Contacts of the strand formed by residues 212 - 220 (chain A) in PDB entry 1A81
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 212 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU 3.9 0.2 - - - +
208A LEU* 3.8 3.5 - - - -
209A HIS* 3.0 35.0 + - + +
210A GLU 2.7 11.6 + - - +
211A GLY* 1.3 75.1 - - - +
213A VAL* 1.3 79.2 + - - +
214A LEU* 3.8 18.1 + - + +
171B GLU* 4.1 15.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A SER 5.7 0.2 - - - -
179A GLU* 2.9 50.6 + - - +
182A VAL* 3.8 28.7 - - + -
183A LEU* 4.8 8.6 - - + +
206A CYS* 4.7 9.0 - - + -
207A LEU 3.8 10.5 - - - +
208A LEU* 4.8 1.3 - - + +
211A GLY 4.0 1.4 + - - -
212A LYS* 1.3 95.6 - - - +
214A LEU* 1.3 63.0 + - - +
215A HIS* 3.3 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU 3.1 1.7 - - - +
206A CYS* 3.0 26.9 - - - -
207A LEU* 3.0 34.0 + - + +
209A HIS* 3.3 41.5 - - + -
212A LYS* 3.9 25.1 - - + +
213A VAL* 1.3 77.7 - - - +
215A HIS* 1.3 63.4 + - - +
216A TYR* 5.0 8.1 - - + +
252A LEU* 4.6 12.3 - - + -
171B GLU* 3.1 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG* 3.4 41.6 + - + +
178A SER* 4.0 2.7 - - - -
179A GLU* 3.5 16.4 + - + +
195A ARG* 2.3 35.3 + - - +
204A ALA* 5.9 0.2 - - + -
205A LEU 3.3 3.3 + - - +
206A CYS* 3.4 23.0 - - + +
213A VAL* 3.3 30.9 - - + +
214A LEU* 1.3 76.6 - - - +
216A TYR* 1.3 61.5 + - - +
169B ASP 4.4 1.7 + - - +
170B PTR 3.3 24.0 - - + -
171B GLU* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ALA* 3.7 0.7 - - - +
205A LEU* 2.9 56.6 + - + +
207A LEU* 4.5 17.9 - - + -
214A LEU* 5.0 5.9 - - + +
215A HIS* 1.3 74.8 - - - +
217A ARG* 1.3 65.4 + - - +
228A ILE* 4.3 21.5 - - + -
250A GLY 4.1 0.5 + - - -
251A LEU* 3.2 40.6 - - + -
252A LEU* 3.2 40.7 + - - +
170B PTR 4.3 2.0 - - - -
171B GLU* 2.8 48.0 - - + -
172B PRO 3.7 10.7 + - - -
173B ILE* 5.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG* 3.8 36.7 - - - +
202A SER* 2.4 32.7 + - - -
203A TYR 4.2 4.6 + - - +
204A ALA* 4.9 0.9 - - - +
216A TYR* 1.3 71.6 - - - +
218A ILE* 1.3 69.5 + - - +
219A ASP* 2.8 26.8 + - - +
228A ILE* 3.2 13.2 - - - +
229A PRO* 3.0 38.6 - - + +
170B PTR 3.9 34.4 - - + +
171B GLU 5.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ILE* 3.8 30.3 - - + -
202A SER* 2.8 14.2 + - - -
203A TYR* 2.6 55.2 + - + +
204A ALA 4.3 0.7 - - - -
205A LEU* 4.1 13.9 - - + +
216A TYR 3.7 6.5 + - - +
217A ARG* 1.3 79.5 + - - +
219A ASP* 1.3 67.3 + - - +
226A LEU* 4.4 21.3 - - + -
227A SER 4.4 4.3 - - - +
228A ILE* 4.1 14.1 - - + -
237A LEU* 4.6 3.6 - - + -
240A LEU* 3.7 25.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
201A GLY 4.3 0.4 - - - -
202A SER* 3.5 8.5 - - - +
217A ARG* 2.8 38.0 + - - +
218A ILE* 1.3 83.0 - - - +
220A LYS* 1.3 61.4 + - - +
221A ASP* 3.5 5.3 + - - +
225A LYS 3.7 0.7 - - - +
226A LEU* 3.4 3.7 - - - -
227A SER* 2.8 44.6 + - - +
229A PRO* 3.6 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A THR* 5.9 4.9 - - - +
200A ASN 5.4 2.9 - - - +
201A GLY* 3.3 37.0 + - - +
202A SER* 4.7 0.2 - - - +
203A TYR* 5.8 2.5 - - - -
219A ASP* 1.3 71.3 - - - +
221A ASP* 1.3 61.7 + - - +
224A GLY* 3.5 33.0 + - - -
225A LYS 4.1 6.7 - - - -
226A LEU* 3.4 24.6 - - + +
235A ASP 5.6 1.0 + - - -
----------------------------------------------------------
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