Contacts of the strand formed by residues 217 - 224 (chain A) in PDB entry 2ATW
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 ARG 217 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLU* 2.9 32.7 + - - +
216A HIS* 1.3 80.1 + - - +
218A SER* 1.3 70.9 + - - +
219A LYS* 5.0 2.7 - - - +
253A GLU* 3.7 4.6 - - - +
254A LYS* 3.0 28.7 - - - +
256A ASP* 2.8 28.6 + - - -
274A PRO* 5.8 0.9 - - - +
308A GLN* 3.0 39.0 + - - +
309A ASN* 5.4 3.6 - - - +
312A LEU* 3.6 21.2 - - + +
3B A 2.7 38.2 + - - +
4B C 3.6 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A VAL* 3.9 16.5 - - - +
210A VAL* 4.9 1.3 - - - -
211A ALA 3.3 7.6 - - - -
212A ARG* 3.1 23.6 - - - +
217A ARG* 1.3 77.4 - - - +
219A LYS* 1.3 66.5 + - - +
220A ILE* 4.8 1.6 - - - -
253A GLU* 2.7 23.9 + - - -
254A LYS 2.7 12.0 + - - +
255A ILE* 3.3 14.6 - - - +
256A ASP* 2.8 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A VAL* 3.4 3.6 - - - +
211A ALA* 2.9 35.0 + - + +
217A ARG* 5.3 0.7 - - - +
218A SER* 1.3 74.7 - - - +
220A ILE* 1.3 63.8 + - - +
256A ASP* 2.7 34.0 + - + +
258A ILE* 4.4 2.2 - - + +
271A ALA 3.0 21.1 + - - +
273A SER 2.6 30.7 + - - -
309A ASN* 2.7 41.9 + - - +
312A LEU* 3.8 26.9 - - + +
313A ALA* 3.8 11.2 - - - +
316A LEU* 3.5 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A VAL* 3.9 27.4 - - + -
193A PHE* 3.9 29.8 - - + -
207A ILE* 4.7 11.2 - - + -
209A ALA 3.3 6.7 - - - +
210A VAL* 4.0 15.3 - - + -
218A SER* 4.1 1.8 - - - -
219A LYS* 1.3 80.2 - - - +
221A ALA* 1.3 59.9 + - - +
222A VAL* 3.8 21.7 + - + -
235A CYS* 4.8 1.6 - - - -
255A ILE* 4.4 7.2 - - + -
256A ASP 3.0 8.6 + - - +
257A ILE* 3.8 30.5 - - + +
258A ILE* 2.8 29.1 + - - +
316A LEU* 4.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ILE* 3.4 2.3 - - - -
208A VAL* 2.8 29.1 + - + -
209A ALA* 2.7 22.0 + - + +
220A ILE* 1.3 72.5 - - - +
222A VAL* 1.3 66.1 + - - +
258A ILE* 3.3 7.4 - - + +
260A TYR* 4.3 7.2 - - + -
267A PHE* 3.7 36.3 - - + -
316A LEU* 3.9 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 4.4 7.2 - - + -
206A GLU 3.1 12.1 - - - +
207A ILE* 4.2 9.2 - - + -
208A VAL* 4.5 0.2 - - - -
220A ILE* 3.8 28.0 - - + -
221A ALA* 1.3 80.6 - - - +
223A ARG* 1.3 63.3 + - - +
231A ALA* 4.1 5.8 - - + +
232A LYS* 4.1 21.8 - - - +
235A CYS* 4.0 11.7 - - - -
257A ILE* 4.0 15.5 - - + -
258A ILE 3.0 14.4 + - - +
259A ASP* 3.8 6.4 - - - +
260A TYR* 2.7 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 3.4 3.5 - - - +
206A GLU* 2.8 65.9 + - + +
208A VAL* 3.7 18.6 - - + -
222A VAL* 1.3 79.2 - - - +
224A SER* 1.3 74.2 + - - +
225A ASN* 2.5 30.4 + - - +
231A ALA* 3.6 9.0 - - - -
260A TYR* 4.0 27.1 - - + +
262A ASP* 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A SER 3.7 6.1 + - - -
205A VAL* 4.4 0.4 - - - -
223A ARG* 1.3 91.7 + - - +
225A ASN* 1.3 61.0 + - - +
226A VAL 3.0 22.3 + - - -
229A LEU* 2.9 34.2 + - - +
231A ALA* 3.6 12.8 - - - +
----------------------------------------------------------
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