Contacts of the strand formed by residues 45 - 49 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36H TYR* 3.1 11.1 - - - +
37H GLN* 2.9 48.4 + - + +
38H GLN* 4.8 0.4 - - - +
43H ALA 3.9 2.6 + - - -
44H PRO* 1.3 74.9 - - - +
46H LEU* 1.3 63.4 + - - +
47H LEU* 5.2 1.8 - - + -
58H VAL* 6.0 2.2 - - + -
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Residues in contact with LEU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H ASN* 4.2 10.1 - - + +
35H TRP 4.0 4.9 - - - +
36H TYR* 3.7 33.1 - - + +
44H PRO 4.1 1.2 + - - -
45H LYS* 1.3 73.7 - - - +
47H LEU* 1.3 65.0 + - - +
48H ILE 3.0 31.6 - - - +
49H TYR* 4.0 20.2 - - + +
55H GLN* 3.3 30.1 - - - +
56H SER 4.6 3.1 - - - +
58H VAL* 4.1 8.1 - - - +
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Residues in contact with LEU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H TRP 2.9 20.9 + - - +
36H TYR 4.2 5.6 - - - -
37H GLN* 3.3 42.6 - - + +
45H LYS* 5.0 2.9 - - + +
46H LEU* 1.3 75.5 - - - +
48H ILE* 1.3 73.6 + - + +
54H LEU* 4.4 0.7 - - - +
55H GLN* 3.0 34.8 + - - +
58H VAL* 3.5 31.2 - - + -
62H PHE* 4.3 12.6 - - + -
73H LEU* 3.4 39.9 - - + -
86H TYR* 4.5 1.1 - - + -
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Residues in contact with ILE 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H ASN* 3.6 15.5 + - - +
35H TRP* 3.2 34.8 + - + +
46H LEU* 3.0 21.0 - - - +
47H LEU* 1.3 94.2 - - + +
49H TYR* 1.3 68.1 + - - +
51H ALA 3.3 26.5 - - - +
52H SER* 3.5 17.3 - - - +
53H SER 3.6 3.6 - - - +
54H LEU* 4.4 6.7 - - + -
62H PHE 3.8 22.0 - - - +
63H SER* 4.2 4.5 - - - +
64H GLY* 4.6 3.6 - - - +
73H LEU* 3.6 22.2 - - + -
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Residues in contact with TYR 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G SER* 4.2 21.8 - - - +
32G TYR* 3.2 37.9 - + + -
92G TYR* 4.7 16.5 + + - -
33H LEU 4.1 1.3 - - - -
34H ASN* 3.7 9.6 - - - +
46H LEU* 4.0 22.3 - - + +
48H ILE* 1.3 75.4 - - - +
50H ALA* 1.3 60.6 + - + +
51H ALA* 2.7 4.6 + - - -
52H SER 2.4 33.4 + - - -
53H SER* 3.2 14.1 + - - +
55H GLN* 2.5 46.0 + - + -
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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