Contacts of the helix formed by residues 84 - 97 (chain B) in PDB entry 2B33
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 TYR 84 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP* 3.9 26.6 + - + +
84A TYR* 4.0 0.9 - - - -
87A ARG* 2.8 28.7 + - - -
47B ILE* 3.5 41.1 - - + -
50B LYS* 5.1 0.6 + - - -
79B THR* 5.0 4.5 - - + -
80B THR* 4.6 0.9 - - - -
81B SER* 3.8 31.0 - - - +
82B MET 3.0 1.4 + - - -
83B ASP* 1.3 81.0 - - + +
85B PHE* 1.3 63.3 + - - +
86B GLN 3.4 2.2 - - - -
87B ARG* 3.4 10.5 + - - +
88B VAL* 2.9 38.3 + - + +
105B PHE* 4.7 0.7 - - - -
116B GLU* 2.9 48.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B MET* 2.9 26.8 + - + +
83B ASP 3.4 0.8 - - - -
84B TYR* 1.3 75.9 - - - +
86B GLN* 1.3 77.5 + - + +
88B VAL* 3.8 0.7 - - - +
89B ASN* 2.9 61.0 + - - +
103B ARG* 3.9 10.3 - - - -
105B PHE* 3.8 54.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B MET 4.6 2.4 - - - +
83B ASP* 4.6 6.4 + - - +
84B TYR 3.4 0.6 - - - -
85B PHE* 1.3 97.5 + - + +
87B ARG* 1.3 63.5 - - + +
89B ASN* 3.4 6.2 + - - +
90B GLU* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP* 2.8 39.9 + - - +
46B THR* 4.1 8.3 - - - +
47B ILE* 3.6 21.4 - - + +
48B GLU* 3.2 39.0 + - - +
83B ASP 5.2 8.5 - - - +
84B TYR* 3.4 10.2 + - - +
85B PHE 3.4 0.2 - - - -
86B GLN* 1.3 78.6 - - + +
88B VAL* 1.3 65.5 + - - +
90B GLU* 3.4 9.2 + - - +
91B VAL* 3.4 25.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
47B ILE* 3.7 17.7 - - + -
51B THR* 3.6 33.5 - - + +
77B VAL* 4.5 4.3 - - + -
79B THR* 4.9 0.7 - - + -
84B TYR* 2.9 31.6 + - + +
85B PHE 3.8 2.5 - - - +
87B ARG* 1.3 74.3 - - - +
89B ASN* 1.3 60.3 + - - +
91B VAL* 3.2 4.0 + - - +
92B TYR* 2.8 35.3 + - + +
105B PHE* 3.7 26.0 - - + -
117B ILE* 4.2 20.0 - - + -
119B ILE* 5.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 2.9 51.9 + - - +
86B GLN* 3.5 7.2 - - - +
88B VAL* 1.3 74.3 - - - +
90B GLU* 1.3 59.9 + - - +
92B TYR* 3.7 6.5 - - - +
93B SER* 2.9 32.7 + - - -
103B ARG* 3.1 32.3 + - - +
105B PHE* 3.9 11.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLU* 5.7 3.1 - - + +
86B GLN 3.0 14.9 + - - +
87B ARG* 3.4 13.9 - - - +
88B VAL 3.2 0.2 - - - -
89B ASN* 1.3 76.3 - - - +
91B VAL* 1.3 59.9 + - + +
93B SER* 2.6 24.1 + - - -
94B ARG* 3.6 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLU* 3.4 46.9 - - + +
51B THR* 3.8 20.4 - - + -
52B GLU* 3.9 22.7 - - + +
55B LEU* 4.1 4.7 - - + -
87B ARG 3.4 4.9 + - - +
88B VAL 3.2 6.1 + - - +
90B GLU* 1.3 75.7 - - - +
92B TYR* 1.3 64.3 + - - +
94B ARG* 3.2 29.8 + - - +
95B TYR* 3.3 19.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.7 23.3 - - + +
75B VAL* 3.3 45.1 - - + +
77B VAL* 4.3 11.9 - - + -
88B VAL* 2.8 25.9 + - + +
89B ASN* 3.7 8.7 - - - +
91B VAL* 1.3 73.7 - - - +
93B SER* 1.3 58.9 + - - +
95B TYR* 3.0 8.5 + - - +
96B PHE* 2.9 56.7 + + + -
101B PRO* 3.9 11.6 + - + +
103B ARG* 3.5 41.0 - - - +
119B ILE* 4.6 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ASN 2.9 14.6 + - - -
90B GLU* 2.6 28.6 + - - -
92B TYR* 1.3 78.8 - - - +
94B ARG* 1.3 60.2 + - - +
95B TYR 3.2 0.2 - - - -
96B PHE 4.5 1.3 - - - -
97B GLY* 2.8 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLU* 5.5 2.8 - - - +
90B GLU* 3.6 48.9 + - - +
91B VAL* 3.2 25.5 + - - +
93B SER* 1.3 79.7 + - - +
95B TYR* 1.3 67.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU* 3.6 15.6 + - + +
55B LEU* 3.6 45.3 - - + -
56B GLU* 2.8 38.1 + - - +
59B LYS* 4.3 9.6 - - + -
69B LEU* 3.8 32.8 - - + +
91B VAL* 3.3 29.2 - - + -
92B TYR 3.0 6.3 + - - +
94B ARG* 1.3 86.1 - - + +
96B PHE* 1.3 73.4 + - + +
97B GLY 3.8 1.1 - - - -
99B HIS* 3.3 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.8 24.0 - - + -
58B LEU* 3.9 16.8 - - + -
69B LEU* 3.7 47.8 - - + -
72B VAL* 3.8 20.4 - - + -
75B VAL* 4.5 3.6 - - + -
92B TYR* 2.9 51.9 + + + +
93B SER* 3.9 1.8 - - - -
95B TYR* 1.3 85.0 - - + +
97B GLY* 1.3 58.3 + - - +
98B ASP 3.4 1.8 - - - -
99B HIS* 4.0 7.6 - - + -
100B ARG* 3.0 26.3 + - - +
101B PRO* 3.7 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B SER* 2.8 34.6 + - - -
95B TYR 3.8 1.2 - - - -
96B PHE* 1.3 72.8 - - - +
98B ASP* 1.3 59.8 + - - +
100B ARG* 3.5 19.3 - - - +
----------------------------------------------------------
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