Contacts of the helix formed by residues 273 - 283 (chain C) in PDB entry 5W5T
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 273 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ARG* 3.5 38.4 - - + +
27C LEU* 3.4 12.5 - - - +
272C GLY* 1.3 76.6 - - - +
274C ILE* 1.3 60.1 + - - +
275C ASP* 3.8 7.6 + - - +
276C ALA* 3.2 23.9 + - - +
277C TYR* 2.9 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ARG 4.1 4.2 + - - +
27C LEU* 3.6 36.3 - - + +
28C LYS* 4.1 11.0 - - + -
30C LEU* 5.2 4.0 - - + -
273C THR* 1.3 73.0 - - - +
275C ASP* 1.3 58.2 + - - +
277C TYR* 3.4 6.5 + - + +
278C TRP* 2.9 27.9 + - - +
377C VAL* 4.7 8.1 - - + -
402C ARG* 3.9 28.5 - - + +
404C THR* 3.7 23.1 - - + -
408C ILE* 4.2 14.4 - - + -
410C LEU* 4.0 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C THR* 3.2 6.8 + - - +
274C ILE* 1.3 80.5 - - - +
276C ALA* 1.3 54.7 + - - +
278C TRP* 3.3 10.4 + - - +
279C GLN* 2.7 45.8 + - - +
404C THR* 4.2 11.5 - - + +
406C SER* 2.6 33.4 + - - +
408C ILE* 3.9 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C ARG* 5.9 0.2 - - - -
271C VAL* 3.9 19.2 - - + +
272C GLY 4.3 1.8 - - - +
273C THR* 3.2 23.1 + - - +
275C ASP* 1.3 78.3 + - - +
277C TYR* 1.3 60.4 + - - +
279C GLN* 3.3 6.6 + - - +
280C ALA* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 4.2 10.8 - - + -
30C LEU* 3.5 26.7 - - + -
39C VAL* 3.3 25.1 - - + +
40C TYR* 2.6 33.2 + - - +
41C PHE* 5.0 3.8 - + + -
47C ILE* 5.3 1.6 - - + -
271C VAL* 3.8 27.0 - - + +
273C THR 2.9 16.2 + - - +
274C ILE* 3.6 5.4 - - - +
276C ALA* 1.3 77.7 - - - +
278C TRP* 1.3 64.3 + - - +
280C ALA* 3.4 1.0 + - - +
281C ASN* 3.0 49.0 + - - -
345C PHE* 4.7 1.0 - - - -
360C VAL* 4.7 2.7 - - + -
362C LEU* 3.7 21.7 - - + +
377C VAL* 3.9 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ILE 2.9 17.0 + - - +
275C ASP* 3.5 9.2 - - - +
277C TYR* 1.3 79.0 - - - +
279C GLN* 1.3 103.0 + - - +
281C ASN* 3.9 1.4 - - - +
282C ILE* 3.0 44.0 + - + +
341C ARG* 4.2 12.8 - - - -
358C ASN* 3.0 34.4 + - + -
360C VAL* 3.7 15.4 - - + +
375C ASN* 3.6 22.9 - - - -
376C VAL 3.4 19.1 + - - +
377C VAL* 3.7 19.5 - - + -
408C ILE* 3.5 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ASP* 2.7 29.2 + - - +
276C ALA* 3.6 8.3 - - - +
278C TRP* 1.3 94.6 - - - +
280C ALA* 1.3 57.8 + - - +
282C ILE* 3.4 11.5 + - - +
283C ASP* 2.9 67.0 + - - +
341C ARG* 4.5 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE* 3.8 20.9 - - + -
267C TYR* 4.1 15.1 + - - +
269C ARG* 4.4 15.5 - - + +
271C VAL* 3.7 22.2 - - + -
276C ALA 2.9 20.1 + - - +
277C TYR 4.0 0.9 - - - +
279C GLN* 1.3 74.5 - - - +
281C ASN* 1.3 62.1 + - - +
283C ASP* 3.8 14.0 + - - +
284C LEU* 3.9 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE* 3.5 11.2 - - - -
42C GLY 2.9 30.3 + - - -
277C TYR* 3.0 57.6 + - - +
280C ALA* 1.3 74.3 - - - +
282C ILE* 1.3 65.6 + - - +
283C ASP 3.1 1.6 - - - -
284C LEU* 3.1 18.0 + - - +
285C THR 4.3 0.7 + - - -
343C LEU* 3.3 31.9 - - + +
345C PHE* 4.0 2.9 - - - -
360C VAL* 3.8 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C TRP* 3.0 33.7 + - + +
279C GLN* 3.6 22.4 - - - +
281C ASN* 1.3 78.2 - - - +
283C ASP* 1.3 61.2 + - - +
284C LEU 3.0 0.2 - - - -
285C THR* 2.8 34.7 + - + -
286C ASP* 4.2 1.6 + - - +
341C ARG* 3.5 57.3 + - + +
342C SER* 4.3 4.5 - - - -
343C LEU* 4.5 3.4 - - + +
358C ASN* 3.9 2.9 - - - -
359C ALA 3.8 19.1 - - - +
360C VAL* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C TYR* 6.5 0.9 - - + -
269C ARG* 4.9 8.8 + - - +
279C GLN* 2.9 56.6 + - - +
280C ALA* 3.9 10.6 - - - +
281C ASN 3.1 0.4 - - - -
282C ILE* 1.3 77.3 - - - +
284C LEU* 1.3 60.4 + - - +
285C THR 3.1 0.2 - - - -
286C ASP* 3.2 39.1 + - - +
289C PRO* 3.7 9.1 - - - +
290C ASP* 4.8 16.8 - - + +
341C ARG* 4.9 1.9 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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