Contacts of the strand formed by residues 217 - 224 (chain B) in PDB entry 1K9A
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 ASN 217 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A VAL* 3.6 17.1 - - + +
155A HIS* 3.4 25.9 - - - -
161A ASP* 3.6 25.9 + - - -
53B LYS* 4.3 6.5 - - - +
212B GLY 4.2 0.4 - - - -
213B ASP* 3.5 4.8 + - - -
214B TYR* 2.9 32.6 + - - +
215B ARG 3.4 8.1 + - - -
216B GLY* 1.3 82.9 - - - +
218B LYS* 1.3 69.7 + - - +
219B VAL* 3.5 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 6.0 2.0 - - + -
211B LEU* 3.9 17.7 - - + -
212B GLY 3.2 7.6 - - - +
213B ASP* 4.7 1.1 - - + +
217B ASN* 1.3 79.4 + - - +
219B VAL* 1.3 62.9 + - - +
252B LEU* 5.6 0.7 - - - +
268B TYR* 3.7 43.4 + - + +
270B ALA* 6.2 0.2 - - - +
324B GLU* 5.4 6.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LEU* 4.3 1.8 - - + -
211B LEU* 3.6 4.0 - - - +
212B GLY 2.7 42.8 + - - +
214B TYR* 3.8 20.6 - - + -
217B ASN 4.1 3.1 - - - +
218B LYS* 1.3 76.2 - - - +
220B ALA* 1.3 57.4 + - - +
221B VAL* 4.0 9.6 - - + -
252B LEU* 3.3 22.9 - - + -
265B VAL* 3.1 31.4 - - + -
266B THR 2.8 24.7 - - - +
267B GLU* 4.6 1.3 - - - -
268B TYR* 3.7 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ILE* 4.6 9.2 - - + -
209B VAL* 4.2 16.2 - - + -
210B MET 3.6 4.7 - - - -
219B VAL* 1.3 73.4 - - - +
221B VAL* 1.3 63.2 + - - +
265B VAL* 3.3 6.4 - - - +
266B THR* 2.9 58.1 + - + +
267B GLU 3.8 7.2 - - - +
268B TYR* 4.0 7.4 - - + +
269B MET 5.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LEU* 4.2 15.9 - - + -
197B LEU* 3.9 24.5 - - + -
208B ASP 3.5 1.2 - - - +
209B VAL* 3.2 5.2 - - - +
210B MET* 2.8 46.2 + - + +
212B GLY* 4.3 4.0 - - - -
219B VAL* 4.0 17.7 - - + -
220B ALA* 1.3 81.1 - - - +
222B LYS* 1.3 62.6 + - - +
263B TYR* 3.6 39.5 - - + -
264B ILE 3.7 3.6 - - - +
265B VAL* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE 5.2 0.9 - - - -
207B GLY* 5.1 8.5 - - - -
208B ASP 3.2 13.0 - - - +
209B VAL* 4.3 16.4 - - + -
221B VAL* 1.3 75.8 - - - +
223B CYS* 1.3 64.4 + - - +
224B ILE* 3.7 23.3 - - + +
236B GLU* 2.8 40.5 + - - +
262B LEU 3.7 0.3 - - - +
263B TYR* 3.1 6.8 - - - -
264B ILE* 2.8 47.5 + - + +
266B THR* 6.2 2.7 - - + -
332B ASP* 3.0 30.3 + - - +
334B GLY* 4.9 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLY* 3.4 12.3 - - - -
208B ASP* 3.2 22.6 + - - -
210B MET* 3.6 23.8 - - - -
222B LYS* 1.3 74.2 - - - +
224B ILE* 1.3 70.5 + - - +
225B LYS* 3.9 4.1 - - - +
261B GLY* 6.0 0.9 - - - -
262B LEU 3.4 13.2 - - - +
263B TYR* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE* 3.2 18.8 - - + +
207B GLY* 3.9 0.4 - - - -
222B LYS* 3.7 31.6 - - + +
223B CYS* 1.3 83.0 - - - +
225B LYS* 1.3 81.8 + - - +
227B ASP* 3.8 23.7 - - + +
232B ALA* 3.8 16.2 - - + -
233B PHE* 4.2 28.7 - - + +
236B GLU* 3.8 16.8 - - - +
262B LEU* 4.1 5.0 + - + +
264B ILE* 4.8 6.7 - - + -
----------------------------------------------------------
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