Contacts of the strand formed by residues 45 - 49 (chain I) in PDB entry 2BX5
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36I TYR* 3.4 5.5 - - - -
37I GLN* 3.0 41.7 + - + +
39I LYS* 5.4 12.1 - - + -
42I LYS* 5.6 8.5 - - - +
43I ALA 3.8 13.8 + - - +
44I PRO* 1.3 78.6 - - - +
46I LEU* 1.3 66.8 + - - +
47I LEU* 3.5 9.7 + - + +
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Residues in contact with LEU 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I ASN* 3.7 20.4 - - + +
35I TRP 3.3 11.4 - - - +
36I TYR* 3.0 40.4 - - + +
45I LYS* 1.3 73.3 - - - +
47I LEU* 1.3 61.4 + - - +
48I ILE 3.1 26.2 - - - +
49I TYR* 4.2 23.3 - - + -
55I GLN* 3.6 20.6 - - + +
58I VAL* 4.6 3.5 - - - +
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Residues in contact with LEU 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I TRP* 3.0 18.6 + - + +
36I TYR 4.2 2.7 - - - -
37I GLN* 3.4 47.8 - - + +
45I LYS* 3.8 10.5 - - + +
46I LEU* 1.3 75.3 - - - +
48I ILE* 1.3 72.0 + - + +
54I LEU* 3.8 6.1 - - - +
55I GLN* 3.2 29.5 + - - +
58I VAL* 3.6 33.2 - - + +
62I PHE* 4.9 14.6 - - + -
73I LEU* 5.3 2.2 - - + -
86I TYR* 3.8 26.0 - - + -
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Residues in contact with ILE 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I ASN* 4.6 0.2 - - - -
35I TRP* 3.1 30.6 + - + +
46I LEU* 3.1 21.9 - - - +
47I LEU* 1.3 86.0 - - + +
49I TYR* 1.3 66.8 + - - +
51I ALA* 2.8 38.4 - - - +
52I SER 3.8 5.2 - - - +
53I SER 3.5 10.8 - - - +
54I LEU* 4.2 8.3 - - + -
62I PHE* 3.8 18.4 - - + +
63I SER* 3.6 28.9 - - - +
64I GLY* 3.7 10.5 - - - +
73I LEU* 3.8 19.3 - - + -
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Residues in contact with TYR 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I LEU 4.0 5.6 - - - -
34I ASN* 3.9 13.5 - - - +
46I LEU* 4.2 20.0 - - + -
48I ILE* 1.3 78.7 - - - +
50I ALA* 1.3 72.0 + - + +
51I ALA 2.7 8.9 + - - +
53I SER* 3.1 23.6 + - - +
54I LEU 4.7 2.0 + - - -
55I GLN* 2.2 46.9 + - + -
30J SER* 3.2 39.3 - - - -
32J TYR* 4.5 12.1 - + - +
92J TYR* 3.5 21.9 + + - -
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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