Contacts of the helix formed by residues 406 - 413 (chain B) in PDB entry 3T9K
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 HIS 406 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A SER* 4.9 4.0 - - - -
405B GLY* 1.3 76.8 - - - +
407B VAL* 1.3 87.6 + - + +
409B ALA* 3.4 5.3 + - - +
410B GLN* 2.9 44.8 + - - +
465B TRP* 6.5 0.2 - - + -
470B VAL* 5.8 4.9 - - + +
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Residues in contact with VAL 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLY* 3.5 1.3 - - - -
406B HIS* 1.3 96.5 + - + +
408B VAL* 1.3 61.2 + - - +
410B GLN* 4.4 5.6 - - - +
411B VAL* 2.8 42.7 + - + +
460B LEU* 3.9 22.4 - - + +
463B ASP 5.7 0.7 - - - +
465B TRP* 3.9 40.2 - - + +
470B VAL* 4.5 11.7 - - + -
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Residues in contact with VAL 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ARG 4.2 14.1 - - - +
405B GLY* 3.5 18.1 - - - +
407B VAL* 1.3 79.8 - - - +
409B ALA* 1.3 59.8 + - - +
412B GLN* 2.8 66.5 + - + +
429B GLU* 5.1 5.4 - - + +
460B LEU* 4.1 25.7 + - + +
461B THR* 4.0 27.6 - - + -
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Residues in contact with ALA 409 (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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445A GLY 3.8 10.8 - - - +
448A ARG* 3.9 11.8 - - - -
449A SER* 3.6 39.9 - - - +
503A ARG* 5.2 6.1 - - - +
405B GLY 3.6 1.5 + - - +
406B HIS* 3.4 8.0 + - - +
407B VAL 3.2 0.4 - - - -
408B VAL* 1.3 80.7 - - - +
410B GLN* 1.3 57.0 + - - +
412B GLN* 3.8 0.3 - - - +
413B SER* 2.7 38.2 + - - -
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Residues in contact with GLN 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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406B HIS* 2.9 32.7 + - - +
407B VAL* 3.7 4.0 - - - +
409B ALA* 1.3 77.9 - - - +
411B VAL* 1.3 62.1 + - - +
413B SER* 3.4 12.4 + - - -
414B VAL* 3.5 15.9 + - - +
470B VAL* 3.8 24.8 - - + +
471B LYS* 5.5 5.4 - - - +
474B CYS* 4.0 16.9 - - - -
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Residues in contact with VAL 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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407B VAL* 2.8 28.1 + - + +
408B VAL 4.4 0.4 - - - +
410B GLN* 1.3 71.4 - - - +
412B GLN* 1.3 64.8 + - - +
413B SER 3.3 0.5 + - - -
414B VAL* 3.3 9.2 + - - +
417B ASN* 2.8 33.1 + - - +
438B THR* 3.7 23.6 - - + -
460B LEU* 3.8 24.7 - - + -
465B TRP* 5.2 1.1 - - + -
470B VAL* 4.1 19.5 - - + +
473B MET* 4.0 35.2 - - + -
474B CYS* 4.8 1.6 - - - -
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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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448A ARG* 3.2 35.4 + - - +
408B VAL* 2.8 43.3 + - + +
411B VAL* 1.3 73.8 - - - +
413B SER* 1.3 60.2 + - - +
414B VAL 3.2 4.4 + - - +
417B ASN* 4.0 14.8 - - - +
418B ALA* 3.5 27.5 + - - +
427B ALA* 3.4 29.2 + - - +
428B PRO* 2.7 31.2 + - + +
429B GLU* 4.2 4.8 - - - +
438B THR* 5.0 0.9 - - + -
460B LEU* 4.4 4.7 - - + -
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Residues in contact with SER 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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441A ILE* 5.8 3.8 - - - +
445A GLY* 3.5 27.0 - - - -
448A ARG* 3.5 11.7 + - - +
503A ARG* 5.9 0.3 + - - -
409B ALA 2.7 24.8 + - - -
410B GLN* 3.8 7.4 - - - -
411B VAL 3.1 0.6 - - - -
412B GLN* 1.3 74.1 - - - +
414B VAL* 1.3 64.9 + - - +
415B ASP* 3.7 1.4 + - - -
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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