Contacts of the strand formed by residues 222 - 226 (chain U) in PDB entry 3EXG
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 GLY 222 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14U LEU* 3.7 1.2 - - - -
15U HIS* 2.9 36.1 + - - +
17U LEU* 4.1 6.9 - - - +
214U TYR* 3.6 17.2 + - - -
220U ILE 3.8 0.8 + - - -
221U PRO* 1.3 75.1 - - - +
223U LEU* 1.3 68.5 + - - +
251U ILE* 4.1 0.7 - - - -
252U LEU 3.0 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U CYS* 4.2 6.7 - - + -
13U ASP 3.2 12.6 - - - +
14U LEU* 4.1 7.9 - - + -
17U LEU* 5.1 0.7 - - + -
21U PRO* 4.0 21.8 - - + -
214U TYR* 3.4 10.0 - - - +
222U GLY* 1.3 77.4 - - - +
224U ARG* 1.3 59.5 + - - +
225U VAL* 4.1 3.1 + - + -
236U ALA* 4.4 14.1 - - + +
239U PHE* 3.8 28.3 - - + -
240U ALA* 5.2 0.9 - - + -
251U ILE* 3.6 23.1 - - + -
252U LEU 3.0 16.5 + - - +
253U MET* 3.6 19.3 - - + +
254U GLU 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 224 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10U LYS* 4.8 5.2 - - - +
12U CYS* 3.0 28.1 - - - +
13U ASP* 2.8 49.2 + - + +
211U THR 5.2 1.6 + - - -
212U ASP* 3.0 28.1 + - - +
214U TYR* 3.4 28.4 + - + -
223U LEU* 1.3 72.8 - - - +
225U VAL* 1.3 60.1 + - - +
254U GLU* 3.4 25.2 + - - +
256U GLN* 3.3 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10U LYS* 5.0 5.2 - - - -
12U CYS* 4.0 13.5 - - - -
223U LEU* 4.4 5.6 - - + -
224U ARG* 1.3 77.7 - - - +
226U ASP* 1.3 81.7 + - - +
227U GLY 3.7 0.4 - - - -
232U CYS* 3.9 27.1 - - + +
233U VAL* 4.3 10.5 - - + -
236U ALA* 3.6 23.8 - - + -
253U MET* 4.2 15.0 - - + -
254U GLU 2.8 17.8 + - - +
255U LEU* 4.0 7.4 - - + -
256U GLN* 3.1 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 226 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10U LYS* 4.4 31.3 + - + +
225U VAL* 1.3 84.0 - - - +
227U GLY* 1.3 58.6 + - - +
228U MET* 3.0 32.4 + - - +
229U ASP* 3.3 35.9 + - + +
232U CYS* 4.0 10.2 - - - +
233U VAL* 4.1 1.4 - - - +
256U GLN* 3.9 4.9 - - - +
290U LEU* 5.6 2.1 - - - +
----------------------------------------------------------
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