Contacts of the strand formed by residues 408 - 414 (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 408 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C CYS* 4.2 7.6 - - - -
367C GLU 3.6 15.3 - - - -
368C GLN* 2.9 33.7 + - + -
379C CYS* 3.9 10.1 - - - -
383C VAL* 3.9 4.3 - - - +
402C LEU* 3.3 39.4 - - + +
403C GLU* 4.0 22.6 + - - +
406C MET* 2.3 64.7 + - + +
407C ASN* 1.3 61.0 - - - +
409C THR* 1.3 62.3 + - - +
410C PHE* 3.3 23.4 + + + -
430C ALA 3.7 0.5 - - - +
431C SER* 3.1 20.0 - - - -
432C VAL* 3.1 15.2 + - + +
433C SER* 5.7 1.6 - - - -
434C ILE* 5.9 5.2 - - + -
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Residues in contact with THR 409 (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 4.8 0.2 - - - -
366C CYS* 3.5 1.7 - - - -
367C GLU* 2.7 59.1 + - - +
369C CYS* 4.5 1.0 - - - -
407C ASN* 2.9 23.5 + - - -
408C TYR* 1.3 69.4 - - - +
410C PHE* 1.3 62.6 + - - +
411C THR* 4.8 4.5 - - + +
429C THR* 4.9 13.5 - - + -
430C ALA 5.1 0.4 - - - -
431C SER* 3.0 18.4 - - - +
501C NAG 3.6 23.6 + - - +
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Residues in contact with PHE 410 (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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335C LEU* 5.3 1.6 - - + -
337C ALA* 5.5 0.7 - - + -
344C VAL* 4.7 17.3 - - + -
346C LEU* 4.3 29.6 - - + -
364C VAL* 5.1 2.7 - - + -
365C THR 3.0 21.1 - - - -
366C CYS* 3.2 26.2 - - + -
385C TYR* 4.2 11.0 - + - -
399C VAL* 4.2 30.3 - - + -
402C LEU* 5.1 2.5 - - + -
408C TYR* 3.3 35.8 + + + -
409C THR* 1.3 71.2 - - - +
411C THR* 1.3 63.3 + - - +
412C VAL 5.7 0.2 - - - +
429C THR* 3.2 5.9 - - - +
430C ALA* 2.7 48.4 + - + +
432C VAL* 5.5 9.4 - - + -
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Residues in contact with THR 411 (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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335C LEU* 5.0 0.2 - - - -
363C SER 3.8 2.3 - - - +
364C VAL* 5.6 0.4 - - - -
365C THR* 2.7 56.1 + - - +
366C CYS 5.2 0.4 - - - +
409C THR* 4.8 5.4 - - + +
410C PHE* 1.3 79.1 - - - +
412C VAL* 1.3 58.6 + - - +
413C GLU* 5.2 0.7 - - - +
427C PHE* 3.7 29.6 - - + +
428C ARG 3.7 4.9 - - - -
429C THR* 3.2 26.6 - - + +
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Residues in contact with VAL 412 (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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332C PRO* 3.5 12.9 - - + +
335C LEU* 3.5 35.9 - - + -
346C LEU* 6.1 3.4 - - + -
348C TRP* 3.8 37.0 - - + +
362C TYR* 4.1 10.3 - - + -
363C SER 3.3 9.9 - - - +
364C VAL* 3.8 20.4 - - + +
411C THR* 1.3 73.6 - - - +
413C GLU* 1.3 64.7 + - - +
427C PHE* 3.2 1.5 - - - +
428C ARG 3.1 25.7 + - - +
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Residues in contact with GLU 413 (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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332C PRO* 4.2 1.1 - - - -
361C VAL 3.3 1.9 - - - +
362C TYR* 3.2 15.4 - - - -
363C SER* 2.8 49.0 + - - +
411C THR 5.2 0.9 - - - +
412C VAL* 1.3 77.6 - - - +
414C ALA* 1.3 69.4 + - - +
415C ARG* 3.8 13.6 + - - +
425C ARG* 2.7 62.1 + - - +
426C SER 3.2 17.8 + - - +
427C PHE* 3.5 17.5 - - + +
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Residues in contact with ALA 414 (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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328C PRO* 5.7 0.3 - - - +
329C PRO* 3.4 21.0 - - + +
330C SER 3.6 9.2 - - - +
332C PRO* 3.7 9.2 - - + +
351C PRO* 3.6 31.2 - - + -
360C ILE* 3.9 4.9 - - + -
361C VAL 3.9 3.4 - - - -
362C TYR* 4.1 5.8 - - + -
413C GLU* 1.3 78.5 - - - +
415C ARG* 1.3 62.3 + - - +
419C SER* 4.7 0.2 + - - -
426C SER* 3.1 19.4 + - - +
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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