Contacts of the helix formed by residues 436 - 443 (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 GLU 436 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B SER* 3.2 6.3 + - - +
435B PHE* 1.3 76.5 - - - +
437B ASP* 1.3 66.6 + - - +
438B MET 3.3 1.8 - - - -
439B LYS* 3.6 9.6 - - + +
440B LYS* 3.1 23.4 + - - +
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Residues in contact with ASP 437 (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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429B VAL* 4.0 17.3 - - + -
430B PRO* 3.6 26.1 - - + +
433B PRO* 4.4 2.0 - - + -
434B SER* 2.9 38.3 + - - +
436B GLU* 1.3 78.4 - - - +
438B MET* 1.3 62.6 + - - +
440B LYS* 3.5 5.8 + - - +
441B VAL* 3.2 27.0 + - - +
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Residues in contact with MET 438 (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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373B LYS* 3.4 22.7 - - + +
374B ARG* 3.5 32.5 - - - +
376B MET 5.2 1.8 - - - +
381B LEU* 3.8 23.1 - - + -
425B PHE* 4.0 13.9 - - + -
429B VAL* 3.9 28.0 - - + -
433B PRO* 4.3 9.6 - - + -
434B SER 3.3 14.4 + - - +
435B PHE* 5.0 0.2 - - - -
437B ASP* 1.3 75.3 - - - +
439B LYS* 1.3 57.4 + - - +
441B VAL* 3.2 2.6 + - + +
442B VAL* 2.8 63.0 + - + +
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Residues in contact with LYS 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LEU* 3.7 38.4 + - + +
382B ASP* 4.5 16.8 + - - +
383B GLU* 5.5 3.7 + - - -
435B PHE* 3.4 26.0 + - + +
436B GLU* 3.5 10.3 + - + +
438B MET* 1.3 77.6 - - - +
440B LYS* 1.3 57.0 + - - +
443B CYS* 3.0 39.3 + - + +
444B VAL* 3.2 8.3 + - + +
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Residues in contact with LYS 440 (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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436B GLU 3.1 17.2 + - - +
437B ASP* 3.7 6.7 - - - +
439B LYS* 1.3 78.2 - - - +
441B VAL* 1.3 58.4 + - + +
444B VAL* 3.3 16.9 + - + +
445B ASP* 2.7 58.1 + - - +
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Residues in contact with VAL 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B PHE* 3.8 15.9 - - + -
428B VAL* 3.3 56.8 - - + +
429B VAL* 3.7 7.2 - - + -
437B ASP 3.2 16.3 + - - +
438B MET* 3.2 4.6 + - + +
440B LYS* 1.3 83.1 - - + +
442B VAL* 1.3 61.1 + - + +
445B ASP* 3.5 9.4 - - - +
446B GLN 3.4 4.9 + - - -
447B GLN* 3.0 45.2 + - + +
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Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B MET 4.6 2.0 - - - +
378B PRO* 3.7 38.9 - - + +
381B LEU* 3.9 11.2 - - + -
399B TRP* 3.9 17.0 - - + +
425B PHE* 3.9 22.7 - - + -
438B MET* 2.8 46.7 + - + +
441B VAL* 1.3 74.6 - - + +
443B CYS* 1.3 56.7 + - - +
446B GLN* 2.8 28.5 - - - +
447B GLN 4.0 6.3 + - - +
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Residues in contact with CYS 443 (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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378B PRO* 3.6 33.4 - - - -
381B LEU* 3.8 21.1 - - - -
382B ASP* 4.1 17.0 - - - +
439B LYS* 3.0 22.7 + - + +
442B VAL* 1.3 81.6 - - - +
444B VAL* 1.3 68.2 + - + +
445B ASP 3.6 0.2 - - - -
446B GLN* 3.7 13.9 + - - +
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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