Contacts of the helix formed by residues 459 - 470 (chain B) 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 PRO 459 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457B ALA 4.2 2.5 - - - +
458B ASP* 1.3 84.6 - - + +
460B VAL* 1.3 63.7 + - + +
461B LEU 3.0 4.5 - - - -
462B SER* 3.2 8.0 - - - -
463B GLY* 2.8 31.0 + - - -
492B ILE* 4.3 14.7 - - + +
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Residues in contact with VAL 460 (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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296B PRO* 3.6 38.8 - - + +
297B HIS* 5.7 1.6 - - - +
300B LEU* 4.0 26.1 - - + +
458B ASP* 4.2 10.1 - - + -
459B PRO* 1.3 83.4 - - + +
461B LEU* 1.3 63.6 + - + +
464B LEU* 3.1 31.8 + - - +
489B LEU* 5.5 0.5 - - - +
492B ILE* 3.0 35.8 - - + +
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Residues in contact with LEU 461 (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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296B PRO* 4.8 4.5 - - + -
299B ALA* 4.6 5.2 - - + -
409B ALA* 5.0 3.1 - - + -
412B THR* 3.4 44.0 - - + +
414B VAL* 3.5 22.9 - - + -
455B LEU* 3.4 35.8 - - + +
458B ASP* 3.3 26.1 - - + +
459B PRO 3.0 0.2 - - - -
460B VAL* 1.3 89.3 - - + +
462B SER* 1.3 68.7 + - - +
464B LEU* 4.0 20.1 - - + +
465B ALA* 3.2 20.3 + - - +
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Residues in contact with SER 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B LEU 3.5 9.0 - - - -
456B ALA* 4.8 6.9 + - - +
458B ASP 2.8 24.2 + - - -
459B PRO* 3.2 11.2 - - - -
461B LEU* 1.3 80.0 - - - +
463B GLY* 1.3 63.1 + - - +
465B ALA* 3.1 16.3 - - - +
466B GLN* 3.1 7.9 + - - +
469B ARG* 5.1 0.9 + - - -
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Residues in contact with GLY 463 (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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459B PRO 2.8 16.7 + - - -
462B SER* 1.3 71.0 - - - +
464B LEU* 1.3 65.9 + - - +
466B GLN* 3.0 9.5 + - - +
467B MET* 2.8 29.4 + - - +
488B THR* 5.9 3.5 - - - +
492B ILE* 4.2 17.7 - - - -
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Residues in contact with LEU 464 (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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299B ALA* 4.6 16.2 - - + +
300B LEU* 5.1 2.9 - - + +
303B ALA* 3.9 21.3 - - + -
405B LEU* 3.9 9.1 - - + +
408B ILE* 4.7 8.5 - - + -
409B ALA* 5.0 3.8 - - + -
460B VAL 3.1 27.0 + - - +
461B LEU* 4.1 20.4 - - + -
462B SER 3.4 0.8 - - - -
463B GLY* 1.3 73.8 - - - +
465B ALA* 1.3 57.6 + - - +
467B MET* 3.2 16.2 + - + +
468B MET* 2.8 51.0 + - + +
489B LEU* 3.3 30.3 - - + -
492B ILE* 5.2 1.0 - - - +
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Residues in contact with ALA 465 (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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451B ILE* 3.3 33.6 - - + +
455B LEU* 4.2 8.1 - - + +
461B LEU 3.2 13.4 + - - +
462B SER* 3.1 14.8 + - - +
463B GLY 3.1 0.2 - - - -
464B LEU* 1.3 79.2 - - - +
466B GLN* 1.3 58.5 + - - +
468B MET* 3.4 13.9 - - - +
469B ARG* 3.1 32.0 + - - +
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Residues in contact with GLN 466 (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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462B SER 3.1 7.7 + - - +
463B GLY* 3.0 12.0 + - - +
465B ALA* 1.3 77.2 - - - +
467B MET* 1.3 65.2 + - - +
469B ARG* 2.8 41.9 + - - +
470B GLU* 3.1 65.8 + - - +
473B TYR* 4.5 6.1 + - - -
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Residues in contact with MET 467 (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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405B LEU* 3.1 26.5 - - + -
463B GLY 2.8 20.5 + - - +
464B LEU* 3.6 6.3 - - + +
466B GLN* 1.3 71.2 - - - +
468B MET* 1.3 64.4 + - - +
470B GLU* 3.4 2.1 + - - +
471B CYS* 3.0 31.2 + - - -
480B LEU* 4.0 25.0 - - + +
485B ILE* 3.3 28.9 - - + +
488B THR* 4.4 17.9 - - + -
489B LEU* 3.2 51.1 - - + -
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Residues in contact with MET 468 (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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402B GLY* 3.8 8.7 - - - +
405B LEU* 3.6 29.1 - - + +
406B TRP* 3.8 20.6 - - - -
409B ALA* 3.1 33.2 - - + -
451B ILE* 4.2 15.3 - - + -
452B PRO* 6.4 0.2 - - - -
455B LEU* 5.4 2.2 - - + -
464B LEU* 2.8 43.4 + - + +
465B ALA* 3.4 15.9 - - + +
467B MET* 1.3 72.6 - - - +
469B ARG* 1.3 63.6 + - - +
471B CYS* 3.1 12.3 + - - +
472B TRP* 3.2 40.0 - - + -
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Residues in contact with ARG 469 (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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451B ILE* 3.4 37.6 - - + +
462B SER 5.1 1.0 + - - -
465B ALA* 3.1 15.7 + - - +
466B GLN* 2.8 46.2 + - - +
467B MET 3.3 0.2 - - - -
468B MET* 1.3 79.4 - - - +
470B GLU* 1.3 59.5 + - + +
472B TRP* 2.9 27.4 + - + +
473B TYR* 3.1 26.6 + - + +
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Residues in contact with GLU 470 (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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466B GLN* 3.1 46.5 + - - +
467B MET* 3.8 1.7 - - - +
468B MET 3.3 0.4 - - - -
469B ARG* 1.3 75.1 - - - +
471B CYS* 1.3 57.4 + - - +
472B TRP 3.4 0.2 - - - -
473B TYR* 3.8 29.7 + - + +
478B ALA 4.5 1.9 - - - +
479B ARG* 3.2 10.4 - - - +
480B LEU* 3.2 60.1 + - + +
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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