Contacts of the strand formed by residues 73 - 81 (chain B) in PDB entry 2OMU
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 THR 73 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLN* 5.1 2.1 - - - +
71B ILE* 3.1 18.7 - - - +
72B ALA* 1.3 87.3 - - + +
74B TYR* 1.3 66.5 + - - +
75B THR* 5.5 1.6 + - - -
95B LEU* 3.9 18.2 - - + -
96B ILE 3.2 10.1 - - - +
97B THR* 4.6 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLN* 3.5 27.6 - - + +
42B GLY* 4.0 11.2 - - - -
47B PRO* 4.4 4.4 - - + +
50B VAL* 4.2 7.9 - - + +
51B PHE* 3.5 40.4 - + + -
66B LEU* 3.9 17.4 - - + +
67B ASP 5.7 1.0 + - - -
71B ILE* 3.5 48.0 + - + +
73B THR* 1.3 77.6 - - - +
75B THR* 1.3 61.7 + - - +
76B LEU* 4.0 5.6 - - + -
94B ILE 3.4 2.4 - - - +
95B LEU* 3.5 4.3 - - - +
96B ILE* 2.8 40.8 + - + +
98B VAL* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLY* 3.9 13.2 - - - -
41B GLN* 4.0 8.7 + - - +
73B THR* 5.5 1.4 + - - -
74B TYR* 1.3 73.2 + - - +
76B LEU* 1.3 67.7 + - - +
77B PHE* 3.9 16.7 - - + -
93B GLU* 3.6 37.5 + - + +
94B ILE 3.5 3.4 - - - +
95B LEU* 4.7 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 3.9 20.2 - - + -
39B THR 3.3 11.9 - - - +
41B GLN 3.3 26.9 - - - +
43B ALA* 4.2 11.9 - - + +
51B PHE* 3.8 24.0 - - + -
60B LEU* 4.2 9.0 - - + -
74B TYR* 4.3 8.5 - - + -
75B THR* 1.3 77.8 - - - +
77B PHE* 1.3 66.7 + - - +
93B GLU* 3.4 4.7 - - - -
94B ILE* 2.6 50.6 + - + +
96B ILE* 3.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 3.1 7.1 - - - -
39B THR* 2.8 55.7 + - - +
40B GLY* 5.3 2.9 - - - -
75B THR* 3.9 20.2 - - + -
76B LEU* 1.3 77.4 - - - +
78B SER* 1.3 60.2 + - - +
79B HIS* 3.3 13.1 + - + +
91B PRO* 4.2 14.1 - - + -
92B MET* 3.2 5.6 - - - +
93B GLU* 3.5 51.6 - - + -
94B ILE* 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B TRP* 3.4 27.5 - - - -
4B ILE* 4.0 0.5 - - - +
24B ILE* 4.5 6.7 - - - -
36B TYR* 5.9 0.7 - - - -
37B SER 3.2 9.0 - - - -
38B ILE* 4.1 7.2 - - - -
53B ILE* 5.4 2.5 - - - -
77B PHE* 1.3 70.5 - - - +
79B HIS* 1.3 65.3 + - - +
91B PRO* 3.3 9.9 - - - +
92B MET* 3.0 37.8 + - - +
94B ILE* 3.3 26.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B TRP* 3.6 6.5 - - - -
35B PHE 3.8 0.6 - - - +
36B TYR* 3.3 9.2 - - - +
37B SER* 2.8 53.9 + - - +
39B THR* 2.7 40.1 + - + +
77B PHE* 3.3 13.0 + - + -
78B SER* 1.3 78.0 + - - +
80B ALA* 1.3 63.1 + - - +
81B VAL* 5.5 5.4 - - + -
89B GLU 5.9 0.4 - - - -
90B ASP 5.5 0.4 - - - -
91B PRO* 3.8 34.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B TRP* 3.6 20.3 - - + -
26B SER* 4.4 0.7 - - - -
34B VAL* 3.7 20.2 - - + -
35B PHE 3.6 3.6 - - - -
36B TYR* 4.2 4.7 - - + -
79B HIS* 1.3 76.4 - - - +
81B VAL* 1.3 65.7 + - - +
87B ALA* 3.3 8.0 - - - +
88B VAL* 3.2 28.3 + - + -
89B GLU* 3.8 20.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 3.3 4.5 - - - -
35B PHE* 2.7 58.0 + - + +
37B SER* 6.1 0.9 - - - +
55B ARG* 4.5 11.2 - - - +
79B HIS* 5.5 4.7 - - + -
80B ALA* 1.3 78.0 - - - +
82B SER* 1.3 68.6 + - - +
85B GLY* 3.7 16.6 - - - +
86B ASN 3.2 6.1 - - - +
87B ALA* 3.2 19.7 - - + +
88B VAL* 4.3 4.9 - - - -
----------------------------------------------------------
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