Contacts of the helix formed by residues 144 - 153 (chain A) in PDB entry 2BHT
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 PRO 144 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG* 5.2 8.7 - - - +
142A ASN 3.1 11.9 - - - +
143A ASN* 1.3 86.9 - - - +
145A ASP* 1.3 59.6 + - - +
146A ASN 3.3 0.7 - - - -
147A PRO* 3.8 11.8 - - + +
148A LYS* 3.3 22.0 + - - +
220A ILE* 4.0 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 2.4 28.8 + - - +
48A MET* 3.9 21.0 - - + +
51A GLU* 3.3 33.4 - - - +
52A ALA* 4.6 3.6 + - - +
55A ARG* 2.8 34.0 + - - -
143A ASN* 2.8 29.0 + - - +
144A PRO* 1.3 77.7 - - - +
146A ASN* 1.3 63.2 + - - +
148A LYS* 3.6 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 6.1 1.6 - - - +
44A ALA* 3.6 24.5 - - + +
48A MET* 4.0 13.5 - - - +
72A THR* 5.7 2.4 - - - +
140A GLN* 3.4 19.2 + - - +
143A ASN 3.2 8.8 + - - +
145A ASP* 1.3 75.9 - - - +
147A PRO* 1.3 75.3 - - + +
148A LYS 3.0 0.9 - - - -
149A ALA* 3.0 21.3 + - - +
150A HIS* 3.4 15.4 + - - -
175A THR* 3.0 32.4 + - - +
177A GLY* 3.4 13.5 - - - -
320A PLP 4.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASN 3.3 10.5 - - - +
144A PRO* 3.8 15.0 - - + +
146A ASN* 1.3 97.2 - - + +
148A LYS* 1.3 62.0 + - - +
149A ALA 3.2 0.3 + - - -
150A HIS* 3.4 2.2 + - - +
151A TYR* 3.0 25.2 + - - +
177A GLY* 3.2 35.2 - - - +
180A THR* 4.2 9.4 - - + -
181A GLY* 3.4 13.8 - - - +
184A GLU* 4.4 6.7 - - - +
220A ILE* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 4.5 3.6 - - - +
51A GLU* 2.5 45.9 + - + +
55A ARG* 5.0 2.4 - - - +
144A PRO 3.3 21.0 + - - +
145A ASP* 3.6 11.0 - - - +
146A ASN 3.0 1.6 + - - -
147A PRO* 1.3 77.1 - - - +
149A ALA* 1.3 51.2 + - - +
151A TYR* 4.3 9.9 - - + -
152A THR* 2.3 57.6 + - + +
184A GLU* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 3.4 40.2 - - + +
44A ALA* 4.1 0.9 - - - +
47A SER* 3.7 13.7 - - - -
145A ASP 3.7 1.8 + - - -
146A ASN 3.0 12.6 + - - +
148A LYS* 1.3 78.0 - - - +
150A HIS* 1.3 52.0 + - - +
152A THR* 2.7 6.6 + - - -
153A THR* 2.5 47.5 + - + +
154A THR* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 3.9 18.3 + - + +
43A ARG* 4.6 7.0 - - + -
44A ALA* 4.6 11.0 - - + -
146A ASN* 3.4 31.0 + - - -
147A PRO* 3.4 4.2 + - - +
149A ALA* 1.3 76.9 - - + +
151A TYR* 1.3 63.7 + - - +
152A THR 3.0 1.2 + - - -
153A THR 3.0 0.2 + - - -
154A THR* 3.0 37.6 + - + +
155A GLY 2.7 27.3 + - - -
177A GLY 3.8 5.6 + - - +
178A THR* 2.5 44.9 + - + +
181A GLY 4.4 1.1 - - - -
182A VAL* 4.0 15.9 - - + +
320A PLP 4.7 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PRO 3.0 18.0 + - - +
148A LYS* 3.9 8.7 - - + +
150A HIS* 1.3 76.5 - - - +
152A THR* 1.3 68.5 + - + +
156A PRO* 3.6 13.4 - - - +
181A GLY* 3.1 17.9 + - - +
182A VAL* 4.9 0.2 - - - +
184A GLU* 3.1 28.3 - - + +
185A PHE* 3.0 49.7 - + + +
188A GLU* 3.1 18.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LYS* 2.3 60.4 + - + +
149A ALA* 2.7 17.2 + - - -
150A HIS 3.7 0.2 - - - -
151A TYR* 1.3 89.6 - - + +
153A THR* 1.3 66.3 + - - +
156A PRO* 3.1 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLY* 6.1 0.2 - - - -
43A ARG* 3.4 22.1 + - - +
149A ALA* 2.5 34.0 + - + +
150A HIS 3.0 0.2 + - - -
152A THR* 1.3 86.6 - - - +
154A THR* 1.3 66.0 + - - +
155A GLY 3.2 1.3 + - - -
156A PRO* 3.4 3.5 - - - +
157A GLU* 2.8 39.5 + - - +
----------------------------------------------------------
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