Contacts of the helix formed by residues 192 - 205 (chain A) in PDB entry 2KSB
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 192 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR 6.2 0.2 - - - -
169A SER* 5.4 0.3 - - - -
170A THR* 4.1 0.5 + - - +
187A HIS 5.5 0.2 - - - -
188A PRO 3.0 2.6 + - - -
189A ASN* 2.9 21.1 + - - +
190A LYS* 3.1 28.7 - - - -
191A ILE* 1.4 79.3 - - - +
193A GLU* 1.3 63.5 + - - +
194A LYS 3.5 2.7 - - - +
195A VAL* 4.0 19.3 + - + +
196A TYR* 3.9 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A THR* 2.9 19.3 - - + +
183A GLU* 2.7 29.6 - - + +
184A TRP 4.3 3.1 - - - +
186A GLU 2.5 24.4 - - - +
187A HIS* 2.8 23.2 + - - +
188A PRO* 3.0 28.1 + - + -
191A ILE* 3.4 1.4 - - - -
192A TYR* 1.3 73.0 - - - +
194A LYS* 1.3 82.6 + - - +
196A TYR* 3.0 16.1 + - - +
197A HIS* 3.1 15.5 + - + +
272A TYR* 3.5 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A HIS* 4.9 10.4 - - + +
192A TYR 3.5 0.4 - - - -
193A GLU* 1.3 97.1 + - - +
195A VAL* 1.3 69.7 + - + +
197A HIS* 3.4 9.4 + - - +
198A ILE* 3.5 19.0 + - + +
272A TYR* 2.8 34.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A TYR* 4.0 24.2 + - + +
193A GLU 3.2 0.8 - - - -
194A LYS* 1.3 82.5 - - + +
196A TYR* 1.3 64.6 + - - +
197A HIS 3.3 0.2 + - - -
198A ILE* 3.4 6.8 + - - +
199A CYS* 3.1 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 2.6 33.7 + - + -
164A PRO* 3.6 14.6 - - + +
165A GLN* 3.1 30.0 + - + +
169A SER* 3.7 22.7 - - - -
170A THR* 3.5 17.9 - - + -
182A ILE* 2.9 38.6 - - + -
192A TYR 3.9 6.9 + - - +
193A GLU 3.0 10.9 + - - +
195A VAL* 1.3 79.9 - - - +
197A HIS* 1.3 51.3 + - - +
199A CYS* 3.3 6.1 + - + +
200A VAL* 2.8 57.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A THR* 5.0 0.4 - - + +
182A ILE* 4.6 9.1 - - + +
183A GLU 4.6 2.2 + - - +
184A TRP* 3.7 21.2 + - + +
193A GLU* 3.1 18.1 + - - +
194A LYS 3.5 10.5 - - - +
195A VAL 3.2 0.4 - - - -
196A TYR* 1.3 73.9 - - - +
198A ILE* 1.3 70.8 + - - +
200A VAL* 4.1 0.2 - - - -
201A THR* 3.2 26.3 + - - -
268A PHE* 2.8 50.6 + + - -
269A LEU* 3.2 26.5 - - + +
272A TYR* 2.8 40.1 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LYS* 3.8 16.2 - - + +
195A VAL* 3.4 7.9 + - - +
197A HIS* 1.3 81.3 - - + +
199A CYS* 1.3 65.1 + - - +
201A THR* 4.0 0.3 - - - -
202A VAL* 3.1 39.1 + - + +
269A LEU* 5.1 4.9 - - + -
272A TYR* 3.5 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 4.8 12.3 - - - -
195A VAL* 3.1 21.7 + - + +
196A TYR* 3.5 8.7 - - + +
198A ILE* 1.3 81.2 - - - +
200A VAL* 1.3 64.3 + - + +
203A LEU* 2.7 61.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 5.9 0.4 - - + -
117A PHE* 3.8 15.9 - - + -
161A LEU* 3.0 33.4 - - + -
182A ILE* 3.7 12.6 - - + -
196A TYR* 2.8 67.6 + - + +
197A HIS 4.1 2.5 - - - +
199A CYS* 1.3 74.4 - - + +
201A THR* 1.3 63.8 + - - +
204A ILE* 2.7 39.6 + - + +
268A PHE* 4.8 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A HIS 3.2 8.7 + - - -
198A ILE 4.1 0.9 - - - -
200A VAL* 1.3 78.1 - - - +
202A VAL* 1.3 60.1 + - - +
204A ILE* 4.6 2.0 - - - -
205A TYR* 2.9 27.3 + - - +
206A PHE* 2.9 41.6 + - + -
265A HIS* 4.4 18.6 - - - +
268A PHE* 2.8 38.2 - - + -
269A LEU* 3.3 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 3.1 30.5 + - + +
201A THR* 1.3 79.4 - - - +
203A LEU* 1.3 70.4 + - + +
206A PHE* 3.2 21.1 + - + -
207A LEU* 2.7 34.3 + - + +
269A LEU* 5.7 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR* 3.0 9.3 + - - +
161A LEU* 4.9 5.6 - - + -
198A ILE* 6.1 0.2 - - + -
199A CYS* 2.7 59.0 + - - +
202A VAL* 1.3 88.0 - - + +
204A ILE* 1.3 60.0 + - - +
207A LEU* 3.6 7.9 - - - +
208A PRO* 2.9 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE* 2.9 74.3 - - + -
120A ILE* 3.6 7.8 - - + +
121A TYR* 2.9 29.4 - - + -
157A LEU 5.8 1.1 - - - +
158A ALA* 5.7 1.8 - - - -
161A LEU* 2.9 21.7 - - + +
200A VAL* 2.7 33.9 + - + +
201A THR* 4.2 1.1 - - - +
203A LEU* 1.3 76.3 - - - +
205A TYR* 1.4 70.4 + - + +
208A PRO* 2.8 21.8 - - - +
265A HIS* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 5.7 1.1 - - + -
120A ILE* 4.4 14.3 - - + +
201A THR* 2.9 14.2 + - - +
204A ILE* 1.4 86.9 - - + +
206A PHE* 1.4 82.2 + + - +
208A PRO* 3.6 1.9 - - - +
209A LEU* 3.1 53.6 + - + +
257A PHE* 3.9 23.4 - + - -
258A ALA* 4.3 10.2 - - - +
261A TRP* 4.3 1.3 - - + -
262A LEU* 3.6 32.9 + - + +
265A HIS* 2.9 61.9 - + + +
----------------------------------------------------------
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