Contacts of the strand formed by residues 59 - 65 (chain B) in PDB entry 2OVI
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 59 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLY* 1.3 69.4 - - - -
60B VAL* 1.3 60.2 + - - +
74B SER* 5.4 1.8 - - - -
75B GLY* 3.6 26.0 - - - +
76B GLU* 3.7 11.6 + - - +
138B GLY* 3.5 15.5 - - - -
146B LEU* 4.6 5.1 - - + +
149B GLN* 2.9 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 4.9 5.6 - - + +
57B TRP* 4.6 16.2 - - + -
58B GLY 3.4 8.7 + - - +
59B ASN* 1.3 80.7 - - - +
61B THR* 1.3 63.6 + - - +
62B THR* 3.9 12.8 - - - +
73B PHE 3.5 0.9 - - - +
74B SER* 3.3 4.0 - - - -
75B GLY 3.0 40.2 + - - +
77B LEU* 4.3 18.6 - - + +
135B ILE* 3.7 23.8 - - + -
136B PHE 3.5 11.9 - - - +
137B LEU* 4.8 2.0 - - + -
138B GLY* 4.2 3.8 - - - +
149B GLN* 3.9 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 1.3 74.2 - - - +
62B THR* 1.3 63.8 + - - +
63B LEU* 4.0 8.2 + - + -
72B GLU* 3.6 40.4 - - + +
73B PHE 3.4 2.9 - - - +
74B SER* 3.2 20.6 + - - +
134B LYS 3.8 0.9 - - - +
135B ILE* 3.3 3.2 - - - -
136B PHE* 2.7 52.7 + - + +
137B LEU 5.0 3.2 + - - -
138B GLY* 5.3 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TRP* 5.2 1.3 - - + -
60B VAL* 3.9 7.0 - - - +
61B THR* 1.3 71.1 - - - +
63B LEU* 1.3 65.4 + - - +
72B GLU* 3.3 1.1 - - - -
73B PHE* 2.6 43.3 + - - +
77B LEU* 3.1 16.6 - - + +
95B MET* 3.7 32.9 - - + +
133B LEU* 4.1 21.5 - - + -
134B LYS 3.5 4.3 - - - +
135B ILE* 2.9 29.8 - - + +
71C LEU* 4.5 3.8 - - + +
73C PHE* 5.4 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 4.4 10.5 - - + -
62B THR* 1.3 75.7 - - - +
64B VAL* 1.3 75.2 - - - +
65B HIS* 3.9 11.4 - - + +
70B ILE* 3.9 20.2 - - + -
71B LEU 2.9 20.4 - - - +
72B GLU* 3.8 11.9 - - - +
133B LEU* 3.6 6.4 - - - +
134B LYS* 2.8 70.5 + - + +
136B PHE* 3.8 25.4 - - + -
71C LEU* 4.6 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 1.3 75.7 - - - +
65B HIS* 1.3 61.2 + - - +
66B THR* 4.0 11.7 - - + -
69B VAL* 3.7 2.0 - - + +
70B ILE* 3.4 2.4 - - - -
71B LEU* 3.0 43.2 + - + +
132B MET 3.8 10.8 - - - +
133B LEU* 3.6 16.2 - - + +
64C VAL* 3.3 30.1 - - + -
66C THR* 5.4 3.1 - - + -
69C VAL* 3.7 18.8 - - + -
71C LEU* 3.3 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 3.9 17.4 - - + +
19B GLU* 3.7 39.7 + - + +
63B LEU* 3.9 10.3 - - + +
64B VAL* 1.3 72.3 - - - +
66B THR* 1.3 77.6 + - - +
69B VAL 3.5 4.5 - - - -
70B ILE* 4.4 18.3 - - + +
131B ALA* 4.8 12.8 + - + +
132B MET 5.6 0.2 + - - -
133B LEU* 6.0 0.4 - - - +
134B LYS* 3.8 26.2 + - - +
86C TYR* 5.7 3.0 + - - -
----------------------------------------------------------
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