Contacts of the helix formed by residues 406 - 412 (chain C) in PDB entry 1M7X
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 ALA 406 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339C GLY* 5.0 4.7 - - - -
340C HIS* 3.5 32.3 - - + +
405C ASP* 1.3 79.1 + - - +
407C VAL* 1.3 61.2 + - - +
408C ALA 3.5 2.2 - - - -
409C SER* 2.8 29.3 + - - +
410C MET* 3.1 13.9 + - - +
458C GLU* 3.6 11.3 + - - -
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Residues in contact with VAL 407 (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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404C VAL* 4.1 19.7 - - + +
405C ASP 4.0 4.5 - - - +
406C ALA* 1.3 73.2 - - - +
408C ALA* 1.3 68.7 + - - +
410C MET* 2.7 18.4 + - - +
411C ILE* 2.8 24.5 + - + +
439C LEU* 3.9 25.6 - - + -
457C ALA* 4.2 10.5 - - + -
458C GLU* 3.0 34.7 + - - +
459C GLU* 3.5 20.0 - - + -
466C VAL* 5.7 0.4 - - + -
475C LEU* 4.9 8.3 - - + -
477C PHE* 4.7 2.5 - - + -
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Residues in contact with ALA 408 (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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406C ALA* 3.5 0.6 - - - -
407C VAL* 1.3 77.4 - - - +
409C SER* 1.3 58.0 + - - +
411C ILE* 3.3 5.6 - - - +
412C TYR* 2.8 37.3 + - - +
458C GLU* 5.2 0.4 + - - -
459C GLU* 2.8 30.7 + - - +
460C SER* 3.4 26.5 - - - +
461C THR* 3.7 13.2 - - + -
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Residues in contact with SER 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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339C GLY 5.3 2.6 + - - -
374C ILE* 6.1 0.7 - - - +
406C ALA* 2.8 35.8 + - - +
408C ALA* 1.3 78.8 - - - +
410C MET* 1.3 62.9 + - - +
412C TYR* 3.3 23.0 - - - +
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Residues in contact with MET 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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338C PRO* 4.5 1.8 - - - +
339C GLY* 3.4 34.3 - - - +
377C TYR* 3.7 21.5 - - + +
404C VAL* 4.3 14.8 - - - -
405C ASP 4.6 0.4 - - - +
406C ALA 3.1 12.8 + - - +
407C VAL* 2.7 13.1 + - - +
409C SER* 1.3 85.4 + - - +
411C ILE* 1.3 61.9 + - + +
412C TYR 3.3 1.2 + - - -
432C ASN* 3.5 11.1 + - - +
435C ALA* 3.2 21.6 - - + +
438C PHE* 3.8 21.3 - - + -
439C LEU* 3.4 42.8 - - + -
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Residues in contact with ILE 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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407C VAL* 2.8 33.0 + - + +
408C ALA* 3.3 8.7 - - - +
410C MET* 1.3 74.3 - - - +
412C TYR* 1.3 62.4 + - + +
431C GLU* 3.4 5.5 - - - +
432C ASN* 2.4 33.7 + - - +
435C ALA* 3.8 6.1 - - + -
436C ILE* 3.5 39.5 - - + +
439C LEU* 4.1 19.5 - - + -
459C GLU* 4.0 7.9 - - - +
463C PHE* 3.6 46.7 - - + -
475C LEU* 4.9 1.1 - - + -
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Residues in contact with TYR 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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408C ALA* 2.8 28.8 + - + +
409C SER* 3.3 19.7 - - - +
410C MET 3.2 2.2 - - - -
411C ILE* 1.3 97.9 - - + +
430C ARG* 3.0 36.1 - - - +
431C GLU* 3.1 40.4 + - + -
432C ASN* 4.7 7.0 - - - -
461C THR* 4.1 28.3 + - + -
463C PHE* 4.2 12.5 - + - -
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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