Contacts of the helix formed by residues 198 - 211 (chain A) in PDB entry 2BEW
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 GLU 198 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 3.9 21.2 - - + +
165A ALA* 3.6 13.5 - - + -
194A GLY 5.0 1.1 - - - +
195A ALA* 3.0 22.0 + - - +
196A ALA 4.0 0.5 - - - +
197A SER* 1.3 82.7 - - - +
199A GLY* 1.3 66.4 + - - +
200A ASP* 4.0 4.7 - - + +
201A ALA* 3.0 17.5 + - - +
202A HIS* 3.9 2.9 + - - +
601A THW 3.2 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A SER 3.7 2.0 + - - -
198A GLU* 1.3 74.9 + - - +
200A ASP* 1.3 61.7 + - - +
202A HIS* 3.1 13.7 + - - +
203A ALA* 3.0 19.9 + - - +
75B CYS* 5.4 0.7 - - - -
77B GLN* 3.4 21.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
164A LEU 4.9 1.5 - - - +
165A ALA* 3.4 25.4 - - + +
166A THR* 3.6 15.9 + - - +
168A ILE* 4.0 0.2 - - - +
169A PRO* 3.5 15.9 - - + +
198A GLU* 3.1 3.6 - - + +
199A GLY* 1.3 78.0 - - - +
201A ALA* 1.3 56.4 + - - +
203A ALA* 3.5 4.7 - - - +
204A GLY* 2.9 23.0 + - - -
77B GLN* 3.0 37.8 + - - +
108B ASP* 4.5 3.3 - - - +
109B GLN* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ALA* 4.4 1.0 - - - +
168A ILE* 3.9 27.0 - - + +
195A ALA 4.3 1.8 - - - +
196A ALA* 3.4 36.3 - - + +
198A GLU 3.0 7.3 + - - +
200A ASP* 1.3 77.9 - - - +
202A HIS* 1.3 58.2 + - - +
205A PHE* 3.0 46.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLU 3.9 1.7 + - - +
199A GLY* 3.1 16.2 + - - +
201A ALA* 1.3 76.3 - - - +
203A ALA* 1.4 65.9 + - - +
206A ASN* 3.2 32.5 + - + +
246A TYR* 2.7 44.2 + + - +
75B CYS* 5.6 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PRO* 4.5 4.5 - - + -
199A GLY 3.0 12.0 + - - +
200A ASP* 3.5 13.7 - - - +
202A HIS* 1.4 77.5 - - - +
204A GLY* 1.3 63.1 + - - +
206A ASN* 3.9 0.8 - - - -
207A PHE* 3.0 33.5 + - - -
75B CYS* 3.6 30.7 - - - -
77B GLN* 4.2 1.6 - - + -
78B GLY* 3.7 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ILE* 4.0 5.8 - - - -
169A PRO* 4.0 13.1 - - - +
172A VAL* 3.4 24.0 - - - +
200A ASP 2.9 17.2 + - - -
203A ALA* 1.3 76.6 - - - +
205A PHE* 1.3 62.4 + - - +
207A PHE* 4.7 1.8 - - - -
208A ALA* 3.0 21.3 + - - +
217A PHE* 3.9 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ILE* 4.4 5.8 - - + -
191A PHE* 3.7 29.6 - + - -
196A ALA* 5.6 2.2 - - + -
201A ALA* 3.0 31.8 + - + +
204A GLY* 1.3 75.7 - - - +
206A ASN* 1.3 63.3 + - - +
208A ALA* 3.4 1.0 + - - +
209A ALA* 3.3 16.8 + - - +
217A PHE* 3.8 36.3 - + - -
239A ILE* 4.6 8.3 - - + -
242A ARG* 4.8 11.4 - - + -
243A GLY* 5.2 0.2 - - - -
246A TYR* 3.6 37.9 - + + +
248A ILE* 3.6 29.1 - - + +
280A LEU* 4.1 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A HIS* 3.2 22.4 + - + +
203A ALA* 4.0 2.2 - - - +
205A PHE* 1.3 77.0 - - - +
207A PHE* 1.3 69.6 + - + +
209A ALA* 3.3 2.4 + - - -
210A THR* 3.0 43.1 + - - +
246A TYR* 3.8 25.4 - - + +
73B PRO* 3.6 25.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PRO* 6.1 2.0 - - + -
172A VAL* 4.0 15.0 - - + +
203A ALA* 3.0 29.4 + - - +
204A GLY* 4.1 2.2 - - - +
206A ASN* 1.3 78.1 - - + +
208A ALA* 1.3 59.1 + - - +
210A THR* 4.0 6.1 - - - -
211A LEU* 2.9 51.2 + - + +
72B THR* 3.7 31.0 - - + -
73B PRO* 3.7 23.1 - - + -
75B CYS* 3.7 29.6 - - + -
78B GLY* 3.6 32.3 - - - -
79B ILE* 3.6 7.0 - - + -
82B PHE* 4.0 17.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A VAL* 3.7 13.4 - - + +
204A GLY 3.0 19.5 + - - +
205A PHE 3.8 1.6 - - - +
207A PHE* 1.3 77.3 - - - +
209A ALA* 1.3 58.4 + - - +
212A GLU* 3.1 6.9 + - - -
213A CYS* 3.0 28.6 + - - -
215A ILE* 3.8 17.5 - - + -
217A PHE* 3.6 27.4 - - + -
278A PRO* 3.5 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PHE 3.3 9.2 + - - +
206A ASN* 3.3 7.9 + - - +
207A PHE 3.2 0.2 - - - -
208A ALA* 1.3 80.4 - - - +
210A THR* 1.3 66.3 + - + +
212A GLU* 3.4 17.8 + - - +
246A TYR 3.1 28.3 - - - +
247A GLY 4.7 5.6 - - - +
248A ILE* 4.2 9.6 - - + -
278A PRO* 3.8 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASN* 3.0 36.2 + - - +
207A PHE 3.7 0.9 + - - -
209A ALA* 1.3 77.7 - - + +
211A LEU* 1.3 77.0 + - - +
212A GLU* 3.7 8.0 + - - +
73B PRO* 3.6 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TYR* 3.8 16.4 - - + -
179A LYS* 2.8 27.2 + - - -
207A PHE* 2.9 37.6 + - + +
210A THR* 1.3 87.1 + - - +
212A GLU* 1.4 57.5 + - - +
213A CYS* 3.7 11.9 - - - -
70B PHE* 3.7 29.6 - - + -
71B ASN 3.8 13.7 - - - +
72B THR* 4.6 6.1 - - + -
73B PRO* 4.8 1.6 - - + -
82B PHE* 3.6 33.9 - - + -
----------------------------------------------------------
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