Contacts of the strand formed by residues 81 - 90 (chain B) in PDB entry 2BQ6
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 ALA 81 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL 3.7 0.5 - - - +
67B ARG* 3.3 2.6 - - - -
68B VAL* 3.0 39.8 + - + +
80B GLU* 1.3 74.3 - - - +
82B VAL* 1.3 63.5 + - - +
83B HIS* 4.0 13.8 + - + +
115B ARG* 3.0 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 3.9 15.3 - - + -
65B LYS* 3.9 31.4 - - + +
66B VAL 3.3 8.7 - - - +
67B ARG* 4.3 26.0 - - + +
80B GLU* 5.9 1.6 - - + -
81B ALA* 1.3 76.9 - - - +
83B HIS* 1.3 67.6 + - - +
84B GLU 4.3 0.2 + - - -
110B THR* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LYS* 3.7 1.9 - - - +
66B VAL* 2.8 39.9 + - + +
68B VAL* 4.4 7.9 - - + -
81B ALA* 4.2 24.3 - - + +
82B VAL* 1.3 82.9 + - - +
84B GLU* 1.3 63.5 + - - +
85B VAL 3.8 0.3 + - - -
108B LEU* 4.0 25.6 - - + -
110B THR* 2.6 36.2 + - - +
111B PRO 3.1 30.3 - - - -
112B ILE* 3.8 20.9 - - + +
113B THR 5.0 1.2 + - - -
115B ARG* 6.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 4.6 13.7 + - - -
65B LYS* 4.5 28.6 - - + +
82B VAL 4.3 0.2 + - - -
83B HIS* 1.3 74.1 - - - +
85B VAL* 1.3 60.6 + - - +
108B LEU* 3.6 4.7 - - - +
109B LYS* 3.0 70.8 + - + +
110B THR* 5.0 3.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
64B PHE* 3.7 37.1 + - + +
65B LYS* 4.4 0.9 - - - -
66B VAL* 3.9 27.4 - - + -
84B GLU* 1.3 71.2 - - - +
86B GLU* 1.3 62.7 + - - +
87B VAL 3.6 21.3 - - - +
88B VAL* 3.7 21.5 - - + -
106B LEU* 4.4 12.3 - - + -
107B ARG 3.7 5.8 - - - +
108B LEU* 4.7 2.9 - - + +
109B LYS* 3.3 14.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU 3.5 1.6 + - - -
85B VAL* 1.3 74.2 - - - +
87B VAL* 1.3 74.5 + - + +
107B ARG* 2.6 41.1 + - - +
108B LEU 3.8 1.2 - - - +
109B LYS* 3.4 43.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 3.6 3.9 - - - +
86B GLU* 1.3 107.0 - - + +
88B VAL* 1.3 70.7 + - - +
89B ILE* 3.9 24.2 + - + -
106B LEU* 3.5 3.8 - - - -
107B ARG* 2.8 43.8 + - + -
244B THR* 6.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.4 37.9 - - + -
64B PHE* 4.8 11.0 - - + -
85B VAL* 3.7 19.7 - - + -
87B VAL* 1.3 82.0 - - - +
89B ILE* 1.3 62.6 + - - +
90B LYS* 3.6 7.7 + - + +
105B VAL 4.0 1.8 - - - -
106B LEU* 3.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 4.7 11.0 - - + +
87B VAL* 3.9 20.2 - - + -
88B VAL* 1.3 73.6 - - - +
90B LYS* 1.3 62.1 + - - +
104B ALA* 4.6 1.3 - - - -
105B VAL* 2.9 39.9 + - + +
107B ARG* 5.5 1.8 - - + +
237B TRP* 3.3 18.0 - - + -
241B SER* 3.1 49.6 - - - +
244B THR* 3.9 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA* 4.1 16.2 - - + -
59B LEU* 3.3 32.0 - - + +
60B TYR* 2.6 40.2 + - + +
88B VAL* 3.6 7.9 + - + +
89B ILE* 1.3 81.1 - - - +
91B HIS* 1.3 82.7 + - - +
92B ASN* 3.5 8.2 + - - +
94B PHE* 4.5 4.9 - - + -
104B ALA* 4.2 6.3 - - - -
237B TRP* 3.9 7.2 + - - -
----------------------------------------------------------
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