Contacts of the helix formed by residues 266 - 278 (chain C) in PDB entry 1Z10
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 ASP 266 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C PHE* 3.5 14.7 - - - -
185C ILE 3.3 9.6 - - - +
186C VAL 3.3 10.8 - - - +
187C PHE* 3.1 20.1 - - - +
188C GLY* 3.3 20.6 - - - +
255C ASN* 3.0 24.2 + - - +
264C PRO 3.4 1.2 - - - -
265C ARG* 1.3 90.0 + - - +
267C PHE* 1.3 64.3 + - - +
268C ILE 3.3 1.4 + - - -
269C ASP* 2.9 28.2 + - - +
270C SER* 3.1 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PHE* 3.9 11.0 - + - -
131C SER* 3.7 31.6 - - - -
134C THR* 3.5 39.2 - - + +
135C LEU* 4.5 10.1 - - + -
138C PHE* 3.9 2.0 - - - -
185C ILE* 2.9 15.6 + - + +
186C VAL* 3.7 24.9 - - + -
266C ASP* 1.3 71.6 - - - +
268C ILE* 1.3 65.8 + - + +
270C SER* 3.3 3.3 + - - -
271C PHE* 3.1 38.2 + + + +
294C THR* 3.9 12.8 - - + -
295C THR* 4.0 20.6 - - - -
298C LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C VAL 3.4 16.3 + - - +
187C PHE* 3.9 22.7 - - + -
248C ILE 5.0 0.2 - - - +
251C LYS* 4.1 15.5 - - + +
252C VAL* 3.9 31.6 - - + +
255C ASN* 3.5 26.7 - - + +
266C ASP* 3.2 8.2 + - - +
267C PHE* 1.3 77.1 - - - +
269C ASP* 1.3 59.0 + - - +
271C PHE* 3.2 4.0 + - - +
272C LEU* 2.9 37.9 + - + +
291C LEU* 4.1 10.3 - - + -
295C THR* 3.9 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C ASN* 2.9 22.2 + - - +
259C LEU* 3.4 23.4 - - + +
260C ASP 5.1 0.5 + - - -
263C SER 4.3 1.4 - - - +
264C PRO* 3.6 21.0 - - + +
265C ARG* 2.7 51.6 + - - +
266C ASP* 2.9 20.1 + - - +
268C ILE* 1.3 70.2 - - - +
270C SER* 1.3 67.0 + - - +
272C LEU* 3.2 4.3 + - - +
273C ILE* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PHE* 3.8 8.9 - - - -
134C THR* 3.8 18.6 - - - +
138C PHE* 3.2 26.0 - - - -
264C PRO* 3.5 17.3 - - - +
266C ASP 3.1 3.0 + - - -
267C PHE 3.7 7.4 - - - -
268C ILE 3.3 0.2 - - - -
269C ASP* 1.3 79.8 - - - +
271C PHE* 1.3 62.7 + - - +
273C ILE* 3.3 6.1 + - - +
274C ARG* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C LEU* 3.9 25.4 - - + -
130C PHE* 3.5 31.8 - + + -
131C SER* 5.9 0.2 - - - -
267C PHE* 3.1 23.5 + + + +
268C ILE 3.5 7.9 - - - +
270C SER* 1.3 74.9 - - - +
272C LEU* 1.3 60.2 + - - +
274C ARG* 3.3 1.3 + - - +
275C MET* 2.8 46.1 + - + +
286C PHE* 3.7 24.7 - + - -
287C TYR 3.8 8.3 - - - -
290C ASN* 3.9 5.6 - - + -
291C LEU* 3.5 52.5 - - + -
294C THR* 4.6 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C VAL* 4.6 0.9 - - + +
255C ASN* 4.1 5.4 - - + +
256C GLN* 3.7 56.8 - - + +
259C LEU* 4.4 14.6 - - + -
268C ILE* 2.9 32.4 + - + +
269C ASP* 3.6 13.5 - - - +
271C PHE* 1.3 76.1 - - - +
273C ILE* 1.3 61.2 + - - +
275C MET* 3.3 18.8 + - + +
276C GLN* 3.1 25.7 + - - +
291C LEU* 3.4 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LEU* 4.2 15.7 - - + -
260C ASP 4.2 1.3 - - - +
261C PRO* 3.4 44.9 - - + +
264C PRO* 3.9 27.8 - - + -
269C ASP 2.9 20.4 + - - +
270C SER* 3.7 5.6 - - - +
272C LEU* 1.3 74.5 - - - +
274C ARG* 1.3 66.9 + - - +
276C GLN* 3.0 20.8 + - - +
277C GLU* 3.1 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C GLN* 5.3 5.3 - - - +
129C ARG* 6.1 3.0 - - - +
130C PHE* 3.7 42.2 - - + +
270C SER 3.0 16.3 + - - +
271C PHE 3.7 4.0 - - - +
273C ILE* 1.3 75.3 - - - +
275C MET* 1.3 64.0 + - - +
277C GLU* 3.2 21.0 + - - -
278C GLU* 2.9 44.2 + - - +
286C PHE* 3.6 41.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C GLN* 5.2 4.0 - - - +
271C PHE* 2.8 37.9 + - + +
272C LEU* 3.4 20.4 - - + +
274C ARG* 1.3 76.3 - - - +
276C GLN* 1.3 62.6 + - + +
278C GLU* 3.2 10.4 + - - +
279C GLU* 3.2 18.1 + - - +
286C PHE* 3.3 33.6 - - + +
287C TYR* 3.8 12.3 - - - -
288C LEU* 3.6 25.6 - - + +
291C LEU* 3.9 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LEU* 3.8 24.0 - - - +
261C PRO* 4.1 22.8 - - - +
272C LEU 3.1 15.4 + - - +
273C ILE* 3.0 13.9 + - - +
275C MET* 1.3 78.2 - - + +
277C GLU* 1.3 63.2 + - + +
278C GLU 3.2 1.4 + - - -
279C GLU* 3.2 37.7 + - - +
280C LYS* 4.8 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C ILE* 3.1 30.5 + - + +
274C ARG* 3.7 27.9 + - - +
276C GLN* 1.3 77.4 - - + +
278C GLU* 1.3 61.0 - - - +
279C GLU 3.4 0.4 - - - -
280C LYS* 3.2 33.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C GLN* 6.0 0.3 - - - +
274C ARG* 2.9 39.1 + - - +
275C MET 3.7 4.7 - - - +
276C GLN 3.1 0.2 - - - -
277C GLU* 1.3 80.4 - - - +
279C GLU* 1.3 59.3 + - - +
280C LYS* 3.1 3.6 - - - -
281C ASN* 2.8 54.7 + - - +
284C THR* 2.7 36.8 + - + +
286C PHE* 4.0 19.2 - - + +
----------------------------------------------------------
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