Contacts of the helix formed by residues 481 - 492 (chain C) 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 THR 481 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394C LYS* 6.4 0.4 - - - +
395C TRP* 5.6 8.3 - - - +
398C ILE* 3.9 5.4 - - - -
479C ARG 4.8 4.3 - - - +
480C LEU* 1.3 78.5 - - - +
482C ALA* 1.3 63.8 + - - +
483C LEU* 3.6 9.4 + - - +
484C ARG* 3.1 25.4 + - + +
485C ILE* 3.1 22.5 + - - +
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Residues in contact with ALA 482 (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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307C ALA* 4.4 4.1 - - - +
310C LEU* 4.0 15.0 - - + -
311C ALA* 3.8 29.9 - - - +
314C HIS* 4.0 20.8 + - + +
398C ILE* 3.6 17.2 - - + +
481C THR* 1.3 70.8 - - - +
483C LEU* 1.3 61.8 + - - +
485C ILE* 3.3 7.1 + - - +
486C LYS* 2.9 30.3 + - - +
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Residues in contact with LEU 483 (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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311C ALA* 4.2 11.4 - - + +
315C VAL* 5.2 20.6 - - + -
481C THR* 3.2 9.1 - - - +
482C ALA* 1.3 78.1 - - - +
484C ARG* 1.3 56.5 + - - +
486C LYS* 3.3 26.9 - - + +
487C LYS* 2.9 59.5 + - - +
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Residues in contact with ARG 484 (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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480C LEU* 3.7 28.6 - - + +
481C THR* 3.1 28.7 + - - +
483C LEU* 1.3 75.8 - - - +
485C ILE* 1.3 56.7 + - - +
487C LYS* 3.5 12.8 + - - +
488C THR* 2.9 40.0 + - - +
491C LYS* 5.4 9.1 - - - +
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Residues in contact with ILE 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C ALA* 4.2 9.4 - - + -
398C ILE* 4.3 16.8 - - + -
401C PHE* 3.8 28.3 - - + -
467C MET* 3.6 30.5 - - + -
471C CYS* 4.0 26.5 - - - -
480C LEU* 3.8 24.2 - - + -
481C THR 3.1 16.5 + - - +
482C ALA* 3.6 8.1 - - - +
484C ARG* 1.3 73.2 - - - +
486C LYS* 1.3 69.7 + - - +
488C THR* 3.2 4.6 + - - -
489C LEU* 3.1 22.8 + - + +
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Residues in contact with LYS 486 (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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254B ASP* 3.8 17.7 + - - -
253C HIS* 5.8 3.4 + - - -
304C VAL* 4.6 1.1 - - + +
307C ALA* 4.0 15.8 - - + +
308C CYS* 3.8 33.8 + - - +
311C ALA* 3.9 21.2 - - + +
312C HIS* 5.5 1.8 - - - +
482C ALA 2.9 14.9 + - - +
483C LEU* 3.3 23.0 - - + +
485C ILE* 1.3 74.8 - - - +
487C LYS* 1.3 53.3 + - + +
489C LEU* 2.7 27.9 + - - +
490C GLN* 2.8 56.0 + - - +
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Residues in contact with LYS 487 (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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341B ASN* 6.2 2.2 - - - +
483C LEU* 2.9 52.6 + - + +
484C ARG* 3.8 12.1 - - + +
485C ILE 3.2 0.2 - - - -
486C LYS* 1.3 70.7 - - + +
488C THR* 1.3 65.3 + - - +
489C LEU 2.8 5.4 + - - -
490C GLN* 2.8 21.5 + - + +
491C LYS* 2.9 29.3 + - - +
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Residues in contact with THR 488 (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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463C GLY* 5.7 3.1 - - - +
467C MET* 3.9 27.1 - - + +
480C LEU* 5.4 2.8 - - - +
484C ARG* 2.9 27.3 + - - +
485C ILE* 3.2 5.3 + - - -
487C LYS* 1.3 74.1 - - - +
489C LEU* 1.3 58.9 + - + +
491C LYS* 3.7 25.4 + - + +
492C ILE* 3.5 22.2 + - - +
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Residues in contact with LEU 489 (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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300C LEU* 3.4 42.7 - - + +
303C ALA* 3.8 15.7 - - + +
304C VAL* 3.6 43.5 - - + +
307C ALA* 4.1 10.1 - - + -
401C PHE* 5.4 1.1 - - + -
405C LEU* 5.7 0.2 - - + -
464C LEU* 4.1 16.4 - - + -
467C MET* 4.5 11.2 - - + -
485C ILE* 3.1 22.4 + - + +
486C LYS 2.7 11.9 + - - +
488C THR* 1.3 82.1 - - + +
490C GLN* 1.3 57.4 + - - -
491C LYS 3.5 1.8 - - - -
492C ILE* 3.8 14.6 + - + +
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Residues in contact with GLN 490 (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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254B ASP* 3.4 19.0 + - - -
301B ARG* 2.8 31.0 + - - +
339B LYS* 6.1 0.2 - - - +
341B ASN* 3.3 28.8 - - - +
343B GLN* 5.2 10.4 + - - +
304C VAL* 4.2 12.3 - - + -
308C CYS* 4.4 4.6 - - - -
486C LYS* 2.8 67.4 + - - +
487C LYS* 2.8 14.6 + - + +
489C LEU* 1.3 74.6 - - - +
491C LYS* 1.3 57.3 + - - +
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Residues in contact with LYS 491 (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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301B ARG* 3.7 16.6 + - - +
341B ASN* 5.1 5.4 - - + +
484C ARG* 5.4 9.2 - - - +
487C LYS* 2.9 34.2 + - - +
488C THR* 3.7 27.5 + - + +
490C GLN* 1.3 80.4 - - - +
492C ILE* 1.3 64.8 + - - +
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Residues in contact with ILE 492 (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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301B ARG* 5.6 1.3 - - - -
300C LEU* 4.2 27.7 - - + +
460C VAL* 4.7 14.1 - - + +
488C THR 3.5 15.7 + - - +
489C LEU* 3.8 18.4 + - + +
490C GLN 3.6 1.0 - - - -
491C LYS* 1.3 85.2 - - - +
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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