Contacts of the helix formed by residues 409 - 418 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407B SER 3.8 1.2 + - - -
408B LEU* 1.3 75.9 - - - +
410B LEU* 1.3 64.6 + - - +
411B ALA* 3.5 8.3 + - - +
412B GLN* 3.0 35.0 + - - +
413B ARG* 3.0 22.6 + - - +
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B SER* 1.3 72.7 - - - +
411B ALA* 1.3 58.1 + - - +
413B ARG* 3.2 32.2 + - - +
414B ARG* 2.9 30.6 + - - +
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Residues in contact with ALA 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B SER* 3.2 7.0 + - - +
410B LEU* 1.3 79.5 - - - +
412B GLN* 1.3 59.6 + - + +
414B ARG* 3.7 7.7 - - - +
415B GLY* 2.9 21.1 + - - -
419B THR* 4.9 1.0 + - - -
420B TYR* 4.3 3.7 + - - -
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Residues in contact with GLN 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B PRO* 3.8 23.0 - - + +
401B PHE* 5.9 0.2 - - - -
407B SER 4.7 0.5 - - - +
408B LEU* 3.5 25.0 - - + +
409B SER* 3.0 39.6 + - - +
411B ALA* 1.3 75.0 - - + +
413B ARG* 1.3 61.8 + - - +
415B GLY* 2.9 2.8 + - - -
416B PHE* 2.8 38.8 + - + -
420B TYR* 3.2 22.2 - - - +
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Residues in contact with ARG 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B TRP* 3.7 53.0 + - + +
406B ASN* 3.2 35.3 + - - +
408B LEU* 2.9 34.6 + - + -
409B SER 3.0 14.3 + - - +
410B LEU* 3.6 27.9 - - - +
412B GLN* 1.3 75.9 - - - +
414B ARG* 1.3 58.5 + - - +
416B PHE* 3.1 4.9 + - - +
417B THR* 2.8 34.1 + - - +
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Residues in contact with ARG 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B LEU 2.9 16.6 + - - +
411B ALA* 3.7 8.3 - - - +
413B ARG* 1.3 74.2 - - - +
415B GLY* 1.3 60.3 + - - +
417B THR* 3.8 14.4 - - + -
418B LYS* 2.9 40.5 + - + +
419B THR* 3.0 33.8 + - + +
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Residues in contact with GLY 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B PHE* 4.7 1.0 - - - -
411B ALA 2.9 9.8 + - - -
412B GLN 2.9 8.8 + - - -
414B ARG* 1.3 77.8 - - - +
416B PHE* 1.3 63.2 + - - +
417B THR 3.3 0.3 + - - -
418B LYS 3.7 1.0 + - - -
419B THR* 3.0 20.2 + - - -
420B TYR* 2.9 48.6 + - - +
421B THR 4.5 0.7 + - - -
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Residues in contact with PHE 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B PRO* 3.5 39.7 - - + -
311B ALA* 5.7 0.2 - - + -
312B PHE* 3.7 29.4 - + + -
318B VAL* 3.9 13.9 - - + -
346B TYR* 3.3 38.3 - - + +
384B LEU* 3.7 29.4 - - + -
386B ALA* 5.5 1.6 - - + -
401B PHE* 3.8 23.3 - + - -
405B TRP* 4.2 13.5 - + + -
408B LEU* 4.2 14.1 - - + -
412B GLN 2.8 31.0 + - - -
413B ARG 3.1 4.0 + - - +
415B GLY* 1.3 76.3 - - - +
417B THR* 1.3 61.0 + - - +
418B LYS 5.4 0.2 - - - -
420B TYR* 3.5 10.5 - + - -
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Residues in contact with THR 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B TYR* 4.1 21.1 - - - -
405B TRP* 4.5 8.0 - - - -
413B ARG* 2.8 16.4 + - - +
414B ARG* 3.6 17.5 - - + +
416B PHE* 1.3 79.5 - - - +
418B LYS* 1.3 75.8 + - + +
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Residues in contact with LYS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B ARG* 2.9 33.4 + - + +
415B GLY 4.0 0.9 - - - -
416B PHE 3.5 0.8 - - - -
417B THR* 1.3 89.2 - - + +
419B THR* 1.4 70.4 + - + +
420B TYR 3.9 1.1 - - - -
421B THR* 3.9 19.1 - - - +
422B VAL* 5.1 2.1 - - - +
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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