Contacts of the strand formed by residues 254 - 260 (chain B) in PDB entry 1ZMC
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 ILE 254 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B THR* 3.0 40.6 - - + +
165B ILE* 3.9 17.9 - - + -
246B ALA* 4.6 2.7 - - + -
247B THR 3.5 12.6 - - - +
248B LYS* 4.4 10.8 - - + -
252B GLY 4.0 6.3 - - - +
253B LYS* 1.3 80.7 - - - +
255B ASP* 1.3 71.9 + - - +
256B VAL* 4.4 6.3 - - + -
269B ILE 3.5 1.7 - - - +
270B THR* 3.1 6.2 - - - -
271B CYS* 2.9 47.5 + - - +
272B ASP 3.9 8.5 - - - +
274B LEU* 4.1 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ALA* 3.1 4.5 - - - +
247B THR* 2.8 50.4 + - - +
249B LYS* 2.8 42.1 + - + +
253B LYS 4.3 0.2 - - - -
254B ILE* 1.3 71.2 - - - +
256B VAL* 1.3 62.1 + - - +
257B SER* 4.0 2.2 + - - +
268B VAL* 3.7 22.4 - - + +
269B ILE 3.5 1.6 - - - -
270B THR* 2.9 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B VAL* 4.2 18.4 - - + -
184B ILE* 5.3 0.2 - - + -
207B VAL* 5.9 0.2 - - + -
243B VAL* 3.5 33.0 - - + -
245B GLY 3.7 4.3 - - - +
246B ALA* 3.9 9.2 - - + -
254B ILE* 4.4 3.4 - - + -
255B ASP* 1.3 74.8 - - - +
257B SER* 1.3 63.2 + - - +
258B ILE* 3.7 9.8 + - + +
268B VAL* 3.3 4.9 - - - -
269B ILE* 2.7 50.7 + - + +
271B CYS* 4.3 13.0 - - - -
274B LEU* 4.0 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B VAL* 3.4 4.3 - - - +
244B THR* 2.8 41.4 + - - -
245B GLY* 2.7 20.9 + - - +
246B ALA* 5.5 0.3 - - - -
255B ASP* 4.0 3.0 + - - +
256B VAL* 1.3 73.2 - - - +
258B ILE* 1.3 65.7 + - - +
267B GLU 3.7 6.1 - - - -
268B VAL* 4.0 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B VAL* 4.3 8.5 - - + -
238B LYS* 4.0 19.1 - - + -
241B THR* 3.5 24.2 - - + -
242B LYS 3.3 4.5 - - - +
243B VAL* 4.0 23.1 - - + -
244B THR 4.3 0.9 - - - +
256B VAL* 4.2 13.5 - - + +
257B SER* 1.3 82.0 - - - +
259B GLU* 1.3 63.7 + - - +
265B LYS 3.7 0.4 - - - +
266B ALA* 3.3 4.0 - - - +
267B GLU* 2.6 75.7 + - + +
268B VAL 4.5 0.4 - - - +
269B ILE* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B THR* 3.1 9.8 - - - +
242B LYS* 2.8 54.6 + - - -
244B THR* 3.6 20.1 + - - +
258B ILE* 1.3 79.6 - - - +
260B ALA* 1.3 67.2 + - - +
263B GLY* 4.4 1.1 - - - -
264B GLY* 3.1 31.0 + - - +
265B LYS* 3.7 5.8 - - - -
266B ALA* 4.6 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ASN 3.6 7.6 - - - +
241B THR* 4.4 1.8 - - - +
242B LYS* 4.0 4.6 - - - -
259B GLU* 1.3 79.3 - - - +
261B ALA* 1.3 60.3 + - - +
262B SER* 4.2 10.5 - - - +
263B GLY* 2.8 32.0 + - - +
264B GLY 2.8 14.7 + - - +
265B LYS* 4.1 21.7 + - + +
----------------------------------------------------------
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