Contacts of the helix formed by residues 19 - 27 (chain F) in PDB entry 2GLJ
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 19 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17F ASP* 2.5 32.6 + - - +
18F ASP* 1.3 81.4 - - - +
20F GLN* 1.3 62.3 + - + +
22F LYS* 4.5 7.9 - - - +
23F GLU* 3.6 22.5 + - - +
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Residues in contact with GLN 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 ASP* 2.6 40.5 + - - +
19F LYS* 1.3 73.0 - - + +
21F LEU* 1.3 69.1 + - + +
22F LYS 3.1 0.7 - - - -
23F GLU* 2.8 8.3 + - - +
24F VAL* 2.6 34.6 + - + +
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Residues in contact with LEU 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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15F LYS* 4.0 12.8 - - + +
16F TYR* 3.3 43.7 - - + +
17F ASP 3.5 6.9 + - - +
18F ASP* 3.6 19.3 - - + +
20F GLN* 1.3 77.3 - - + +
22F LYS* 1.3 67.2 + - - +
24F VAL* 3.0 19.6 + - + +
25F PHE* 3.0 16.1 - - - -
453F TYR* 3.1 32.3 - - + +
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Residues in contact with LYS 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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13F TRP* 4.7 18.8 - - + -
14F ASP 5.6 2.9 - - - +
16F TYR* 4.4 4.3 - - + -
17F ASP* 3.3 56.5 + - - +
19F LYS* 4.7 8.5 - - - +
20F GLN 2.8 3.8 + - - -
21F LEU* 1.3 73.9 - - - +
23F GLU* 1.3 52.4 + - - +
25F PHE* 2.7 24.4 + - + -
26F ALA* 2.6 40.9 + - + -
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Residues in contact with GLU 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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19F LYS 3.6 14.9 + - - +
20F GLN* 2.8 11.4 + - - +
22F LYS* 1.3 77.9 - - - +
24F VAL* 1.3 58.0 + - + +
25F PHE 2.8 6.8 + - - -
26F ALA* 4.6 5.6 - - - +
27F LEU* 3.5 32.6 + - + +
28F GLY* 3.5 13.5 + - - -
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Residues in contact with VAL 24 (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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20F GLN* 2.6 43.7 + - + +
21F LEU* 3.2 13.7 - - + +
22F LYS 2.9 0.6 + - - -
23F GLU* 1.3 71.3 - - + +
25F PHE* 1.3 60.8 + - - +
28F GLY* 3.6 10.9 - - - -
29F ASP* 4.5 1.4 + - - +
453F TYR* 4.0 21.0 - - + +
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Residues in contact with PHE 25 (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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13F TRP* 3.3 42.0 - + - -
16F TYR* 3.4 35.0 - + + -
21F LEU 3.0 19.1 - - - -
22F LYS* 2.7 21.7 + - - -
23F GLU 2.8 2.4 + - - -
24F VAL* 1.3 81.8 - - - +
26F ALA* 1.3 83.7 + - + +
27F LEU 2.8 2.0 - - - -
28F GLY* 2.7 15.0 + - - +
29F ASP* 3.1 17.1 + - + +
30F ARG* 3.3 8.5 + - - +
449F LYS* 4.0 18.5 - - + +
450F ALA* 3.9 10.8 - - - -
453F TYR* 3.4 34.3 - + + -
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Residues in contact with ALA 26 (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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13F TRP* 5.7 4.3 - - + -
22F LYS* 2.6 29.7 + - + +
23F GLU* 4.6 3.4 - - - +
25F PHE* 1.3 85.9 - - + +
27F LEU* 1.3 64.8 + - + +
30F ARG* 3.1 21.8 - - - +
449F LYS* 3.4 19.2 + - + +
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Residues in contact with LEU 27 (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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23F GLU* 3.5 34.6 + - + +
25F PHE 3.3 1.3 - - - -
26F ALA* 1.3 83.0 - - + +
28F GLY* 1.3 71.7 + - - +
30F ARG* 3.5 17.5 - - - +
31F PHE* 3.0 26.3 - - + +
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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