Contacts of the helix formed by residues 409 - 418 (chain C) in PDB entry 3MA2
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 409 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407C SER 3.7 1.8 + - - -
408C LEU* 1.3 77.4 - - - +
410C LEU* 1.3 61.4 + - - +
411C ALA* 3.0 19.8 + - - +
412C GLN* 2.9 29.6 + - - +
413C ARG* 2.9 23.8 + - - +
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Residues in contact with LEU 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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409C SER* 1.3 71.0 + - - +
411C ALA* 1.3 58.0 + - - +
412C GLN 3.3 0.2 - - - -
413C ARG* 3.3 29.5 - - - +
414C ARG* 2.8 44.0 + - + +
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Residues in contact with ALA 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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409C SER* 3.0 8.9 + - - +
410C LEU* 1.3 77.5 - - - +
412C GLN* 1.3 53.3 + - + +
414C ARG* 3.1 15.8 + - - +
415C GLY* 2.5 34.5 + - - -
419C THR* 5.1 2.6 - - - +
420C TYR* 4.6 3.5 + - - -
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Residues in contact with GLN 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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308C PRO* 3.9 24.4 - - + +
401C PHE* 5.1 5.1 - - - -
408C LEU* 3.5 21.4 - - + +
409C SER* 2.9 37.1 + - - +
411C ALA* 1.3 79.7 - - + +
413C ARG* 1.4 59.8 + - - +
415C GLY* 3.1 1.9 + - - -
416C PHE* 2.8 40.0 + - + -
420C TYR* 3.4 21.7 - - - +
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Residues in contact with ARG 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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405C TRP* 3.3 59.7 - - + +
406C ASN* 4.9 4.8 + - - +
408C LEU* 3.3 28.4 + - + -
409C SER 2.9 14.8 + - - +
410C LEU* 3.3 31.1 - - - +
411C ALA 3.4 0.2 - - - -
412C GLN* 1.4 74.1 - - - +
414C ARG* 1.3 57.3 + - + +
416C PHE 3.6 0.3 + - - -
417C THR* 2.6 39.3 + - - -
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Residues in contact with ARG 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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410C LEU* 2.8 31.6 + - + +
411C ALA* 3.5 11.5 + - - +
413C ARG* 1.3 78.0 - - + +
415C GLY* 1.3 58.4 + - - +
417C THR* 3.8 6.0 - - - +
418C LYS* 2.8 24.9 + - - +
419C THR* 3.0 28.5 + - - +
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Residues in contact with GLY 415 (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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411C ALA 2.5 15.5 + - - -
412C GLN 3.1 4.8 + - - -
414C ARG* 1.3 69.6 - - - +
416C PHE* 1.3 65.3 + - - +
418C LYS 3.4 1.6 + - - -
419C THR* 3.3 16.5 + - - -
420C TYR* 2.9 55.0 + - - +
421C THR* 4.5 1.2 + - - +
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Residues in contact with PHE 416 (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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308C PRO* 4.1 14.4 - - + -
312C PHE* 3.6 31.8 - + + -
318C VAL* 3.8 13.0 - - + -
346C TYR* 3.4 36.4 - - + +
384C LEU* 3.7 34.5 - - + -
386C ALA* 5.3 2.7 - - + -
401C PHE* 4.0 27.4 - + + -
405C TRP* 4.1 6.5 - + + -
408C LEU* 4.0 16.8 - - + -
412C GLN* 2.8 30.1 + - + +
413C ARG 4.0 3.1 - - - +
415C GLY* 1.3 72.7 - - - +
417C THR* 1.3 64.2 + - - +
418C LYS* 4.4 0.5 - - - -
420C TYR* 3.5 24.7 - + - -
421C THR* 4.6 2.9 - - - +
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Residues in contact with THR 417 (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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344C LYS* 6.3 0.9 - - - -
346C TYR* 4.0 22.6 + - + +
405C TRP* 3.7 15.4 - - - -
413C ARG* 2.6 25.2 + - - +
414C ARG* 3.8 8.1 - - - -
416C PHE* 1.3 79.4 - - - +
418C LYS* 1.3 65.8 + - + +
421C THR* 4.9 1.9 - - - +
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Residues in contact with LYS 418 (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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414C ARG 2.8 13.9 + - - +
415C GLY 3.4 3.0 + - - -
417C THR* 1.3 80.3 - - + +
419C THR* 1.3 63.9 + - - +
420C TYR 3.6 1.6 - - - -
421C THR* 3.5 21.0 + - + +
422C VAL* 4.5 2.8 + - - +
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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