Contacts of the strand formed by residues 362 - 366 (chain C) in PDB entry 3MX0
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 TYR 362 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C PRO* 4.3 5.6 - - + -
348C TRP* 3.4 34.5 - + + -
350C PRO* 3.3 18.2 - - - +
351C PRO* 3.3 24.6 - - + +
360C ILE* 3.7 20.0 + - + +
361C VAL* 1.3 75.5 - - - +
363C SER* 1.3 60.0 + - - +
389C PRO 3.3 8.8 - - - +
390C HIS* 3.8 4.0 - - - -
391C GLY 3.9 1.5 + - - -
392C LEU* 2.9 59.4 + - + +
393C THR 5.1 2.5 - - - -
394C ARG 3.2 20.9 - - - -
395C THR* 4.1 7.6 - - + -
412C VAL* 4.1 5.4 - - + -
413C GLU 3.2 18.6 - - - +
414C ALA* 4.2 17.7 - - + -
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Residues in contact with SER 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C VAL 4.1 0.6 + - - -
362C TYR* 1.3 72.6 - - - +
364C VAL* 1.3 61.0 + - - +
365C THR* 4.9 5.2 - - - +
390C HIS* 3.8 21.3 - - - -
411C THR 3.8 1.9 - - - +
412C VAL* 3.3 3.3 - - - -
413C GLU* 2.8 64.0 + - - +
415C ARG* 4.5 12.6 - - - +
425C ARG* 4.9 0.9 + - - -
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Residues in contact with VAL 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C LEU* 4.9 17.0 - - + -
348C TRP* 4.7 5.6 - - + -
363C SER* 1.3 75.8 - - - +
365C THR* 1.3 72.4 + - - +
385C TYR* 3.8 35.0 + - + -
389C PRO* 3.7 21.0 + - + +
390C HIS* 4.3 13.2 - - - -
392C LEU* 4.1 20.4 - - + -
397C VAL* 5.0 2.0 - - + -
410C PHE* 5.1 2.0 - - + -
411C THR 4.1 1.1 - - - -
412C VAL* 3.8 24.0 - - + -
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Residues in contact with THR 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C SER* 4.9 4.9 - - - +
364C VAL* 1.3 83.4 - - - +
366C CYS* 1.3 62.5 + - - +
385C TYR* 5.4 0.2 - - - -
390C HIS* 6.2 1.1 - - + -
410C PHE* 3.0 20.5 - - - -
411C THR* 2.7 59.5 + - - +
413C GLU* 6.6 0.2 - - + -
425C ARG* 5.7 7.9 - - - +
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Residues in contact with CYS 366 (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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365C THR* 1.3 75.1 + - - +
367C GLU* 1.3 68.5 + - - +
378C PRO* 4.3 2.1 - - - +
379C CYS* 2.0 64.1 + - + +
383C VAL* 5.2 0.9 - - - -
385C TYR* 3.7 13.0 - - - +
408C TYR* 4.2 5.8 - - - -
409C THR 3.5 7.0 - - - -
410C PHE* 3.2 29.4 - - + -
411C THR* 6.3 0.2 - - - -
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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