Contacts of the helix formed by residues 79 - 93 (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 ASN 79 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.5 1.7 - - - +
65B GLU* 3.4 43.1 + - - +
69B TRP* 3.5 14.4 - - - +
75B LYS 3.7 2.6 + - - +
76B LEU 3.2 7.7 + - - +
77B LEU 3.2 1.8 - - - -
78B ALA* 1.3 78.3 - - - +
80B GLN* 1.3 62.0 + - - +
81B THR* 3.2 16.8 + - - -
82B GLY 2.9 24.5 + - - +
83B GLN* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ASP* 3.4 47.0 + - + +
78B ALA 4.2 2.0 + - - -
79B ASN* 1.3 73.4 - - - +
81B THR* 1.3 57.9 + - - +
83B GLN* 3.3 23.5 + - - +
84B ASN* 3.1 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 5.4 0.9 - - + -
186A LEU* 4.3 12.2 + - + -
189A ASP* 4.0 15.1 + - - +
190A LEU* 3.8 24.3 - - + +
61B LEU* 3.8 32.3 - - + -
69B TRP* 4.0 4.3 - - + -
79B ASN* 3.2 11.5 + - - -
80B GLN* 1.3 75.0 - - - +
82B GLY* 1.3 60.6 + - - +
84B ASN* 3.1 9.2 + - - +
85B VAL* 2.8 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TRP* 3.3 24.3 - - - -
76B LEU* 3.3 23.4 - - - +
79B ASN* 2.9 16.4 + - - -
81B THR* 1.3 74.0 - - - +
83B GLN* 1.3 61.4 + - - +
86B PHE* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU 3.8 1.2 + - - -
77B LEU* 2.8 40.1 + - + +
78B ALA 5.3 0.4 - - - -
79B ASN 2.8 19.6 + - - +
80B GLN* 3.3 24.3 + - - +
82B GLY* 1.3 72.9 - - - +
84B ASN* 1.3 57.4 + - - +
86B PHE* 4.8 1.1 - - - -
87B GLY* 2.8 31.9 + - - -
99B ILE* 3.6 15.8 - - + +
102B TRP* 4.6 2.8 - - - -
103B LEU* 3.5 38.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE 5.4 1.8 - - - +
185A ASN* 3.1 41.8 + - - +
186A LEU* 3.6 20.0 + - + +
189A ASP* 2.9 33.8 + - - +
80B GLN* 3.1 14.7 + - - +
81B THR* 3.1 9.1 + - - +
83B GLN* 1.3 79.0 - - - +
85B VAL* 1.3 58.6 + - - +
87B GLY* 3.4 1.7 + - - -
88B SER* 2.9 33.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 5.7 2.2 - - + -
81A THR* 6.2 2.0 - - + -
85A VAL* 5.8 4.0 - - + -
186A LEU* 4.1 20.9 - - + -
61B LEU* 5.4 0.2 - - + -
69B TRP* 4.2 7.0 - - + -
81B THR* 2.8 28.9 + - + +
82B GLY 4.1 2.0 - - - +
84B ASN* 1.3 69.9 - - - +
86B PHE* 1.3 64.9 + - - +
88B SER* 3.2 9.3 + - - -
89B PHE* 3.1 19.8 + - - +
177B PHE* 3.9 20.1 - - + -
182B ILE* 4.1 23.1 - - + +
183B TYR* 5.1 0.2 - - - -
186B LEU* 4.1 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.9 16.2 - - + -
76B LEU* 3.6 20.0 - - + -
77B LEU* 4.1 6.1 - - + -
82B GLY 2.9 18.6 + - - +
83B GLN* 4.1 1.6 - - - +
85B VAL* 1.3 77.1 - - - +
87B GLY* 1.3 56.9 + - - +
89B PHE* 3.1 4.2 + + - +
90B LEU* 2.9 62.1 + - + +
99B ILE* 4.0 16.4 - - + -
169B MET* 4.0 13.7 - - + -
173B SER* 3.8 13.5 - - - -
174B TYR* 4.0 20.0 - - + -
177B PHE* 3.5 44.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE* 5.7 0.2 - - - -
83B GLN 2.8 23.8 + - - -
84B ASN* 3.6 2.7 - - - -
85B VAL 3.3 0.2 - - - -
86B PHE* 1.3 72.6 - - - +
88B SER* 1.3 55.0 + - - +
90B LEU* 3.3 2.9 + - - +
91B LYS* 2.8 39.8 + - - +
96B GLU* 4.2 1.1 - - - +
99B ILE* 4.2 22.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 4.4 6.4 - - - +
88A SER* 3.3 21.8 - - - -
182A ILE* 3.6 37.6 + - - +
84B ASN 2.9 18.8 + - - -
85B VAL* 3.2 10.1 + - - -
87B GLY* 1.3 72.3 - - - +
89B PHE* 1.3 57.7 + - - +
91B LYS* 3.4 2.6 + - - +
92B SER 3.0 23.0 + - - -
182B ILE* 4.0 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER* 4.9 1.6 - - - -
85B VAL 3.1 8.7 + - - +
86B PHE* 3.4 8.1 - + - +
88B SER* 1.3 76.9 - - - +
90B LEU* 1.3 73.4 + - + +
92B SER* 2.6 28.3 + - - -
93B GLU* 3.3 42.3 + - + +
173B SER* 3.5 21.5 - - - -
176B ARG* 3.8 11.0 - - + -
177B PHE* 3.6 40.6 - + + -
180B SER* 3.7 30.3 - - - -
182B ILE* 4.2 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 2.9 45.3 + - + +
87B GLY 3.7 3.4 - - - +
89B PHE* 1.3 78.4 - - + +
91B LYS* 1.3 65.1 - - - +
93B GLU* 3.0 11.3 + - - +
95B SER* 2.9 45.7 + - - +
96B GLU* 3.7 16.6 - - + -
98B ASN* 5.0 1.1 - - + +
99B ILE* 3.8 33.0 - - + +
169B MET* 4.3 6.1 - - - -
173B SER* 3.4 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER 4.8 0.4 - - - +
92A SER* 3.8 30.9 - - - +
181A ASP* 3.8 27.3 + - - +
182A ILE* 3.5 38.9 - - + +
185A ASN* 5.5 1.8 - - - +
87B GLY* 2.8 21.2 + - - +
88B SER 3.5 5.6 - - - +
90B LEU* 1.3 75.0 - - - +
92B SER* 1.3 63.4 + - - +
93B GLU 3.0 1.6 + - - -
94B PHE* 3.0 13.3 + - - -
96B GLU* 3.4 29.2 - - + +
100B GLU* 3.9 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER* 3.8 29.6 + - - -
91A LYS* 3.3 40.9 - - - +
88B SER 3.0 13.4 + - - -
89B PHE* 2.6 30.4 + - - -
91B LYS* 1.3 76.1 - - - +
93B GLU* 1.3 59.0 + - - +
94B PHE* 3.6 7.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 3.3 39.9 - - + +
90B LEU* 3.0 6.7 + - - +
92B SER* 1.3 81.1 - - - +
94B PHE* 1.3 75.3 + - - +
95B SER* 3.2 17.4 + - - +
173B SER* 4.3 2.8 - - - -
176B ARG* 2.7 45.0 + - - -
----------------------------------------------------------
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