Contacts of the helix formed by residues 481 - 491 (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 THR 481 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314D HIS* 5.9 0.2 - - - -
394D LYS* 6.0 3.8 - - - +
395D TRP* 5.4 9.0 - - + +
398D ILE* 3.9 4.9 - - - -
479D ARG 4.8 4.3 - - - +
480D LEU* 1.3 77.7 - - - +
482D ALA* 1.3 63.8 + - - +
483D LEU* 3.6 9.4 + - - +
484D ARG* 3.1 25.1 + - + +
485D ILE* 3.1 22.5 + - - +
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Residues in contact with ALA 482 (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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307D ALA* 4.4 3.3 - - - +
310D LEU* 3.9 13.5 - - + -
311D ALA* 3.6 31.3 - - - +
314D HIS* 3.8 26.3 + - + +
398D ILE* 3.6 12.6 - - + +
481D THR* 1.3 70.3 - - - +
483D LEU* 1.3 60.4 + - - +
485D ILE* 3.3 8.3 + - - +
486D LYS* 2.9 30.1 + - - +
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Residues in contact with LEU 483 (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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311D ALA* 4.1 18.0 - - + +
314D HIS* 6.0 0.4 - - - +
315D VAL* 5.1 23.6 - - + -
481D THR* 3.2 8.9 - - - +
482D ALA* 1.3 78.5 - - - +
484D ARG* 1.3 57.5 + - - +
486D LYS* 3.4 12.7 + - + +
487D LYS* 3.0 61.5 + - + +
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Residues in contact with ARG 484 (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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480D LEU* 3.9 23.4 - - + +
481D THR* 3.1 28.2 + - + +
483D LEU* 1.3 73.4 - - - +
485D ILE* 1.3 60.4 + - - +
487D LYS* 3.8 11.8 - - + +
488D THR* 2.9 40.4 + - - +
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Residues in contact with ILE 485 (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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307D ALA* 4.0 11.9 - - + -
310D LEU* 5.9 0.7 - - + -
398D ILE* 4.0 19.5 - - + -
401D PHE* 3.9 26.0 - - + -
467D MET* 3.7 29.2 - - + -
471D CYS* 3.9 26.0 - - - -
480D LEU* 3.8 23.8 - - + -
481D THR 3.1 16.4 + - - +
482D ALA* 3.6 7.9 - - - +
484D ARG* 1.3 73.8 - - - +
486D LYS* 1.3 68.7 + - - +
488D THR* 3.2 2.8 + - - -
489D LEU* 3.1 23.3 + - + +
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Residues in contact with LYS 486 (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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253D HIS* 6.0 2.1 + - - -
304D VAL* 4.7 2.3 - - + +
307D ALA* 4.0 12.7 - - + +
308D CYS* 3.7 41.1 - - - +
311D ALA* 4.0 17.5 - - + -
482D ALA 2.9 14.0 + - - +
483D LEU* 3.4 17.9 - - + +
485D ILE* 1.3 78.0 - - - +
487D LYS* 1.3 63.8 + - + +
489D LEU* 3.4 3.2 + - - +
490D GLN* 3.0 55.0 + - + +
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Residues in contact with LYS 487 (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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483D LEU* 3.0 50.2 + - + +
484D ARG* 3.8 11.4 - - + +
485D ILE 3.2 0.2 - - - -
486D LYS* 1.3 76.3 - - + +
488D THR* 1.3 64.0 + - - +
490D GLN* 3.0 25.4 + - - +
491D LYS* 3.1 12.8 + - - +
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Residues in contact with THR 488 (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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463D GLY* 6.3 4.0 - - - -
467D MET* 4.0 25.0 - - + +
480D LEU* 5.4 2.6 - - - +
484D ARG* 2.9 25.3 + - - +
485D ILE* 3.2 4.0 + - - -
487D LYS* 1.3 77.5 - - - +
489D LEU* 1.3 63.9 + - + +
491D LYS 3.1 23.0 + - - -
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Residues in contact with LEU 489 (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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300D LEU* 4.0 28.6 - - + +
303D ALA* 3.7 37.7 - - + +
304D VAL* 3.9 18.5 - - + +
307D ALA* 4.3 2.5 - - + -
401D PHE* 5.1 2.0 - - + -
405D LEU* 5.2 0.2 - - + -
464D LEU* 3.4 32.3 - - + -
467D MET* 3.7 25.4 - - + -
485D ILE* 3.1 25.0 + - + +
486D LYS 3.9 2.9 - - - +
488D THR* 1.3 77.0 - - + +
490D GLN* 1.3 60.5 + - - +
491D LYS* 3.5 1.9 + - - -
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Residues in contact with GLN 490 (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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304D VAL* 4.1 15.4 - - + +
308D CYS* 4.5 6.5 - - - -
486D LYS* 3.0 55.4 + - + +
487D LYS* 3.0 22.6 + - - +
489D LEU* 1.3 77.8 - - - +
491D LYS* 1.3 58.9 + - - +
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Residues in contact with LYS 491 (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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487D LYS 3.1 7.9 + - - +
488D THR* 3.1 18.6 + - - -
489D LEU 3.3 1.7 - - - -
490D GLN* 1.3 80.5 - - - +
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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