Contacts of the strand formed by residues 273 - 276 (chain B) in PDB entry 1ZMD
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 VAL 273 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ASP 5.0 2.7 - - - +
164B THR* 3.4 18.4 - - - +
166B VAL* 4.1 16.2 - - + -
174B LEU* 4.4 23.8 - - + -
176B LYS 5.8 0.2 - - - +
178B PRO* 3.6 28.3 - - + -
180B LYS 3.3 2.4 + - - -
181B MET* 3.3 15.5 - - + +
182B VAL 3.0 23.7 + - - -
254B ILE* 4.2 0.4 - - - -
271B CYS* 3.4 6.0 - - - -
272B ASP* 1.3 87.2 - - + +
274B LEU* 1.3 70.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ILE* 4.3 9.0 - - + -
164B THR 3.0 6.8 + - - +
165B ILE* 3.5 19.8 - - + +
166B VAL* 2.8 34.5 + - - +
182B VAL* 3.3 39.0 - - + +
184B ILE* 4.0 23.1 - - + -
246B ALA* 3.9 28.3 - - + -
254B ILE* 3.8 18.5 - - + +
256B VAL* 3.9 10.8 - - + -
271B CYS* 4.3 3.4 - - - -
273B VAL* 1.3 75.6 - - - +
275B LEU* 1.3 56.0 + - - +
276B VAL* 4.4 7.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
166B VAL* 3.4 8.7 - - + +
167B SER 3.5 33.4 - - - +
168B SER* 3.7 6.1 - - - +
171B ALA* 4.1 11.0 - - + -
181B MET* 4.4 13.9 - - + -
182B VAL 2.9 14.1 + - - +
183B VAL* 3.3 23.2 - - + -
184B ILE* 2.8 32.7 + - - +
189B ILE 5.1 0.2 - - - +
193B LEU* 3.9 30.3 - - + -
194B GLY 5.1 0.2 - - - +
273B VAL* 4.1 0.4 - - + -
274B LEU* 1.3 73.0 - - - +
276B VAL* 1.3 67.2 + - - +
277B CYS* 3.8 16.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B VAL* 4.7 5.9 - - - +
153B THR 4.7 7.9 - - - +
155B PHE* 3.7 35.0 - - + +
158B ILE* 4.1 24.9 - - + -
160B ILE* 4.0 23.6 - - + -
165B ILE* 4.3 8.3 - - + -
166B VAL 2.9 13.7 + - - +
167B SER* 3.7 13.7 - - - -
168B SER 4.4 0.5 + - - -
184B ILE* 4.2 16.6 - - + -
274B LEU* 4.4 3.8 - - + -
275B LEU* 1.3 79.3 - - - +
277B CYS* 1.3 65.1 + - - +
278B ILE* 4.8 5.6 - - + +
----------------------------------------------------------
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