Contacts of the strand formed by residues 211 - 217 (chain A) in PDB entry 3OPY
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 211 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LYS* 1.4 73.3 - - - +
212A LYS* 1.3 61.2 + - - +
213A ILE* 5.0 4.0 - - + -
240A GLY 4.3 3.2 + - - +
241A CYS* 3.2 22.5 - - - +
242A LYS 2.8 27.7 + - - +
306A ASP* 3.4 31.9 + - - +
307A ALA* 5.9 0.7 - - + -
352A THR* 5.3 7.7 + - - -
519A VAL* 5.1 18.3 + - + +
520A LEU* 4.4 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLU* 3.8 37.7 + - + +
210A LYS 4.0 6.3 + - - +
211A LYS* 1.3 72.4 - - - +
213A ILE* 1.3 59.6 + - - +
242A LYS* 3.4 17.3 - - + +
244A TYR* 3.6 40.1 + - + -
303A ASN 3.4 28.3 + - - +
304A GLY* 3.5 17.9 - - - +
305A ILE* 3.6 16.2 - - + +
306A ASP* 2.8 36.2 + - - +
307A ALA 3.5 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LYS* 3.6 6.3 + - + +
212A LYS* 1.3 75.5 - - - +
214A ALA* 1.4 63.6 + - - +
232A VAL* 4.9 11.0 - - + -
236A GLY* 4.9 3.6 - - - -
241A CYS* 3.7 34.1 - - + -
242A LYS 3.1 8.5 + - - +
243A VAL* 3.5 13.2 - - + +
244A TYR* 2.9 27.0 + - - +
305A ILE* 4.8 0.2 - - - -
307A ALA* 3.6 23.6 - - + +
309A VAL* 4.0 27.1 - - + -
516A VAL* 4.6 18.4 - - + -
519A VAL* 3.9 21.8 - - + -
520A LEU* 4.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LYS 3.9 1.0 + - - -
213A ILE* 1.4 74.1 - - - +
215A ILE* 1.3 55.3 + - - +
244A TYR* 3.2 11.0 - - + +
246A CYS* 5.0 4.3 - - + -
253A LEU* 5.4 2.7 - - + -
260A LEU* 4.7 15.0 - - + -
305A ILE* 3.6 23.6 - - + -
307A ALA 2.8 12.2 + - - +
308A LEU* 3.4 16.7 - - + +
309A VAL* 2.7 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ALA* 1.3 73.0 - - - +
216A ILE* 1.3 67.4 + - - +
228A ALA 5.3 0.4 - - - -
229A VAL* 4.1 18.2 - - + +
232A VAL* 3.8 30.1 - - + -
233A THR* 4.7 3.4 - - - +
243A VAL* 3.8 21.5 - - + -
244A TYR 3.1 13.3 + - - +
246A CYS 3.2 23.4 + - - -
263A LEU* 4.1 8.5 - - + -
279A ILE* 3.6 28.5 - - + +
309A VAL* 3.4 33.0 - - + +
311A CYS* 4.8 9.6 - - + -
356A LEU* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ILE* 1.3 74.4 - - - +
217A THR* 1.3 56.5 + - - +
218A SER* 3.7 28.0 - - - -
246A CYS* 3.3 44.4 - - + +
249A GLY 4.3 9.2 - - - +
250A TYR* 3.7 35.9 - - + -
253A LEU* 4.9 3.6 - - + -
279A ILE* 4.6 0.2 - - - -
308A LEU* 3.8 18.6 - - + -
309A VAL 2.7 10.5 + - - +
310A VAL* 3.7 23.6 - - + -
311A CYS* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ILE* 5.3 0.7 - - + -
216A ILE* 1.3 73.7 - - - +
218A SER* 1.3 59.5 + - - +
225A MET* 4.1 21.8 - - + -
229A VAL* 3.8 24.7 - - + -
246A CYS 4.9 0.2 + - - -
249A GLY* 3.5 7.0 - - - -
277A THR* 2.6 39.8 + - - +
279A ILE* 3.3 15.6 - - + +
280A GLY 3.2 15.2 + - - +
281A THR* 3.4 10.4 - - - -
311A CYS* 3.3 21.1 - - + +
----------------------------------------------------------
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