -
405D LEU* 3.5 24.5 - - + -
463D GLY 3.0 11.8 + - - +
464D LEU* 3.7 10.5 - - + +
466D GLN* 1.3 73.5 - - - +
468D MET* 1.3 60.6 + - - +
470D GLU* 3.0 10.4 + - - +
471D CYS* 3.0 36.6 + - - -
480D LEU* 3.6 21.9 - - + +
485D ILE* 3.7 29.4 - - + +
488D THR* 4.0 26.2 - - + -
489D LEU* 3.7 34.8 - - + -
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Residues in contact with MET 468 (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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402D GLY* 4.0 16.4 - - - +
405D LEU* 4.0 13.9 - - + +
406D TRP* 4.0 29.8 - - - +
409D ALA* 4.0 13.2 - - + -
451D ILE* 3.8 25.4 - - + -
452D PRO* 5.0 0.4 - - + -
455D LEU* 3.6 30.7 - - + -
464D LEU* 2.9 30.2 + - + +
465D ALA* 3.4 13.5 - - - +
467D MET* 1.3 74.5 - - - +
469D ARG* 1.3 62.0 - - - +
470D GLU 3.2 0.9 + - - -
471D CYS* 3.2 15.1 + - - +
472D TRP* 3.3 27.6 + - + -
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Residues in contact with ARG 469 (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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451D ILE* 3.9 28.2 - - + +
465D ALA* 3.2 32.3 + - - +
466D GLN* 3.4 35.9 + - - +
468D MET* 1.3 78.6 - - - +
470D GLU* 1.4 60.6 + - + +
471D CYS 3.3 0.4 - - - -
472D TRP* 3.2 23.9 + - + +
473D TYR* 3.5 18.1 + - + -
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Residues in contact with GLU 470 (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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466D GLN* 3.1 45.1 + - - +
467D MET* 3.0 11.0 + - - +
469D ARG* 1.4 73.7 - - + +
471D CYS* 1.3 60.5 + - - +
472D TRP 3.4 0.4 - - - -
473D TYR* 3.9 28.7 + - + +
478D ALA 5.6 0.7 - - - +
479D ARG* 3.2 12.3 - - - +
480D LEU* 3.2 54.9 + - + +
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Residues in contact with CYS 471 (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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398D ILE* 3.6 36.6 - - + +
399D TRP* 3.4 14.4 - - - -
401D PHE* 4.5 4.7 - - - -
402D GLY* 3.8 25.1 - - - -
405D LEU* 5.2 2.5 - - - -
467D MET* 3.0 19.6 + - - -
468D MET 3.2 8.0 + - - +
470D GLU* 1.3 79.0 - - - +
472D TRP* 1.3 57.8 + - + +
473D TYR 3.6 1.6 - - - -
479D ARG* 3.2 20.9 + - - -
480D LEU* 5.4 1.6 - - - -
485D ILE* 3.9 20.4 - - - -
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Residues in contact with TRP 472 (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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399D TRP* 3.5 53.6 + + + -
402D GLY* 3.5 23.6 - - - -
403D LEU* 3.4 33.2 - - + +
406D TRP* 4.3 11.0 - + + -
448D THR* 4.0 26.6 - - + +
449D PRO* 3.6 39.3 - - + -
451D ILE* 4.0 18.6 - - + -
468D MET* 3.3 24.9 - - + +
469D ARG* 3.2 14.4 + - + +
471D CYS* 1.3 82.8 - - + +
473D TYR* 1.3 66.4 + - - +
474D PRO* 3.2 8.0 - - - +
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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