Contacts of the helix formed by residues 66 - 70 (chain F) in PDB entry 3BXB
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 SER 66 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F MET* 3.9 0.9 - - - -
39F GLN* 2.6 43.2 + - - -
62F PHE 3.7 5.2 - - - -
63F NRQ 1.3 95.0 + - - -
67F LYS* 1.3 64.0 + - - +
68F THR 3.3 2.9 - - - -
69F PHE* 3.3 15.2 + - - +
70F ILE* 4.9 1.4 - - - +
117F TYR* 2.7 33.4 + - - -
215F GLU* 5.5 0.4 - - - -
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Residues in contact with LYS 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F NRQ 3.8 30.6 + - + +
66F SER* 1.3 72.6 - - - +
68F THR* 1.3 63.7 + - - +
69F PHE 3.1 3.2 + - - -
70F ILE* 3.4 40.6 + - - +
72F HIS* 4.8 1.4 - - - -
78F ASP* 5.1 0.5 - - - +
80F PHE* 3.5 41.7 - - + +
88F PHE* 3.9 15.9 - - + -
90F TRP* 4.3 7.4 - - + -
92F ARG* 4.7 0.8 - - - +
145F GLU* 3.1 26.0 + - - -
147F LEU* 5.3 1.1 - - - -
178F TYR* 3.1 39.0 + - + -
197F ARG* 5.0 3.6 - - - +
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Residues in contact with THR 68 (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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5F ILE* 4.1 26.5 - - + -
9F MET* 5.6 0.2 - - - -
34F PRO* 3.5 6.2 - - + +
66F SER 3.3 0.6 + - - -
67F LYS* 1.3 78.0 - - - +
69F PHE* 1.3 61.7 + - + +
70F ILE 3.3 0.2 - - - -
80F PHE* 4.3 6.7 - - - -
81F LYS* 3.1 32.9 + - + -
84F PHE* 3.3 35.8 - - + -
88F PHE* 3.4 10.7 - - - -
108F THR* 4.6 1.7 - - - +
115F LEU* 4.1 26.5 - - + +
117F TYR* 4.8 2.4 + - - -
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Residues in contact with PHE 69 (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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9F MET* 4.2 10.5 - - + -
11F MET* 3.7 26.2 - - + -
32F GLY* 3.5 28.0 - - - -
34F PRO* 3.8 29.6 - - + -
37F GLY* 3.0 26.8 - - - +
38F THR 3.7 18.6 - - - +
39F GLN* 3.5 28.1 + - + +
66F SER* 3.3 20.3 + - - -
67F LYS 3.1 1.6 - - - -
68F THR* 1.3 78.9 - - - +
70F ILE* 1.3 60.9 + - - +
115F LEU* 3.6 20.9 - - + -
117F TYR* 3.3 21.1 - - - -
217F ALA* 4.1 2.9 - - - +
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Residues in contact with ILE 70 (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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34F PRO 3.9 3.4 - - - -
39F GLN* 6.2 0.2 - - - +
66F SER 4.9 1.1 - - - +
67F LYS* 3.4 51.3 + - + +
68F THR 3.3 4.9 + - - -
69F PHE* 1.3 78.9 - - - +
71F ASN* 1.3 60.6 + - - +
72F HIS* 2.9 30.2 + - + -
80F PHE* 4.6 4.7 - - + -
81F LYS* 3.0 20.6 + - - -
145F GLU* 5.5 0.2 - - - +
147F LEU* 6.3 0.7 - - + -
195F VAL* 4.0 21.8 - - + -
197F ARG* 6.1 0.2 - - - -
215F GLU* 5.5 1.1 - - - +
217F ALA* 3.7 26.7 - - + +
219F ALA* 3.8 28.7 - - + +
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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