Contacts of the helix formed by residues 198 - 211 (chain A) in PDB entry 4BKR
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 GLY 198 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLY* 1.3 71.7 - - - -
199A GLU* 1.3 62.8 + - - +
200A ASP 3.4 2.2 - - - -
201A TRP* 3.4 9.6 + - - +
202A GLN* 3.0 23.2 + - - +
246A ASP* 2.8 14.8 + - - -
247A LEU* 3.8 15.5 - - - +
250A LYS* 3.4 27.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ARG* 2.7 37.8 + - - +
146A HIS* 3.4 17.0 + - - -
193A VAL 5.4 2.0 + - - +
194A ALA* 5.2 3.8 + - - +
197A GLY 3.6 2.2 - - - -
198A GLY* 1.3 77.1 - - - +
200A ASP* 1.3 59.2 + - - +
202A GLN* 3.1 10.7 + - - +
203A MET* 2.8 46.7 + - + +
246A ASP* 4.2 0.6 + - - +
250A LYS* 3.7 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA 3.8 1.3 - - - +
113A PHE* 3.4 37.7 - - + +
118A LYS* 2.8 26.5 + - - -
137A TYR* 2.6 24.7 + - - +
139A LEU* 3.8 2.4 - - - +
144A ARG* 4.2 11.9 + - - +
194A ALA 5.6 0.4 + - - -
195A VAL 5.7 0.4 - - - +
197A GLY 4.9 2.3 + - - +
198A GLY 3.4 0.2 - - - -
199A GLU* 1.3 75.7 - - - +
201A TRP* 1.3 55.9 + - - +
203A MET* 3.1 10.5 + - - +
204A TRP* 2.8 54.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 5.5 2.0 - - + -
137A TYR* 3.7 45.7 + + + +
197A GLY 5.3 0.2 + - - -
198A GLY* 3.5 9.3 - - - +
200A ASP* 1.3 76.7 - - - +
202A GLN* 1.3 62.9 + - - +
204A TRP* 3.3 4.8 + - + +
205A ILE* 3.1 28.5 + - + +
220A THR* 2.9 35.9 + - + +
221A THR* 3.9 6.3 - - - -
222A ALA* 3.6 40.2 - - + -
247A LEU* 4.0 33.4 - - + -
250A LYS* 4.4 7.6 - - + -
251A VAL* 3.9 22.4 - - + -
254A ILE* 3.7 17.5 - - + -
267A ARG 3.8 14.8 - - - -
268A VAL* 4.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLY 3.0 11.9 + - - +
199A GLU* 3.2 13.8 + - - +
201A TRP* 1.3 74.6 - - - +
203A MET* 1.3 66.2 + - + +
205A ILE* 3.2 3.0 + - - +
206A ASP* 3.0 45.1 + - - +
250A LYS* 3.3 38.4 - - + +
253A ALA* 4.2 20.6 - - - +
254A ILE* 4.4 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASP* 5.7 1.8 - - - +
118A LYS* 4.0 14.9 - - + +
144A ARG* 3.4 20.4 - - - +
146A HIS* 4.1 11.4 - - + +
147A PRO* 3.7 25.1 - - + -
148A LYS* 5.3 7.2 - - + -
199A GLU* 2.8 47.0 + - + +
200A ASP* 3.1 13.0 + - - +
202A GLN* 1.3 74.8 - - + +
204A TRP* 1.3 55.8 + - - +
206A ASP* 3.9 5.4 - - - +
207A ALA* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 4.3 10.5 - - + -
47A ILE* 3.7 33.6 - - + +
72A VAL* 4.3 7.4 - - + -
112A ALA* 2.9 44.1 + - + -
117A ILE* 4.1 6.1 - - + -
118A LYS* 3.5 38.3 - - + +
121A THR* 3.5 42.6 - - + -
137A TYR* 3.8 10.3 - + + -
200A ASP* 2.8 41.1 + - - -
201A TRP* 3.4 9.9 - - + +
202A GLN 3.2 0.2 - - - -
203A MET* 1.3 72.3 - - - +
205A ILE* 1.3 65.9 + - + +
207A ALA* 3.3 2.8 + - + +
208A LEU* 3.0 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 4.1 25.1 - - + -
201A TRP* 3.1 26.9 + - + +
202A GLN* 3.2 4.5 + - - +
204A TRP* 1.3 76.7 - - + +
206A ASP* 1.3 61.1 + - - +
208A LEU* 3.5 4.9 + - + +
209A LEU* 2.9 39.6 + - + +
214A LEU* 3.9 19.0 - - + +
220A THR* 3.8 27.8 - - + +
254A ILE* 4.0 29.6 - - + -
257A SER* 4.7 2.7 - - - +
258A LEU* 4.6 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLN* 3.0 37.7 + - - +
203A MET* 3.9 6.2 + - - +
205A ILE* 1.3 80.1 - - - +
207A ALA* 1.3 51.9 + - - +
209A LEU* 3.3 13.5 + - - +
210A ASP* 2.8 48.8 + - - +
257A SER* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LYS* 4.4 19.5 - - + -
122A ILE* 3.6 17.7 - - + +
203A MET 3.0 19.6 + - - +
204A TRP* 3.7 4.5 - - + +
206A ASP* 1.3 76.5 - - - +
208A LEU* 1.3 63.4 + - + +
210A ASP* 3.5 7.5 + - - +
211A ALA* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 3.9 17.5 - - + -
121A THR* 4.8 3.1 - - + -
122A ILE* 4.1 13.0 - - + -
125A ILE* 3.9 17.5 - - + -
132A VAL* 5.0 0.7 - - + -
135A VAL* 3.8 30.7 - - + -
204A TRP* 3.0 37.0 + - + +
205A ILE* 3.8 7.2 - - - +
207A ALA* 1.3 73.0 - - + +
209A LEU* 1.3 66.0 + - - +
211A ALA* 3.4 0.9 + - - -
212A GLY 3.1 3.5 + - - -
213A VAL* 3.0 50.5 + - + +
214A LEU* 3.8 18.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ILE* 2.9 27.6 + - + +
206A ASP* 3.3 16.8 + - - +
208A LEU* 1.3 74.0 - - - +
210A ASP* 1.3 70.1 + - - +
212A GLY* 2.9 15.7 + - - -
214A LEU* 4.1 25.5 - - + +
257A SER* 4.2 28.3 - - - +
258A LEU* 4.8 7.0 - - + -
261A HIS* 5.5 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP* 2.8 35.4 + - - +
207A ALA* 3.9 7.8 - - - +
209A LEU* 1.3 77.0 - - - +
211A ALA* 1.3 60.7 + - - +
212A GLY* 3.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 3.7 36.1 - - + -
126A LYS* 2.9 29.8 + - - +
207A ALA 3.1 18.2 + - - +
208A LEU 3.4 3.8 + - - +
209A LEU 3.2 0.2 - - - -
210A ASP* 1.3 75.8 - - - +
212A GLY* 1.3 62.2 + - - +
213A VAL* 3.4 3.9 + - + +
----------------------------------------------------------
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