Contacts of the helix formed by residues 408 - 418 (chain W) in PDB entry 5XTE
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 PRO 408 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406W TYR* 3.6 25.5 - - + +
407W MET* 1.3 87.0 - - + +
409W PRO* 1.3 73.3 - - + +
410W SER* 3.2 10.3 - - - +
411W THR* 2.9 49.5 + - + +
412W VAL* 3.3 4.3 + - - +
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Residues in contact with PRO 409 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382W TYR* 3.8 29.4 - - + +
383W LEU* 3.9 20.4 - - + -
386W VAL* 5.6 8.3 - - + -
406W TYR* 3.9 15.9 - - + +
407W MET 3.7 0.6 - - - +
408W PRO* 1.3 85.5 - - + +
410W SER* 1.3 59.8 + - - +
412W VAL* 3.0 6.3 + - + +
413W LEU* 2.9 35.0 + - - +
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Residues in contact with SER 410 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408W PRO* 4.3 9.4 - - - +
409W PRO* 1.3 81.8 - - - +
411W THR* 1.3 62.7 + - - +
413W LEU* 3.2 16.3 + - - +
414W GLN* 2.9 36.1 + - - +
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Residues in contact with THR 411 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407W MET* 3.9 17.9 - - + -
408W PRO* 2.9 33.3 + - + +
410W SER* 1.3 78.7 + - - +
412W VAL* 1.3 60.1 + - - +
414W GLN* 3.0 14.5 + - + +
415W GLN* 2.9 36.7 + - + +
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Residues in contact with VAL 412 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1O MET* 4.0 35.9 - - + -
382W TYR* 4.1 34.8 - - + +
399W GLN* 5.9 1.3 - - - +
407W MET* 3.9 26.2 - - + +
408W PRO 3.8 11.4 - - - +
409W PRO* 3.0 9.8 + - + +
411W THR* 1.3 76.2 - - - +
413W LEU* 1.3 58.7 + - + +
415W GLN* 3.0 12.2 + - + +
416W ILE* 2.9 29.0 + - + +
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Residues in contact with LEU 413 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379W LYS* 3.6 46.4 - - + -
382W TYR* 4.7 10.1 - - + -
383W LEU* 4.7 26.0 - - + -
409W PRO 2.9 27.8 + - - +
410W SER* 3.3 16.6 - - - +
412W VAL* 1.3 76.3 - - + +
414W GLN* 1.3 62.3 + - - +
416W ILE* 3.1 7.5 - - + +
417W ASP* 2.9 41.3 + - - +
136Y LEU* 6.0 1.3 - - + -
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Residues in contact with GLN 414 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410W SER* 2.9 25.9 + - - +
411W THR* 3.0 16.6 + - + +
413W LEU* 1.3 79.7 - - - +
415W GLN* 1.3 59.3 + - + +
417W ASP* 3.7 13.0 + - - +
418W SER* 2.9 30.5 + - - -
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Residues in contact with GLN 415 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1O MET* 4.5 8.8 - - - +
281W ALA* 6.1 0.5 - - - +
284W ASN* 4.0 21.3 + - - +
407W MET* 3.2 43.9 - - - +
411W THR* 2.9 23.0 + - + +
412W VAL* 3.0 18.3 + - + +
414W GLN* 1.3 79.0 - - + +
416W ILE* 1.3 59.9 + - - +
418W SER* 3.7 12.0 - - - -
419W VAL* 3.6 13.9 - - - +
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Residues in contact with ILE 416 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284W ASN* 5.2 5.1 - - + +
288W VAL* 3.8 12.3 - - + -
375W LYS* 2.2 60.7 + - + +
378W LEU* 3.4 44.4 - - + -
379W LYS* 4.0 11.4 - - + -
412W VAL* 2.9 12.0 + - + +
413W LEU* 3.1 29.6 - - + +
415W GLN* 1.3 73.4 - - - +
417W ASP* 1.3 65.4 - - - +
418W SER 3.1 1.6 - - - -
419W VAL* 3.0 13.2 + - - +
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Residues in contact with ASP 417 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372W GLN* 5.6 2.6 + - - -
375W LYS* 3.6 16.3 + - - +
379W LYS* 4.0 25.0 + - - +
413W LEU* 2.9 28.2 + - - +
414W GLN* 3.8 15.4 + - - +
416W ILE* 1.3 85.0 - - - +
418W SER* 1.3 61.6 + - - +
419W VAL 3.3 6.2 + - - +
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Residues in contact with SER 418 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281W ALA* 6.0 1.6 - - - +
414W GLN 2.9 17.3 + - - -
415W GLN* 3.7 12.1 - - - -
416W ILE 3.1 0.2 - - - -
417W ASP* 1.3 80.2 - - - +
419W VAL* 1.3 61.3 + - - +
420W ALA* 3.5 4.2 + - - +
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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