Contacts of the strand formed by residues 161 - 173 (chain A) in PDB entry 3KJO
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 TYR 161 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLN* 1.3 86.2 - - - +
162A PHE* 1.3 66.8 + - - +
243A SER* 3.7 19.7 - - - +
244A LEU 3.1 5.2 - - - +
245A HIS* 3.4 37.4 - + + -
266A HIS* 4.5 7.6 - + - -
273A ARG* 5.2 0.4 - - - -
9B T 3.0 78.8 - + + +
10B T 2.9 37.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 3.7 35.4 - - + -
152A LYS 5.5 0.4 - - - -
153A LEU* 4.3 9.4 - - + -
156A VAL* 3.6 22.9 - - + -
160A GLN* 4.2 8.3 - - + +
161A TYR* 1.3 78.4 - - - +
163A ASP* 1.3 73.5 + - - +
164A LEU* 3.6 35.2 - - + -
243A SER* 3.3 2.1 + - - +
244A LEU* 2.8 59.2 + - + +
246A THR* 3.5 30.5 - - + -
263A PHE* 4.3 1.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LYS* 6.1 0.7 - - - +
75A ASN* 5.6 3.5 + - - -
150A LEU* 5.9 1.9 - - - +
151A LEU* 4.7 10.7 + - - +
162A PHE* 1.3 84.1 - - - +
164A LEU* 1.3 59.4 + - - +
165A THR* 4.0 2.3 + - - -
240A ARG* 4.5 11.8 - - + +
241A ILE 3.3 6.5 - - - +
242A TYR* 3.4 27.0 - - + +
243A SER* 2.9 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU 4.5 7.2 - - - +
153A LEU* 3.9 27.4 - - + -
162A PHE* 3.6 19.6 + - + -
163A ASP* 1.3 73.2 - - - +
165A THR* 1.3 77.3 + - - +
166A CYS* 3.8 12.2 + - + -
183A VAL* 4.0 26.7 - - + -
185A ASP* 4.1 6.7 - - + +
218A ILE* 4.1 10.5 - - + -
220A ILE* 4.1 2.2 - - + -
239A LEU 3.5 1.9 - - - +
240A ARG* 3.2 4.9 - - - -
241A ILE* 2.8 42.4 + - + +
244A LEU* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 3.6 34.2 - - + +
151A LEU 5.2 0.4 + - - -
152A LYS* 5.7 0.3 + - - -
163A ASP 4.0 2.6 + - - -
164A LEU* 1.3 80.2 - - - +
166A CYS* 1.3 65.7 + - - +
185A ASP* 3.7 11.6 - - - +
239A LEU 3.3 4.3 - - - +
240A ARG* 3.0 32.6 + - - +
278A LEU* 3.8 22.4 - - + -
284A ASP* 4.7 10.3 - - + +
285A VAL* 5.4 0.7 - - + +
288A LEU* 4.1 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 4.0 21.1 - - + -
165A THR* 1.3 78.1 - - - +
167A GLN* 1.3 59.9 + - - +
183A VAL* 3.6 34.8 - - + -
184A TRP 3.2 20.6 - - - +
185A ASP* 4.6 0.4 - - - -
238A PHE* 3.4 5.0 - - - +
239A LEU* 2.9 42.0 + - - +
241A ILE* 4.3 12.1 - - - -
288A LEU* 3.7 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A CYS* 1.3 75.8 - - - +
168A LEU* 1.3 69.3 + - - +
169A LEU* 3.9 10.0 - - - +
183A VAL* 3.3 6.6 - - - -
184A TRP* 2.9 64.6 + - + +
209A HIS* 5.4 1.0 - - - -
236A GLY* 3.1 26.4 + - - +
237A SER 3.5 12.1 - - - +
238A PHE* 3.7 30.6 - - + -
288A LEU* 4.1 0.6 - - - +
292A LEU* 3.7 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A CYS 4.3 0.4 + - - -
167A GLN* 1.3 73.5 - - - +
169A LEU* 1.3 58.4 + - - +
170A GLY 3.4 26.0 - - - +
171A LYS* 4.0 14.6 - - + -
181A LEU* 3.8 18.2 - - + -
182A LYS 3.6 9.2 - - - +
183A VAL* 3.9 13.5 - - + -
233A LEU* 3.6 33.9 - - + -
234A LYS 3.7 18.6 - - - +
235A VAL* 4.1 3.1 - - - -
236A GLY* 2.7 33.7 + - - +
237A SER* 2.9 15.9 + - - +
239A LEU* 3.8 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLN* 3.6 12.3 + - - +
168A LEU* 1.3 75.8 - - - +
170A GLY* 1.3 59.3 + - - +
182A LYS* 2.8 13.3 + - + +
183A VAL 5.0 0.7 - - - -
184A TRP* 3.5 36.8 - - + +
205A GLY* 3.7 10.6 - - - -
206A ASP* 4.1 4.7 + - + +
209A HIS* 3.8 22.4 - - + +
210A ILE* 3.8 22.0 - - + +
213A LEU* 3.4 31.0 - - + -
217A THR* 3.8 16.2 - - + -
235A VAL* 3.4 20.7 - - + +
236A GLY* 5.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 3.4 11.6 - - - +
169A LEU* 1.3 79.5 - - - +
171A LYS* 1.3 64.2 + - - -
181A LEU* 3.6 0.9 - - - -
182A LYS* 2.9 33.3 + - - +
203A LEU* 4.2 6.7 - - - -
204A GLU 3.3 10.8 - - - -
210A ILE* 4.2 11.7 - - - -
235A VAL* 4.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 4.0 15.7 - - + -
170A GLY* 1.3 78.6 - - - +
172A ALA* 1.3 64.3 + - - +
179A PHE* 3.7 14.1 - - + -
180A LEU 3.4 6.3 - - - -
181A LEU* 4.1 9.9 - - + -
202A VAL 3.7 1.0 - - - +
203A LEU* 3.2 3.3 - - - +
204A GLU* 2.8 61.6 + - + +
230A ALA 3.5 10.5 - - - +
231A ARG 2.8 27.9 + - - -
232A SER 4.2 0.6 - - - -
233A LEU 2.7 30.0 + - - +
235A VAL* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LYS* 1.3 78.2 - - - +
173A GLU* 1.3 64.3 + - - +
179A PHE* 3.6 9.2 - - - -
180A LEU* 2.9 42.6 + - + +
198A ILE* 3.7 30.3 - - + -
202A VAL* 4.2 5.6 - - + -
203A LEU* 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ALA* 1.3 80.0 - - - +
174A VAL* 1.3 64.5 + - - +
176A GLY* 4.8 9.5 + - - -
178A SER 5.0 0.7 - - - +
179A PHE* 3.2 22.4 - - + -
198A ILE* 4.0 6.1 - - - +
199A GLN 5.7 0.5 + - - -
202A VAL* 3.7 26.2 + - + +
227A VAL* 5.3 0.2 - - - +
231A ARG* 2.8 44.0 + - - +
----------------------------------------------------------
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