Contacts of the strand formed by residues 215 - 221 (chain A) in PDB entry 2YZ2
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 215 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU* 3.0 53.7 + - + +
26A VAL* 4.7 0.2 - - - -
44A SER 4.5 0.2 + - - -
211A LEU* 3.2 6.3 - - - -
212A GLU* 2.8 38.9 + - - +
213A LYS* 3.8 10.1 - - + +
214A GLY* 1.3 83.7 - - - +
216A LYS* 1.3 65.5 + - - +
217A VAL* 3.5 8.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU 5.2 0.4 + - - -
26A VAL* 4.2 25.6 - - + +
27A SER* 2.7 31.8 + - - +
28A LEU* 4.6 2.9 - - + +
209A VAL* 3.7 20.4 - - + -
210A VAL 3.4 4.5 - - - +
211A LEU* 4.4 4.5 - - + +
215A LYS* 1.3 73.5 - - - +
217A VAL* 1.3 60.7 + - - +
218A PHE 3.5 17.0 - - - +
219A ASP* 2.9 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A VAL* 2.9 28.0 + - + +
212A GLU* 3.9 23.1 - - + +
215A LYS* 3.9 14.4 - - + +
216A LYS* 1.3 75.0 - - - +
218A PHE* 1.3 63.9 + - - +
229A TYR* 3.7 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL 3.4 13.7 - - - -
209A VAL* 3.4 2.3 - - - -
210A VAL* 3.0 32.1 + - + -
216A LYS* 3.5 10.5 - - - +
217A VAL* 1.3 82.7 - - - +
219A ASP* 1.3 75.3 + - - +
220A GLY* 3.2 30.5 - - - -
224A GLU* 3.6 15.3 - - + -
225A PHE* 3.4 50.9 - + + -
228A LYS* 4.2 16.2 - - + -
229A TYR* 3.8 31.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER 4.6 0.3 - - - +
28A LEU* 4.1 6.6 - - - +
29A VAL 5.1 0.9 + - - -
207A ARG* 3.0 39.0 + - - -
208A VAL 3.6 4.7 - - - -
209A VAL* 3.7 8.6 - - - +
216A LYS* 2.9 37.1 + - + +
218A PHE* 1.3 83.8 - - - +
220A GLY* 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG* 2.9 24.3 - - - +
208A VAL 3.0 17.8 + - - +
218A PHE* 3.2 12.9 - - - -
219A ASP* 1.3 78.3 + - - +
221A THR* 1.3 62.7 + - - -
224A GLU* 3.3 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP 3.5 13.7 - - - +
207A ARG* 3.8 5.2 - - + -
208A VAL 4.5 0.2 - - - -
220A GLY* 1.3 77.4 - - - -
222A ARG* 1.3 55.3 + - - +
223A MET* 3.4 9.5 + - - +
224A GLU* 2.7 45.0 + - - +
225A PHE* 2.5 37.1 + - - +
----------------------------------------------------------
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