Contacts of the helix formed by residues 434 - 443 (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 SER 434 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373C LYS* 4.2 3.8 - - - +
432C ASP 3.3 3.7 + - - -
433C PRO* 1.3 75.1 - - - +
435C PHE* 1.3 57.7 + - - +
436C GLU* 3.7 11.5 + - - +
437C ASP* 2.4 66.5 + - - +
438C MET* 2.9 13.1 + - - +
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Residues in contact with PHE 435 (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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373C LYS* 3.8 24.4 - - - +
376C MET* 4.2 17.3 - - + -
380C VAL* 3.8 9.2 - - + -
381C LEU* 2.8 62.4 - - + +
383C GLU* 4.0 20.9 - - + -
434C SER* 1.3 71.9 - - - +
436C GLU* 1.3 55.1 + - + +
438C MET* 3.9 2.3 - - - +
439C LYS* 2.7 56.7 + - + +
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Residues in contact with GLU 436 (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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434C SER* 2.9 9.2 - - - +
435C PHE* 1.3 82.9 - - + +
437C ASP* 1.3 66.9 + - - +
439C LYS* 3.7 8.7 - - + +
440C LYS* 3.0 24.6 + - - +
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Residues in contact with ASP 437 (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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429C VAL* 4.6 9.9 - - + -
430C PRO* 3.7 26.0 - - + +
433C PRO* 3.9 8.5 - - + +
434C SER* 2.4 53.6 + - - +
436C GLU* 1.3 72.4 - - - +
438C MET* 1.3 59.0 + - - +
440C LYS* 3.6 6.1 + - - +
441C VAL* 3.2 28.6 + - - +
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Residues in contact with MET 438 (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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373C LYS* 3.5 20.6 - - + +
374C ARG* 3.4 31.6 - - - +
376C MET 5.1 1.1 - - - +
381C LEU* 3.8 24.7 - - + -
425C PHE* 4.0 13.5 - - + -
429C VAL* 4.2 20.6 - - + -
433C PRO* 3.9 24.5 - - + -
434C SER 2.9 15.9 + - - +
435C PHE 4.5 0.2 - - - -
437C ASP* 1.3 74.2 - - - +
439C LYS* 1.3 58.3 + - - +
440C LYS 3.2 0.2 - - - -
441C VAL* 3.2 1.7 + - + -
442C VAL* 2.7 62.0 + - + +
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Residues in contact with LYS 439 (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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381C LEU* 3.3 41.2 + - + +
382C ASP* 4.1 21.0 + - - +
383C GLU* 6.0 0.4 - - - +
435C PHE* 2.7 37.8 + - + +
436C GLU* 3.7 8.7 - - + +
438C MET* 1.3 70.4 - - - +
440C LYS* 1.3 59.5 + - - +
443C CYS* 2.9 40.1 + - + +
444C VAL* 3.2 9.2 + - + +
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Residues in contact with LYS 440 (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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436C GLU 3.0 17.2 + - - +
437C ASP* 3.7 6.7 - - - +
439C LYS* 1.3 77.2 - - - +
441C VAL* 1.3 58.1 + - + +
444C VAL* 3.3 19.9 + - + +
445C ASP* 2.8 58.2 + - - +
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Residues in contact with VAL 441 (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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425C PHE* 3.8 26.7 - - + -
428C VAL* 3.8 23.6 - - + +
429C VAL* 3.5 22.9 - - + -
437C ASP 3.2 16.1 + - - +
438C MET* 3.2 5.8 + - + +
440C LYS* 1.3 83.6 - - + +
442C VAL* 1.3 62.7 + - + +
445C ASP* 3.5 13.7 - - - +
446C GLN 3.4 5.5 + - - -
447C GLN* 2.9 43.0 + - + +
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Residues in contact with VAL 442 (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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376C MET 4.5 1.8 - - - +
377C ALA 4.5 0.4 - - - -
378C PRO* 3.6 43.7 - - + +
381C LEU* 3.8 11.2 - - + -
399C TRP* 4.0 12.8 - - + -
425C PHE* 3.8 23.3 - - + -
438C MET* 2.7 46.5 + - + +
441C VAL* 1.3 75.0 - - + +
443C CYS* 1.3 57.2 + - - +
446C GLN* 3.0 25.0 - - - +
447C GLN 4.1 6.4 - - - +
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Residues in contact with CYS 443 (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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378C PRO* 3.4 36.3 - - - -
381C LEU* 3.6 22.2 - - - -
382C ASP* 3.6 29.4 - - - +
439C LYS* 2.9 19.2 + - + +
442C VAL* 1.3 78.8 - - - +
444C VAL* 1.3 68.0 + - + +
446C GLN* 3.0 19.3 + - - +
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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