Contacts of the helix formed by residues 406 - 412 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339D GLY* 6.3 1.3 - - - -
340D HIS* 3.9 14.4 - - - +
405D ASP* 1.3 85.1 - - - +
407D VAL* 1.3 63.2 + - - +
408D ALA* 3.0 4.7 - - - +
409D SER* 2.6 39.0 + - - +
410D MET* 3.5 6.9 + - - +
458D GLU* 2.9 24.0 + - - -
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Residues in contact with VAL 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404D VAL* 3.9 26.2 - - + +
405D ASP 2.8 7.1 + - - +
406D ALA* 1.3 73.7 - - - +
408D ALA* 1.3 60.7 + - - +
410D MET* 3.2 16.6 + - - +
411D ILE* 3.2 18.5 + - + +
439D LEU* 4.0 22.0 - - + -
457D ALA* 3.9 20.6 - - + -
458D GLU 3.1 20.4 + - - +
459D GLU* 3.5 20.0 - - + -
475D LEU* 4.5 10.5 - - + -
477D PHE* 4.4 7.2 - - + -
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Residues in contact with ALA 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D ALA* 3.0 2.4 - - - -
407D VAL* 1.3 80.2 - - - +
409D SER* 1.3 62.0 + - - +
411D ILE* 4.0 2.5 - - - -
412D TYR* 3.0 31.2 + - - +
458D GLU* 5.5 0.4 - - - +
459D GLU* 3.4 25.9 - - - +
460D SER* 3.2 32.3 - - - +
461D THR* 4.0 10.5 - - + -
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Residues in contact with SER 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D GLY 4.8 6.9 + - - -
340D HIS* 5.0 2.6 + - - -
374D ILE* 5.5 6.9 - - - +
406D ALA* 2.6 35.2 + - - +
408D ALA* 1.3 78.4 - - - +
410D MET* 1.3 60.8 + - - +
412D TYR 3.3 17.9 - - - +
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Residues in contact with MET 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D PRO* 4.3 5.8 - - + +
339D GLY* 3.6 33.2 - - - +
377D TYR* 3.6 35.4 - - + +
404D VAL* 4.4 14.4 - - - -
405D ASP 4.8 0.2 - - - +
406D ALA 4.0 7.9 - - - +
407D VAL* 3.2 12.5 + - - +
408D ALA 3.1 0.6 - - - -
409D SER* 1.3 77.5 + - - +
411D ILE* 1.3 67.9 + - + +
412D TYR 3.2 3.1 + - - -
432D ASN* 3.3 10.7 + - - +
435D ALA* 3.2 24.3 - - + +
438D PHE* 4.3 9.0 - - + -
439D LEU* 3.8 36.8 - - + -
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Residues in contact with ILE 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407D VAL* 3.3 16.6 - - + +
408D ALA* 3.6 0.9 - - - +
410D MET* 1.3 77.2 - - - +
412D TYR* 1.3 76.0 + - + +
431D GLU* 3.3 8.1 - - - +
432D ASN* 2.6 32.0 + - - -
435D ALA* 4.5 0.4 - - - -
436D ILE* 3.3 32.3 - - + +
439D LEU* 3.7 28.0 - - + -
459D GLU* 3.5 28.0 - - + +
463D PHE* 3.8 28.7 - - + -
475D LEU* 5.1 4.5 - - + -
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Residues in contact with TYR 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D ALA* 3.0 22.6 + - + +
409D SER* 3.3 20.7 - - - +
410D MET 4.6 1.3 - - - -
411D ILE* 1.3 103.7 - - + +
413D ARG* 1.3 54.8 + - - +
414D ASP* 2.8 24.1 + - - +
430D ARG* 4.2 18.6 - - + -
431D GLU* 3.5 32.5 + - + -
461D THR* 3.5 34.7 + - + -
463D PHE* 3.4 26.2 - + - +
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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