Contacts of the helix formed by residues 158 - 172 (chain B) in PDB entry 2BV1
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 PHE 158 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 4.3 10.1 - + + -
105B CYS* 3.5 24.5 - - + -
108B TYR* 3.6 27.4 - + + -
120B ALA* 3.6 39.0 - - + -
123B ILE* 3.7 34.8 - - + -
124B TYR 4.5 1.1 - - - -
128B VAL* 4.3 9.2 - - + -
146B THR* 3.8 27.8 - - + -
150B ILE* 3.6 14.6 - - + -
155B PRO 5.0 0.4 + - - -
156B THR 3.2 0.8 - - - -
157B CYS* 1.3 80.7 - - - +
159B ASP* 1.3 55.5 + - - +
160B GLU 3.3 2.9 - - - -
161B ALA* 3.2 6.1 + - + +
162B GLN* 2.7 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LYS* 3.5 25.5 + - - +
149B LYS* 5.9 0.4 - - - +
155B PRO 4.5 1.7 - - - +
156B THR* 3.0 46.3 + - - +
157B CYS 3.5 0.2 - - - -
158B PHE* 1.3 77.0 - - - +
160B GLU* 1.3 58.9 + - + +
162B GLN* 3.8 6.5 - - - +
163B LYS* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR* 4.1 20.0 + - + +
145B SER* 3.3 22.8 + - - -
146B THR* 5.1 2.0 - - - +
149B LYS* 4.2 23.1 + - - +
158B PHE 3.3 0.6 - - - -
159B ASP* 1.3 77.3 - - + +
161B ALA* 1.3 66.3 + - - +
163B LYS* 3.4 6.2 + - - +
164B VAL* 3.2 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 3.8 20.4 - - + -
128B VAL* 5.4 0.9 - - + -
136B ILE* 4.6 0.7 - - + -
138B ILE* 4.0 21.2 - - + +
142B THR* 3.9 9.5 - - - +
146B THR* 3.9 22.7 + - + +
158B PHE* 3.2 10.1 + - - +
160B GLU* 1.3 78.2 - - - +
162B GLN* 1.3 63.1 + - - +
164B VAL* 3.3 4.2 + - - +
165B ILE* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 3.8 8.2 - - - -
102B TRP* 3.3 49.9 + - + +
105B CYS* 3.5 22.8 - - + +
106B GLU* 2.8 23.4 + - - +
109B LYS* 2.9 24.1 + - - -
158B PHE 2.7 20.6 + - - +
159B ASP* 3.8 8.8 - - - +
161B ALA* 1.3 72.0 - - - +
163B LYS* 1.3 59.3 + - - +
165B ILE* 3.4 2.5 + - - +
166B TYR* 2.9 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ASP 3.0 16.1 + - - +
160B GLU* 3.9 5.6 - - - +
161B ALA 3.3 0.2 - - - -
162B GLN* 1.3 74.7 - - - +
164B VAL* 1.3 63.3 + - - +
166B TYR* 3.4 8.5 + - + +
167B THR* 2.8 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ASN 4.1 11.4 - - - +
138B ILE* 3.8 23.1 - - + -
139B ASP* 4.3 17.3 - - - +
142B THR* 4.4 12.3 - - + +
160B GLU 3.2 16.3 + - - +
161B ALA 3.5 8.1 - - - +
162B GLN 3.3 0.2 - - - -
163B LYS* 1.3 76.8 - - + +
165B ILE* 1.3 57.7 + - - +
167B THR* 3.2 6.7 + - - -
168B LEU* 2.9 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASN* 3.5 51.1 - - + +
101B PHE* 3.6 24.0 - - + -
102B TRP* 5.0 2.9 - - + -
136B ILE* 3.6 25.8 - - + -
137B ASN 3.9 13.9 - - - +
138B ILE* 3.8 13.7 - - + -
161B ALA 3.1 16.1 + - - +
162B GLN 3.9 3.8 - - - +
164B VAL* 1.3 72.9 - - - +
166B TYR* 1.3 65.8 - - - +
168B LEU* 3.5 8.8 - - + +
169B MET* 3.1 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B SER* 5.5 0.3 - - - -
73B LEU* 3.5 29.2 - - + +
74B GLU* 3.0 38.8 + - + +
77B LEU* 4.1 10.3 - - + -
102B TRP* 3.5 31.1 - + - +
162B GLN* 2.9 18.9 + - + +
163B LYS* 3.7 8.5 - - + +
164B VAL 3.3 0.2 - - - -
165B ILE* 1.3 77.2 - - - +
167B THR* 1.3 61.2 + - - +
169B MET* 3.2 12.6 + - + +
170B GLU* 2.8 55.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LYS* 2.8 27.4 + - - +
164B VAL* 3.5 6.0 - - - -
166B TYR* 1.3 80.0 - - - +
168B LEU* 1.3 59.2 + - + +
170B GLU* 3.2 10.9 + - - +
171B LYS* 2.9 53.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASN* 4.9 12.3 - - - +
137B ASN* 3.4 46.0 - - + +
164B VAL* 2.9 22.2 + - + +
165B ILE* 3.5 17.0 - - + +
167B THR* 1.3 79.3 - - + +
169B MET* 1.3 61.7 + - + +
171B LYS* 4.1 2.4 - - + -
172B ASP* 3.2 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.9 14.6 - - + -
77B LEU* 4.6 8.1 - - + -
86B PHE* 4.0 22.4 - - + -
90B LEU* 4.3 3.8 - - + -
98B ASN* 3.8 34.1 - - + +
99B ILE* 4.0 12.8 - - + -
102B TRP* 4.2 28.5 - - + -
165B ILE* 3.1 18.0 + - + +
166B TYR* 3.6 14.8 - - - +
168B LEU* 1.3 78.6 - - - +
170B GLU* 1.3 64.7 + - - +
171B LYS 3.3 0.5 + - - -
172B ASP 3.4 3.1 + - - -
173B SER* 3.4 18.2 - - - +
174B TYR* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B SER* 5.5 3.6 - - - -
73B LEU* 3.8 27.1 + - + +
166B TYR* 2.8 44.8 + - - +
167B THR* 3.2 11.4 + - - +
169B MET* 1.3 73.0 - - - +
171B LYS* 1.3 76.9 + - + +
174B TYR* 3.8 11.5 - - + -
175B PRO* 3.3 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B THR* 2.9 32.6 + - + +
168B LEU* 4.4 3.1 - - + +
170B GLU* 1.3 100.1 + - + +
172B ASP* 1.3 59.3 + - + +
175B PRO* 3.8 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 3.2 19.0 + - + +
169B MET 3.4 1.2 + - - -
171B LYS* 1.3 79.1 - - + +
173B SER* 1.3 69.3 + - - +
174B TYR 3.4 0.7 - - - -
175B PRO* 3.4 9.6 - - - +
176B ARG* 3.2 48.1 + - - +
----------------------------------------------------------
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