Contacts of the helix formed by residues 372 - 376 (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 372 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330C ASP* 2.8 27.3 + - - -
332C LYS* 2.8 36.8 + - + +
370C VAL 3.8 0.4 + - - -
371C GLY* 1.3 70.0 - - - -
373C LYS* 1.3 67.1 + - - +
374C ARG* 4.1 9.2 - - + +
375C TYR* 3.0 37.9 + - + +
376C MET* 3.5 8.8 + - - +
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Residues in contact with LYS 373 (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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370C VAL* 4.8 13.6 - - - +
371C GLY 3.2 2.6 + - - +
372C THR* 1.3 73.5 - - - +
374C ARG* 1.3 64.0 + - - +
375C TYR 3.1 1.4 + - - -
376C MET* 3.2 39.3 + - + +
432C ASP* 5.2 2.5 - - - +
433C PRO* 3.1 30.5 - - + +
434C SER* 4.2 1.8 - - - +
435C PHE* 3.8 27.4 - - + +
438C MET* 3.5 21.4 - - + +
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Residues in contact with ARG 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C THR* 3.3 7.4 - - + +
373C LYS* 1.3 76.9 - - - +
375C TYR* 1.3 76.4 + - + +
376C MET 3.5 0.7 - - - +
403C LEU* 4.0 2.3 - - - +
423C PRO* 3.7 34.2 - - - +
424C PRO* 2.7 51.2 + - + +
425C PHE* 3.8 20.8 - - + -
426C TYR* 4.1 2.4 - - - +
429C VAL* 3.9 17.2 + - - +
430C PRO 3.8 9.1 + - - -
431C ASN* 3.3 26.5 + - - +
433C PRO* 4.0 16.0 - - + +
438C MET* 3.4 25.8 - - + +
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Residues in contact with TYR 375 (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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286C TYR* 5.8 0.2 - - - -
330C ASP* 5.9 0.7 - - - +
331C PHE 3.9 20.2 - - - +
332C LYS* 3.4 34.1 - - + -
333C SER* 3.0 14.2 + - - -
372C THR* 3.0 26.6 + - + +
374C ARG* 1.3 92.8 - - + +
376C MET* 1.3 64.6 + - - +
377C ALA 3.5 0.5 + - - -
396C THR 4.9 1.4 - - - +
399C TRP* 3.3 18.2 - - - -
400C ALA* 4.0 12.4 - - + +
403C LEU* 3.4 36.3 - - + -
404C VAL* 4.2 4.0 - - + -
407C GLU* 2.3 35.6 + - - -
421C TYR* 4.8 0.7 + - - -
423C PRO* 5.7 0.3 - - - +
424C PRO* 3.9 12.2 - - + +
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Residues in contact with MET 376 (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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370C VAL* 4.0 19.1 - - + -
371C GLY* 3.3 31.4 - - - +
372C THR 3.5 13.2 - - - +
373C LYS* 3.2 25.3 + - + +
374C ARG 3.5 1.8 - - - +
375C TYR* 1.3 77.3 - - - +
377C ALA* 1.3 64.7 + - - +
380C VAL* 3.9 25.4 - - + -
381C LEU* 3.5 42.4 - - + +
399C TRP* 3.4 11.2 + - - -
435C PHE* 4.2 12.8 - - + -
438C MET* 5.1 0.2 - - - +
442C VAL* 4.5 3.5 - - - +
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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