Contacts of the strand formed by residues 64 - 68 (chain B) in PDB entry 2ODY
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 LEU 64 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.0 14.4 - - + -
34B PHE 3.4 3.4 - - - +
36B LYS* 3.5 14.9 + - - -
41B LEU* 3.3 34.3 - - + -
59B LEU* 3.5 29.6 - - + -
60B THR* 3.4 38.3 - - + +
61B VAL 3.6 10.1 + - - +
62B ASP 3.4 1.0 - - - -
63B ASP* 1.3 84.1 - - - +
65B LEU* 1.3 67.3 + - - +
84B MET* 4.6 6.2 - - - +
85B LEU* 3.8 29.6 + - + +
88B ILE* 4.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B MET 3.7 0.2 - - - +
33B LEU* 3.8 3.8 - - - +
34B PHE* 2.7 44.3 + - + +
36B LYS* 4.1 24.0 - - + +
64B LEU* 1.3 82.8 - - - +
66B VAL* 1.3 69.3 + - - +
67B ARG* 5.1 0.9 - - + -
82B ILE* 4.0 6.7 - - + -
83B SER 3.7 9.6 - - - +
84B MET* 3.9 9.0 - - + +
85B LEU* 5.6 2.0 - - - -
133E GLU* 3.6 39.3 - - + +
137E LEU* 3.8 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 3.7 25.1 - - + -
32B MET 3.3 2.7 - - - +
33B LEU* 4.0 17.7 - - + -
52B VAL* 4.8 2.9 - - + -
65B LEU* 1.3 77.9 - - - +
67B ARG* 1.3 62.6 + - - +
68B ILE* 3.9 11.0 - - + -
81B LYS 3.5 1.4 - - - +
82B ILE* 3.5 4.3 - - - +
83B SER* 3.0 49.0 + - - +
85B LEU* 4.0 19.7 - - + +
106B LEU* 4.3 7.2 - - + -
108B LEU* 3.6 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLN 4.4 0.5 - - - +
31B VAL* 3.7 1.4 - - - -
32B MET* 2.9 43.9 + - + +
34B PHE* 3.6 55.7 - - + -
65B LEU* 5.1 1.3 - - + -
66B VAL* 1.3 77.6 - - - +
68B ILE* 1.3 61.3 + - - +
70B LYS* 3.6 26.3 - - + +
74B THR 5.0 2.2 + - - -
75B ARG 4.2 1.4 + - - -
76B TYR* 4.1 16.4 - - - +
80B GLU* 2.7 45.9 + - - +
81B LYS 3.4 4.7 - - - -
82B ILE* 4.0 17.8 - - + +
141B TRP* 5.2 0.7 - - - -
80E PHE* 4.4 15.2 - - - +
81E GLU 4.9 4.9 + - - -
137E LEU* 4.2 15.7 - - + +
138E VAL* 5.5 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PRO 4.5 4.9 - - - +
30B GLN 4.2 12.1 - - - +
31B VAL* 3.9 27.6 - - + -
46B LEU* 4.4 9.9 - - + -
52B VAL* 5.0 0.7 - - + -
66B VAL* 3.9 22.4 - - + -
67B ARG* 1.3 75.9 - - - +
69B GLY* 1.3 64.0 + - - +
70B LYS 3.4 2.5 - - - -
80B GLU* 3.2 5.4 - - - +
81B LYS* 2.8 40.3 + - + +
83B SER* 4.8 1.8 - - - +
108B LEU* 4.4 12.8 - - + -
112B ILE* 3.5 28.0 - - + -
118B ILE* 3.7 31.4 - - + +
----------------------------------------------------------
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