Contacts of the helix formed by residues 274 - 283 (chain C) in PDB entry 1NTZ
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 PHE 274 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C PHE* 4.8 0.7 - + - -
124C MET* 3.7 50.7 - - + -
128C PHE* 4.3 14.8 - - + -
270C PRO* 3.8 10.5 - - + -
271C GLU* 3.1 12.0 + - + -
273C TYR* 1.3 111.9 - + - +
275C LEU* 1.3 54.7 + - - +
276C PHE* 3.2 7.4 - + - -
277C ALA* 3.0 8.9 + - + +
278C TYR* 2.7 34.4 + - - +
383C UQ2 3.0 66.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C LYS* 4.4 11.7 - - + +
270C PRO* 3.6 36.6 - - + +
271C GLU 3.8 0.4 + - - +
272C TRP* 3.1 38.8 + - + +
274C PHE* 1.3 77.7 - - - +
276C PHE* 1.3 56.4 + - - +
278C TYR* 3.3 4.8 + - + +
279C ALA* 2.8 29.5 + - - +
336C THR* 3.5 31.4 - - - +
339C GLY* 3.4 21.9 - - - +
340C GLY* 3.9 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C TYR* 3.7 21.3 - + - -
124C MET* 6.0 2.2 - - - -
273C TYR 3.5 24.9 - - - -
274C PHE* 4.4 1.3 - + - -
275C LEU* 1.3 74.0 - - - +
277C ALA* 1.3 79.8 + - + +
279C ALA* 3.4 3.3 + - - +
280C ILE* 3.0 39.2 + - + +
297C SER* 4.3 20.9 - - - -
298C ILE* 4.4 20.4 - - + -
332C LEU* 3.7 27.1 - - + -
335C LEU* 3.7 24.5 - - + +
336C THR* 3.5 23.8 - - + +
358C TYR* 4.6 5.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C PHE* 3.0 12.4 + - + +
276C PHE* 1.3 95.7 - - + +
278C TYR* 1.3 60.6 + - - +
280C ILE* 3.3 4.5 + - - +
281C LEU 2.9 24.3 + - - -
294C LEU* 3.4 29.3 - - + +
297C SER* 4.1 16.2 - - - +
298C ILE* 5.8 2.9 - - + -
383C UQ2 5.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C VAL* 5.1 6.8 - - + +
268C ILE* 3.0 22.4 + - + +
269C LYS* 4.0 6.5 - - + -
270C PRO* 3.4 28.7 - - + -
274C PHE 2.7 13.2 + - - +
275C LEU* 3.3 8.3 - - + +
277C ALA* 1.3 76.7 - - - +
279C ALA* 1.3 62.6 + - - +
281C LEU* 3.3 10.2 + - + +
282C ARG* 3.1 73.7 + - + +
294C LEU* 4.5 0.2 - - - +
339C GLY 3.2 23.1 - - - -
383C UQ2 3.1 39.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C LEU 2.8 10.2 + - - +
276C PHE 3.6 5.4 - - - +
277C ALA 3.3 0.2 - - - -
278C TYR* 1.3 74.5 - - - +
280C ILE* 1.3 57.5 + - - +
282C ARG* 3.7 7.4 + - - +
283C SER* 2.3 35.0 + - - -
335C LEU* 3.1 39.9 - - + +
338C ILE* 4.0 11.6 - - + +
339C GLY* 3.7 13.5 - - - +
351C GLY 4.4 0.6 - - - +
355C SER* 4.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C PHE* 3.0 16.9 + - + +
277C ALA* 3.3 8.9 + - - +
279C ALA* 1.3 77.2 - - - +
281C LEU* 1.3 63.2 + - - +
283C SER* 3.3 15.1 + - - -
284C ILE* 3.8 9.2 - - + +
293C ALA* 3.7 30.7 - - + +
294C LEU* 4.7 0.4 - - - -
297C SER* 3.7 22.9 - - - +
335C LEU* 4.0 19.5 - - + -
355C SER* 3.4 22.8 - - - +
358C TYR* 3.8 26.2 - - + -
359C PHE* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C VAL* 5.9 3.4 - - + -
149C LEU* 3.7 34.8 - - + -
277C ALA 2.9 16.9 + - - +
278C TYR* 3.5 13.0 - - + +
280C ILE* 1.3 80.4 - - - +
282C ARG* 1.3 62.3 + - + +
283C SER 3.1 3.5 + - - -
284C ILE* 3.3 18.0 + - - +
286C ASN 5.7 0.4 - - - +
287C LYS 5.5 0.9 - - - +
290C GLY* 3.4 38.3 - - - +
291C VAL* 3.8 1.3 - - - +
294C LEU* 4.0 10.7 - - + +
383C UQ2 3.6 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C HIS 5.9 0.2 + - - -
268C ILE 4.9 2.0 + - - -
278C TYR* 3.1 56.9 + - + +
279C ALA* 4.2 6.3 - - - +
281C LEU* 1.3 78.8 - - + +
283C SER* 1.3 58.8 + - - +
284C ILE 3.0 12.8 + - - +
338C ILE* 3.1 13.9 + - + +
339C GLY* 2.8 25.1 + - - -
341C GLN 2.4 30.9 + - - -
342C PRO* 4.7 1.6 - - - +
343C VAL* 3.4 47.1 - - + +
348C ILE* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ALA 2.3 28.0 + - - -
280C ILE 3.4 9.6 - - - -
281C LEU 3.1 1.2 + - - -
282C ARG* 1.3 75.8 - - - +
284C ILE* 1.3 60.6 + - - +
285C PRO* 3.7 7.4 - - - +
348C ILE* 5.6 3.8 - - - -
351C GLY 3.0 15.9 + - - -
352C GLN* 3.5 32.5 - - - +
355C SER* 3.0 23.3 + - - -
----------------------------------------------------------
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