Contacts of the strand formed by residues 222 - 227 (chain A) in PDB entry 3DB4
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 222 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLY 3.6 5.8 + - - +
221A GLN* 1.3 74.8 - - - +
223A VAL* 1.3 61.9 + - - +
240A ASP* 5.9 2.0 - - + -
241A ALA 3.2 11.7 - - - +
242A GLU* 4.4 18.8 - - + +
280A ILE* 3.6 18.3 + - + +
282A ARG* 3.4 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 3.8 27.6 - - + -
221A GLN* 4.0 7.6 - - + -
222A VAL* 1.3 80.6 - - - +
224A MSE 1.3 59.2 + - - +
225A LEU* 3.6 26.7 - - + -
240A ASP* 3.2 4.9 - - - -
241A ALA 2.8 39.7 + - - +
243A ILE* 3.7 29.4 - - + -
277A VAL* 3.5 14.4 - - + -
278A PHE 3.4 9.0 - - - +
280A ILE* 3.7 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASP* 4.6 9.9 - - - +
151A TRP* 3.8 22.0 - - - +
205A ARG* 3.6 19.7 - - - +
208A ALA* 3.8 25.1 - - + -
223A VAL* 1.3 72.3 - - - +
225A LEU* 1.3 63.5 + - - +
238A TRP* 3.8 37.7 - - + +
239A TYR 3.4 13.5 - - - +
240A ASP* 3.7 13.0 - - - +
277A VAL* 3.7 0.2 - - - -
278A PHE* 2.7 58.5 + - + +
279A LYS 5.7 0.2 - - - +
280A ILE* 3.8 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A VAL* 3.6 23.8 - - + -
224A MSE 1.3 76.4 - - - +
226A ASN* 1.3 64.3 + - - +
227A TYR* 3.7 11.8 + - + -
238A TRP* 3.4 12.3 - - - -
239A TYR* 2.9 36.1 + - + +
241A ALA* 3.7 27.1 - - + -
243A ILE* 5.2 1.1 - - + -
255A LEU* 5.0 4.3 - - + -
257A ALA* 4.4 4.5 - - + -
259A VAL* 4.4 2.7 - - + -
271A ILE* 3.7 44.4 - - + -
273A PHE 5.3 0.4 - - - +
276A GLU 4.6 1.3 - - - -
277A VAL* 4.1 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 1.3 75.4 - - - +
227A TYR* 1.3 65.2 + - - +
235A ARG* 3.6 15.3 - - - +
236A GLY 2.9 38.7 + - - -
237A PHE 3.6 2.7 - - - -
238A TRP* 3.1 49.6 - - + +
271A ILE* 4.2 11.3 - - - +
272A ILE 5.0 0.7 + - - -
273A PHE* 3.7 33.8 + - + +
276A GLU 5.0 1.0 + - - -
301A SO4 3.6 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 3.7 14.1 + - + -
226A ASN* 1.3 76.7 + - - +
228A ASN* 1.3 69.6 + - - +
229A PRO* 3.7 30.2 + - + +
232A PRO* 3.5 39.1 - - + +
234A GLU 4.8 2.0 - - - -
236A GLY* 4.0 3.4 - - - -
237A PHE 2.9 31.0 + - - +
239A TYR* 3.5 14.5 - + + -
259A VAL* 4.1 15.5 - - + -
266A LEU* 4.2 10.7 - - + +
269A CYS* 3.5 37.3 - - + +
270A ARG 3.7 20.9 + - - -
271A ILE* 3.7 18.2 - - + -
272A ILE* 5.6 0.9 - - + -
273A PHE* 5.4 1.6 - - - -
----------------------------------------------------------
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