Contacts of the helix formed by residues 265 - 275 (chain B) in PDB entry 1ZXN
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 LYS 265 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B PRO 4.1 1.8 + - - -
264B VAL* 1.3 72.1 - - - +
266B GLY* 1.3 56.6 + - - +
268B ARG* 5.8 0.7 - - - +
269B SER* 2.8 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ALA 3.9 11.7 + - - -
248B GLY* 3.5 9.4 - - - -
250B THR 5.1 5.6 + - - -
264B VAL* 3.7 7.0 - - - +
265B LYS* 1.3 73.1 - - - +
267B PHE* 1.3 66.1 + - - -
268B ARG 3.4 2.0 - - - -
269B SER* 3.0 16.5 + - - -
270B TYR* 3.2 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B GLY 3.0 22.3 + - - +
266B GLY* 1.3 70.5 - - - -
268B ARG* 1.3 59.4 + - - +
270B TYR* 2.8 18.6 + + - +
271B VAL* 2.8 38.5 + - + +
298B GLU* 3.4 55.6 + - + +
300B CYS* 4.6 7.4 - - - -
311B ILE 4.6 0.7 - - - -
313B PHE* 3.7 27.1 - + - -
363B PHE* 3.7 34.5 - + + -
364B VAL 3.8 5.6 - - - -
365B ASN* 3.8 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LYS 5.8 0.4 - - - +
266B GLY 3.4 0.8 - - - -
267B PHE* 1.3 77.8 - - - +
269B SER* 1.3 57.6 + - - +
271B VAL* 3.3 9.1 + - - +
272B ASP* 3.0 34.0 + - - +
290B HIS* 3.5 33.2 - - + +
298B GLU* 3.9 4.2 + - - +
300B CYS* 4.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B PRO 5.1 3.5 - - - +
264B VAL* 3.4 7.8 - - - +
265B LYS* 2.8 46.0 + - - -
266B GLY 3.0 6.2 + - - -
267B PHE 3.3 0.4 - - - -
268B ARG* 1.3 75.6 - - - +
270B TYR* 1.3 66.3 + - - +
272B ASP* 3.5 23.3 - - - +
273B MET* 3.7 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 4.6 4.9 - - + +
241B ARG* 4.5 0.5 + - - -
244B TYR* 3.6 35.0 - - + -
245B ASP* 2.5 31.5 + - - -
248B GLY* 3.6 22.2 - - - -
264B VAL* 4.0 8.5 - - + -
266B GLY 3.2 1.1 + - - +
267B PHE* 2.8 26.8 + + - +
269B SER* 1.3 79.9 + - - +
271B VAL* 1.3 71.8 + - + +
273B MET* 2.9 30.2 + - - +
274B TYR* 2.6 43.9 + + - -
311B ILE* 4.3 5.3 - - + +
313B PHE* 3.5 28.5 - + - -
363B PHE* 5.4 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PHE* 2.8 28.8 + - + +
268B ARG 3.6 7.4 - - - +
270B TYR* 1.3 76.7 - - + +
272B ASP* 1.3 65.1 + - - +
274B TYR* 3.1 25.7 + - - +
275B LEU* 3.6 16.2 + - + +
288B VAL* 4.9 5.6 - - + -
300B CYS* 3.6 30.1 - - + -
363B PHE* 3.7 50.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ARG* 3.0 20.1 + - - +
269B SER* 3.5 18.2 - - - +
270B TYR 3.0 0.6 + - - -
271B VAL* 1.3 80.5 - - - +
273B MET* 1.3 50.6 + - - +
275B LEU* 2.5 42.8 + - - +
276B LYS 5.0 0.7 - - - -
288B VAL* 5.5 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.2 37.7 - - + +
69B GLY* 5.8 0.2 - - - -
70B ILE* 3.5 32.0 - - + +
244B TYR* 3.5 34.1 - - + -
263B PRO* 5.3 5.8 - - + -
264B VAL* 4.2 11.2 - - + -
269B SER 3.7 9.8 + - - +
270B TYR* 2.9 20.4 + - - +
272B ASP* 1.3 77.5 - - - +
274B TYR* 1.3 65.1 + - + +
275B LEU 3.2 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TRP* 3.3 55.1 - + - +
70B ILE* 3.2 27.4 - - + +
241B ARG* 3.9 10.7 + - - -
270B TYR* 2.6 58.1 + + - -
271B VAL* 3.1 10.8 + - - +
273B MET* 1.3 77.9 - - + +
275B LEU* 1.3 71.2 + - + +
276B LYS* 5.9 0.2 - - - +
311B ILE* 3.4 29.8 - - + +
361B TRP* 4.1 11.9 - - + -
363B PHE* 3.9 14.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B VAL* 3.7 20.4 - - + +
272B ASP* 2.5 30.8 + - - +
273B MET* 3.1 7.5 - - - +
274B TYR* 1.3 99.6 - - + +
276B LYS* 1.3 69.4 + - - +
288B VAL* 3.2 35.2 - - + -
302B THR* 4.8 11.9 - - + +
361B TRP* 4.4 13.9 - - + -
363B PHE* 4.1 13.2 - - + -
----------------------------------------------------------
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