Contacts of the helix formed by residues 260 - 270 (chain C) in PDB entry 2POZ
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 TYR 260 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C GLY 4.3 4.7 - - - +
86C GLY* 4.0 10.3 - - - -
87C ALA* 3.3 43.7 - - + +
90C PHE* 4.1 17.3 - - + -
257C GLU 4.2 1.8 - - - -
258C ARG* 3.4 39.3 - - - +
259C VAL* 1.3 88.6 - - - +
261C THR* 1.3 80.4 + - + +
264C GLY* 3.1 14.0 + - - -
283C THR* 3.3 40.8 - - + +
284C ALA* 4.3 2.0 - - - +
81G TRP* 3.6 13.3 + + - -
83G LYS 4.8 2.4 + - - -
84G ASN* 4.0 19.9 + - - +
85G GLY* 5.7 0.4 - - - -
237G PHE* 3.6 5.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TRP* 4.5 6.5 - - + -
90C PHE* 3.5 46.4 - - + -
259C VAL 4.3 0.2 + - - -
260C TYR* 1.3 80.2 + - - +
262C ARG* 1.3 58.7 + - - +
263C PHE* 3.2 28.3 + - + +
264C GLY 3.4 2.1 + - - -
265C PHE* 2.9 30.0 + - - -
284C ALA* 2.8 27.8 + - - +
289C GLU* 3.6 10.5 - - - -
293C ILE* 3.5 10.8 - - - +
237G PHE* 3.6 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TRP* 4.0 15.0 - - - -
261C THR* 1.3 72.9 - - - +
263C PHE* 1.3 83.1 + - + +
265C PHE* 3.7 2.3 - - - +
266C ARG* 2.9 32.1 + - - +
289C GLU* 2.7 42.6 + - - +
292C LYS* 3.9 33.2 - - + +
293C ILE* 3.7 17.6 - - + +
296C MSE 3.8 26.8 - - - +
295H ALA* 2.9 37.2 + - - +
298H GLU* 3.0 32.3 + - - +
299H ALA* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TRP* 4.5 8.1 - + - -
76C TYR* 3.7 31.9 - + - -
261C THR* 3.1 14.3 - - - +
262C ARG* 1.3 106.6 - - + +
264C GLY* 1.3 59.2 + - - +
266C ARG* 3.8 15.4 - - - +
267C LYS* 3.4 13.9 + - - +
175G ARG* 4.6 10.5 - - - -
237G PHE* 3.5 48.7 - + + +
298H GLU* 3.6 32.3 - - + -
299H ALA* 3.5 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C VAL* 3.5 17.1 - - - +
260C TYR 3.1 20.9 + - - -
261C THR 3.0 4.2 + - - -
263C PHE* 1.3 79.4 - - - +
265C PHE* 1.3 61.8 + - - +
266C ARG 3.3 0.3 + - - -
267C LYS* 3.2 36.8 + - - +
268C ILE* 3.9 2.4 + - - +
237G PHE* 3.8 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C VAL 5.1 0.2 - - - -
256C GLY* 3.5 37.2 - - - -
259C VAL* 3.3 34.5 - - + -
260C TYR* 4.3 0.9 - - - -
261C THR 2.9 26.8 + - - +
262C ARG* 4.1 3.4 - - - +
264C GLY* 1.3 71.6 - - - +
266C ARG* 1.3 65.7 + - - +
267C LYS 3.1 2.7 - - - -
268C ILE* 2.9 12.7 + - + +
269C PHE* 2.9 43.9 + + + -
277C ILE* 3.9 32.5 - - + -
279C PRO* 3.9 19.7 - - + -
284C ALA* 4.6 1.1 - - + -
293C ILE* 3.7 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ARG 2.9 17.0 + - - +
263C PHE* 3.8 10.3 - - - +
264C GLY 3.2 0.2 - - - -
265C PHE* 1.3 76.6 - - - +
267C LYS* 1.3 66.7 + - + +
269C PHE* 3.3 12.5 + - - +
270C GLU* 3.0 49.4 + - - +
296C MSE 4.5 7.9 - - + -
238G ASP* 3.1 25.6 + - - +
240G GLY* 3.9 10.0 - - - +
272H GLN* 2.5 33.1 + - - +
299H ALA* 2.7 38.4 + - + -
300H TYR* 3.3 43.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ASN* 4.5 6.3 + - - -
239C ASN* 3.9 21.7 + - - +
263C PHE 3.4 13.5 - - - +
264C GLY* 3.2 21.8 + - - +
266C ARG* 1.3 83.5 - - + +
268C ILE* 1.3 59.2 + - + +
270C GLU* 3.9 8.3 + - - +
271C LEU* 3.1 28.6 + - - +
84G ASN* 5.7 4.8 + - - +
237G PHE* 3.5 37.2 + - - +
239G ASN* 5.8 4.5 - - - +
267G LYS* 4.8 17.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
236C PRO 5.9 0.4 - - - +
239C ASN* 3.6 27.1 - - - +
242C LEU* 4.5 7.6 - - + -
255C VAL* 4.0 27.4 - - + -
259C VAL* 4.0 38.1 - - + -
264C GLY 4.2 2.0 - - - +
265C PHE* 2.9 15.1 + - + +
267C LYS* 1.3 76.9 - - + +
269C PHE* 1.3 67.8 + - + +
271C LEU* 3.1 23.1 + - + +
272C GLN* 3.5 3.6 + - - -
273C ALA 4.8 1.0 + - - -
274C CYS* 4.4 12.8 + - + -
277C ILE* 4.6 16.2 - - + -
302C MSE 4.7 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C PHE* 2.9 38.4 + + + +
266C ARG* 3.6 4.7 - - - +
268C ILE* 1.3 78.5 - - + +
270C GLU* 1.3 62.2 + - + +
272C GLN* 3.1 15.5 + - - +
277C ILE* 4.0 12.6 - - + -
293C ILE* 3.5 22.9 - - + -
296C MSE 3.4 48.0 - - + -
297C ALA* 3.6 22.9 - - + -
300C TYR* 3.3 47.1 - + + +
302C MSE 3.8 23.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ARG* 3.0 47.9 + - + +
267C LYS* 4.4 8.3 - - - +
268C ILE 3.3 0.2 - - - -
269C PHE* 1.3 75.7 - - + +
271C LEU* 1.3 62.4 + - + +
272C GLN* 4.5 7.6 + - - +
300C TYR* 4.5 6.7 - - - +
270H GLU* 4.6 20.6 - - - +
300H TYR* 3.1 26.0 + - - +
----------------------------------------------------------
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