Contacts of the strand formed by residues 17 - 23 (chain F) in PDB entry 1M06
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 HIS 17 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15F LEU 2.9 22.7 + - - +
16F SER* 1.3 77.4 - - - +
18F LEU* 1.3 74.5 + - - +
19F ALA* 5.1 2.9 - - + -
32F SER* 3.0 26.8 + - - -
33F TRP 5.6 1.4 + - - -
34F THR* 4.8 7.6 - - - -
412F ARG* 3.7 3.9 - - - +
413F TYR* 2.7 61.4 + + + +
414F ASN* 5.1 0.6 - - - +
415F VAL* 4.3 8.7 - - + -
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Residues in contact with LEU 18 (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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17F HIS* 1.3 85.8 - - - +
19F ALA* 1.3 64.0 + - - +
20F PHE* 4.1 27.8 - - + -
411F ALA 3.5 16.2 - - - +
412F ARG* 3.9 27.6 - - + -
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Residues in contact with ALA 19 (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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17F HIS* 5.1 4.3 - - + -
18F LEU* 1.3 79.8 - - - +
20F PHE* 1.3 65.4 + - - +
21F ASP* 3.9 1.2 + - + -
31F VAL* 4.1 17.9 - - + +
32F SER* 5.3 0.2 - - - -
409F LYS* 3.8 7.2 + - - +
410F GLN* 3.2 4.5 - - - -
411F ALA 3.1 27.8 + - - +
413F TYR* 3.9 25.1 - - + -
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Residues in contact with PHE 20 (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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18F LEU* 4.1 33.0 - - + -
19F ALA* 1.3 76.0 - - - +
21F ASP* 1.3 62.1 + - - +
409F LYS 3.5 4.0 - - - +
410F GLN* 3.3 43.5 - - + -
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Residues in contact with ASP 21 (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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19F ALA* 3.9 1.5 + - + -
20F PHE* 1.3 76.4 - - - +
22F CYS* 1.3 75.9 + - - +
29F LYS* 2.8 43.9 + - - +
30F THR 3.4 10.6 - - - +
31F VAL* 3.5 28.9 - - + +
404F LEU* 5.7 0.4 - - - +
407F TRP* 4.2 4.7 - - + -
408F ASN* 3.2 2.6 - - - +
409F LYS* 2.8 41.8 + - + +
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Residues in contact with CYS 22 (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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21F ASP* 1.3 92.2 + - - +
23F GLY* 1.3 56.9 + - - +
29F LYS* 3.7 11.3 - - - +
404F LEU* 3.8 25.6 - - + +
405F LEU* 3.5 23.8 - - - +
407F TRP* 3.1 29.4 - - - +
408F ASN* 3.3 13.5 - - + +
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Residues in contact with GLY 23 (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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22F CYS* 1.3 77.9 - - - +
24F MET* 1.3 57.4 + - - -
29F LYS* 4.9 4.3 - - - -
159F TYR* 5.1 5.4 - - - -
405F LEU* 3.4 16.8 - - - +
406F GLN 3.1 8.1 + - - -
407F TRP* 3.0 51.3 + - - -
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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