Contacts of the helix formed by residues 80 - 92 (chain B) in PDB entry 2VBJ
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 80 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 4.3 10.3 - - + +
78B LEU* 4.4 5.6 - - + +
79B SER* 1.3 75.8 - - - +
81B ILE* 1.3 64.7 + - - +
82B LYS* 4.7 2.4 - - + +
83B PRO* 3.4 28.2 - - + +
84B LEU* 2.9 22.2 + - - +
4C G 3.5 39.0 - - - +
5C C 4.1 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 4.1 20.6 - - + +
79B SER 3.0 9.1 + - - +
80B GLU* 1.3 71.2 - - - +
82B LYS* 1.3 64.6 + - + +
84B LEU* 3.3 3.9 + - + +
85B HIS* 2.9 27.7 + - - +
109B ILE* 3.6 43.4 - - + +
112B LEU* 4.1 18.4 - - + -
3C T 5.1 2.2 - - - +
4C G 3.3 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU* 4.7 2.1 - - + +
81B ILE* 1.3 82.8 - - + +
83B PRO* 1.3 67.7 - - + +
85B HIS* 3.3 7.7 + - - +
86B ASN* 3.0 26.9 + - - +
4C G 5.0 0.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 5.4 0.7 + - - -
64B VAL* 3.9 34.6 - - + +
78B LEU* 4.1 5.6 - - + +
80B GLU* 3.4 46.4 - - + +
82B LYS* 1.3 94.8 - - + +
84B LEU* 1.3 54.3 + - - +
86B ASN* 3.7 7.8 + - + +
87B PHE* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 3.8 39.3 - - + +
42B THR 4.6 1.3 - - - +
43B PHE* 3.7 29.4 - - + +
78B LEU* 3.9 25.0 - - + +
79B SER 4.0 8.5 - - - +
80B GLU 2.9 19.7 + - - +
81B ILE* 3.6 5.8 - - + +
83B PRO* 1.3 75.5 - - - +
85B HIS* 1.3 58.9 + - - +
87B PHE* 3.8 0.8 - - + +
88B LEU* 2.9 51.2 + - + +
105B VAL* 4.4 5.2 - - + -
109B ILE* 4.4 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ILE 2.9 14.7 + - - +
82B LYS* 3.4 10.3 - - - +
84B LEU* 1.3 77.8 - - - +
86B ASN* 1.3 64.0 + - - +
89B THR* 2.8 45.8 + - + -
106B LEU* 3.5 22.4 - - + +
109B ILE* 3.5 34.9 - - + +
110B GLU* 2.7 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASN* 3.4 36.0 + - - +
3B THR* 2.8 35.9 + - - +
5B TYR* 3.8 12.1 + - - -
82B LYS 3.0 16.0 + - - +
83B PRO* 3.7 7.8 + - + +
85B HIS* 1.3 81.7 + - - +
87B PHE* 1.3 62.5 + - - +
89B THR* 3.7 4.9 - - - -
90B GLN* 3.0 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 3.9 30.7 - + + +
9B PHE* 4.9 1.6 - + - -
10B LEU* 4.8 5.8 - - + -
13B LEU* 3.6 33.4 - - + -
43B PHE* 3.5 35.9 - + - -
62B ILE* 3.8 22.2 - - + -
78B LEU* 4.0 20.9 - - + -
83B PRO 2.9 17.6 + - - +
84B LEU* 3.8 2.9 - - + +
86B ASN* 1.3 74.6 - - - +
88B LEU* 1.3 76.7 + - + +
90B GLN* 3.0 6.1 + - - +
91B LEU* 3.0 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 4.2 26.0 - - + -
43B PHE* 4.4 9.4 - - + -
84B LEU* 2.9 38.4 + - + +
87B PHE* 1.3 93.2 - - + +
89B THR* 1.3 58.6 - - - +
91B LEU* 4.3 10.1 - - + -
92B GLN* 2.9 34.7 + - - +
102B ALA* 4.4 16.4 - - + +
105B VAL* 3.4 39.9 - - + -
106B LEU* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B HIS* 2.8 44.1 + - + -
86B ASN* 3.7 7.4 - - - -
87B PHE 3.2 0.2 - - - -
88B LEU* 1.3 76.6 - - - +
90B GLN* 1.3 65.4 - - + +
92B GLN* 3.8 6.0 + - - +
93B PRO* 3.5 15.8 - - - +
106B LEU* 3.6 18.6 - - + +
110B GLU* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B THR 2.9 25.5 + - - -
4B LYS* 3.8 16.4 + - - +
5B TYR* 2.9 41.5 + - + +
10B LEU* 3.5 25.9 - - + +
86B ASN* 3.0 30.0 + - - +
87B PHE 3.0 8.0 + - - +
89B THR* 1.3 82.7 - - + +
91B LEU* 1.3 61.8 + - - +
93B PRO* 3.4 9.9 - - - +
94B PHE* 3.7 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.7 39.2 - - + +
13B LEU* 4.3 10.5 - - + -
14B ALA* 3.8 14.4 - - - +
17B VAL* 4.3 14.8 - - + -
23B ILE* 5.8 0.2 - - + -
43B PHE* 4.4 5.2 - - + -
87B PHE* 3.0 41.0 + - + +
88B LEU* 4.1 9.6 - - + +
90B GLN* 1.3 72.9 - - - +
92B GLN* 1.3 68.7 + - - +
93B PRO* 3.2 4.5 - - - -
94B PHE* 2.9 20.1 + - - +
95B LEU* 3.5 31.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU 2.9 21.6 + - - +
89B THR* 3.8 7.2 + - - +
91B LEU* 1.3 78.1 - - - +
93B PRO* 1.4 87.8 - - + +
94B PHE 3.0 1.2 + - - -
95B LEU* 3.2 16.8 + - + +
99B GLN* 2.9 29.9 + - + +
102B ALA* 3.9 21.1 - - + -
103B ASN* 3.2 36.2 + - - +
106B LEU* 4.3 7.9 - - + -
----------------------------------------------------------
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