Contacts of the helix formed by residues 379 - 393 (chain C) in PDB entry 5T0H
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 THR 379 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C LEU* 4.9 1.3 - - - -
339C THR* 5.9 1.6 - - - -
375C ARG* 4.3 18.8 - - - +
378C VAL* 1.3 78.7 - - - +
380C GLN* 1.3 67.1 + - - +
381C GLU* 3.1 23.2 + - + +
382C ASP* 3.2 18.1 + - + +
383C PHE* 3.4 14.8 + - - -
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Residues in contact with GLN 380 (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 LEU* 5.1 1.8 - - - +
341C GLY 4.7 0.9 - - - +
342C ILE* 3.4 22.1 - - + +
343C ASN* 2.6 55.4 + - - +
346C LYS* 3.3 27.5 - - + +
347C ILE* 3.5 21.1 - - + +
379C THR* 1.3 77.5 + - - +
381C GLU* 1.3 51.7 + - - +
383C PHE* 3.7 9.5 - - - -
384C GLU* 2.4 38.6 + - + +
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Residues in contact with GLU 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C THR* 3.1 17.4 + - + +
380C GLN* 1.3 77.7 - - - +
382C ASP* 1.3 58.6 + - - +
384C GLU* 3.0 20.8 + - - +
385C MET* 2.6 60.8 + - - +
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Residues in contact with ASP 382 (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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366C ALA* 3.0 36.5 - - - +
369C TYR* 3.7 14.9 - - - +
370C ALA* 3.1 14.1 + - - +
375C ARG* 3.0 32.0 + - - +
378C VAL* 3.6 11.7 - - + -
379C THR* 3.2 4.7 + - + +
381C GLU* 1.3 85.9 + - - +
383C PHE* 1.3 61.1 + - - +
385C MET* 3.1 12.8 + - - +
386C ALA 3.1 17.3 + - - -
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Residues in contact with PHE 383 (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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336C MET* 4.5 5.2 - - + -
338C LEU* 3.4 43.1 - - + -
342C ILE* 3.7 17.9 - - + -
347C ILE* 3.9 16.6 - - + -
362C VAL* 4.6 4.3 - - + +
363C CYS* 3.5 39.3 - - + -
366C ALA* 3.4 19.7 - - + -
367C GLY* 4.9 1.6 - - - -
378C VAL* 3.6 30.5 - - + -
379C THR 3.4 14.1 + - - -
380C GLN* 3.1 9.8 + - - +
382C ASP* 1.3 77.8 - - - +
384C GLU* 1.3 55.6 + - - +
386C ALA* 3.3 4.0 + - - +
387C VAL* 2.9 31.8 + - - +
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Residues in contact with GLU 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C LYS* 6.5 0.7 - - + -
347C ILE* 4.6 1.7 - - + +
350C LEU* 4.6 17.9 - - + -
380C GLN* 2.4 33.3 + - + +
381C GLU* 3.0 33.8 - - - +
383C PHE* 1.3 66.3 - - - +
385C MET* 1.3 71.5 + - - +
387C VAL* 3.2 22.9 - - + +
388C ALA* 3.3 7.8 + - - +
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Residues in contact with MET 385 (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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369C TYR* 5.9 7.6 - - + -
381C GLU* 2.6 45.2 + - - +
382C ASP* 3.1 19.0 + - - +
384C GLU* 1.3 82.4 - - - +
386C ALA* 1.3 57.7 + - - +
388C ALA* 3.1 12.3 + - + +
389C LYS* 2.9 38.9 + - + +
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Residues in contact with ALA 386 (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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361C GLY 4.3 2.0 - - - +
362C VAL* 3.2 27.6 - - - +
365C GLU* 4.0 12.6 - - + -
366C ALA* 3.3 27.8 - - + +
369C TYR* 6.4 0.2 - - + -
382C ASP 3.1 6.1 + - - -
383C PHE 3.3 0.6 + - - +
385C MET* 1.3 72.1 - - - +
387C VAL* 1.3 65.0 + - - +
388C ALA 3.1 1.3 - - - -
389C LYS* 3.5 11.2 - - + +
390C VAL* 3.1 29.6 + - + +
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Residues in contact with VAL 387 (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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347C ILE* 3.9 22.7 - - + -
350C LEU* 3.5 49.6 - - + +
351C MET* 4.6 14.4 - - + -
358C GLU* 5.3 2.5 - - - -
362C VAL* 5.0 5.4 + - + +
383C PHE 2.9 19.5 + - - +
384C GLU* 3.2 15.5 - - + +
385C MET 3.2 0.2 - - - -
386C ALA* 1.3 75.8 - - - +
388C ALA* 1.3 61.0 + - + +
390C VAL* 4.8 2.5 - - - -
391C MET* 3.2 29.4 - - - +
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Residues in contact with ALA 388 (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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384C GLU* 3.3 7.6 + - - +
385C MET* 3.1 12.4 + - + +
386C ALA 3.1 0.4 - - - -
387C VAL* 1.3 80.7 - - + +
389C LYS* 1.3 55.0 + - + +
391C MET* 2.9 6.5 + - - -
392C GLN* 2.5 57.5 + - + +
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Residues in contact with LYS 389 (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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365C GLU* 4.9 11.9 - - + -
369C TYR* 3.6 38.3 + - + +
385C MET* 2.9 30.9 + - + +
386C ALA* 3.2 16.7 + - + -
388C ALA* 1.3 75.2 - - + +
390C VAL* 1.3 63.5 + - + +
392C GLN* 2.9 32.3 + - + +
393C LYS* 4.1 7.4 + - - +
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Residues in contact with VAL 390 (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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358C GLU* 3.2 38.1 - - - +
361C GLY* 3.2 36.6 - - - +
362C VAL* 5.1 0.9 - - - -
365C GLU* 4.2 19.7 - - + -
386C ALA 3.1 16.4 + - - +
387C VAL 4.3 0.2 - - - +
389C LYS* 1.3 73.6 - - - +
391C MET* 1.3 62.7 + - + +
392C GLN 3.8 0.3 + - - -
393C LYS* 4.3 20.0 + - - +
394C ASP* 5.0 5.2 - - - +
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Residues in contact with MET 391 (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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350C LEU 3.3 20.6 - - - +
351C MET* 3.7 23.1 - - - -
352C PRO* 3.6 32.3 - - + +
354C ALA* 4.4 10.3 - - + -
358C GLU* 3.7 16.8 - - - +
387C VAL* 3.2 22.9 - - - +
388C ALA* 2.9 5.1 + - - +
390C VAL* 1.3 77.8 - - + +
392C GLN* 1.3 62.2 + - - +
393C LYS 3.2 2.6 + - - -
394C ASP* 4.1 20.9 + - - +
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Residues in contact with GLN 392 (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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388C ALA* 2.5 47.9 + - + +
389C LYS* 2.9 19.6 + - + +
391C MET* 1.3 74.4 - - - +
393C LYS* 1.3 66.5 + - + +
394C ASP 4.4 2.8 - - - -
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Residues in contact with LYS 393 (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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389C LYS 4.6 7.9 - - - +
390C VAL* 4.5 15.0 - - - +
391C MET 3.2 1.4 - - - -
392C GLN* 1.3 80.1 - - + +
394C ASP* 1.3 71.8 + - - +
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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