Contacts of the strand formed by residues 45 - 51 (chain F) 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 LYS 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39F PHE* 4.0 6.1 - - - -
40F ASN* 2.9 26.5 + - - +
43F THR* 3.3 31.6 - - + +
44F GLY* 1.3 80.6 - - - +
46F CYS* 1.3 64.9 + - - +
47F THR* 3.1 15.2 + - - +
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Residues in contact with CYS 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F PHE* 4.5 2.9 - - + -
38F TYR 3.3 4.9 - - - -
39F PHE* 4.2 11.2 - - - -
45F LYS* 1.3 77.7 - - - +
47F THR* 1.3 58.2 + - - +
64F ILE* 3.8 36.7 - - + +
67F CYS* 2.1 50.5 - - + -
68F GLN* 3.3 25.8 - - + +
72F GLY* 5.2 0.7 - - - -
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Residues in contact with THR 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F PHE* 3.3 3.5 - - - -
38F TYR* 2.6 61.4 + - + +
40F ASN* 3.6 11.5 + - - +
43F THR* 4.1 4.9 + - - -
45F LYS* 3.1 18.5 + - - +
46F CYS* 1.3 73.6 - - - +
48F MET* 1.3 74.7 + - - +
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Residues in contact with MET 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F PRO* 4.5 18.2 - - + -
36F ARG 3.2 14.6 - - - +
37F PHE* 3.9 25.6 - - + -
38F TYR* 4.5 0.7 - - - -
47F THR* 1.3 86.6 - - - +
49F PHE* 1.3 69.1 + - - +
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Residues in contact with PHE 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F ALA* 4.2 9.2 - - + -
26F ASP 3.5 33.7 - - - -
27F GLU* 4.6 1.8 - - + -
34F ILE 3.8 0.2 - - - +
35F PRO* 3.8 3.3 - - - +
36F ARG* 2.8 58.7 + - + +
37F PHE 3.9 6.1 - - - -
38F TYR* 3.7 42.6 - + + -
48F MET* 1.3 79.4 - - - +
50F SER* 1.3 79.7 + - - +
51F TYR* 4.0 6.1 - - + -
59F ASN 4.1 6.5 - - - -
60F ASN* 3.7 26.2 - - + -
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Residues in contact with SER 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F GLU* 3.1 33.7 + - - +
32F ALA 4.8 0.2 + - - -
33F LEU* 4.0 31.5 - - - +
34F ILE 3.8 5.3 + - - -
35F PRO* 5.0 0.9 - - - -
49F PHE* 1.3 79.7 - - - +
51F TYR* 1.3 60.0 + - - +
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Residues in contact with TYR 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ASP 3.7 11.4 - - - -
27F GLU* 3.5 10.1 - - - -
32F ALA 3.3 2.8 - - - +
34F ILE* 2.8 49.0 + - + +
36F ARG* 3.6 43.3 - - + -
49F PHE* 3.7 10.0 + - + -
50F SER* 1.3 72.5 - - - +
52F GLY* 1.3 66.8 + - - +
53F GLY* 3.5 24.7 + - - -
54F CYS* 3.3 29.1 + - - -
55F GLY 2.9 29.6 + - - -
56F GLY* 4.5 0.2 - - - -
60F ASN* 3.3 25.4 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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