Contacts of the helix formed by residues 18 - 25 (chain A) in PDB entry 4F9K
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 CYS 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LYS* 3.6 22.2 - - - -
17A GLY* 1.3 81.0 - - - +
19A GLU* 1.3 62.7 + - - +
20A LEU 3.1 3.7 + - - -
21A TYR* 3.4 5.6 + - + +
22A VAL* 3.4 23.1 + - - +
39B CYS* 2.0 53.4 - - + +
42B LYS* 3.5 24.0 - - + +
44D GLU* 4.4 0.2 - - - -
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS* 2.8 50.6 + - + +
17A GLY* 3.4 1.3 - - - -
18A CYS* 1.3 78.4 - - - +
20A LEU* 1.3 63.1 + - + +
22A VAL* 3.6 11.7 + - - +
23A GLN* 3.4 34.6 + - - +
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLY 5.0 1.0 + - - +
18A CYS 3.1 0.6 - - - -
19A GLU* 1.3 77.2 - - + +
21A TYR* 1.3 66.3 + - - +
22A VAL 3.1 2.3 + - - -
23A GLN* 3.1 10.6 + - - +
24A LEU* 3.0 32.9 + - + +
65C ILE* 4.6 30.7 - - + -
69C GLN* 5.7 1.2 - - + +
44D GLU* 3.5 40.8 + - + +
45D ARG* 4.0 27.4 - - + -
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Residues in contact with TYR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A CYS 3.6 7.9 - - - +
20A LEU* 1.3 77.3 - - - +
22A VAL* 1.3 67.6 + - + +
24A LEU* 3.4 9.4 + - + +
25A HIS* 3.0 59.1 + + - +
27A ILE* 4.6 9.6 - - + -
38B LEU* 3.8 22.3 - - + +
39B CYS* 5.2 1.8 - - - -
42B LYS* 3.7 51.6 - - + -
43B PRO* 2.5 39.1 + - - +
46B PRO* 3.4 20.8 - - + +
44D GLU* 3.4 13.6 + - + +
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS* 5.9 4.3 - - + -
18A CYS 3.4 15.9 + - - +
19A GLU* 3.6 11.0 - - - +
20A LEU 3.1 0.8 + - - -
21A TYR* 1.3 83.0 - - + +
23A GLN* 1.3 64.1 + - + +
25A HIS 3.6 0.2 + - - -
26A GLY 3.2 26.7 + - - +
27A ILE* 3.5 15.5 + - + +
28A GLN* 3.8 41.5 - - + +
35B ILE* 4.1 23.3 - - + -
38B LEU* 6.5 0.7 - - + -
39B CYS* 4.8 8.7 - - + -
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Residues in contact with GLN 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLU* 3.4 33.3 + - - +
20A LEU* 3.1 9.9 + - - +
22A VAL* 1.3 76.5 - - - +
24A LEU* 1.3 66.2 + - - +
25A HIS 3.2 1.0 + - - -
26A GLY* 3.4 12.0 + - - +
28A GLN* 4.0 20.6 + - + +
65C ILE* 5.4 3.8 - - - +
69C GLN* 3.5 60.8 + - + +
70C LYS* 5.3 0.4 - - - -
72C ASN* 5.1 7.6 - - - +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.0 27.4 + - + +
21A TYR* 3.6 11.0 - - + +
23A GLN* 1.3 78.3 - - - +
25A HIS* 1.3 76.1 + - + +
26A GLY 3.8 0.5 + - - -
24C LEU* 3.6 38.1 - - + +
25C HIS* 4.4 17.0 - - + +
69C GLN* 4.8 5.0 - - - +
44D GLU* 5.7 4.5 - - + +
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Residues in contact with HIS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.0 48.4 + + + +
22A VAL 3.6 0.6 + - - -
23A GLN 3.2 0.2 - - - -
24A LEU* 1.3 99.2 - - + +
26A GLY* 1.3 48.8 + - - +
27A ILE* 2.7 42.5 + - + +
30A VAL* 4.1 7.6 - - - +
43B PRO 4.0 2.7 - - - -
44B GLU* 3.3 21.4 + - - -
46B PRO* 3.5 24.9 - - + +
47B MSE 5.0 5.0 - - - +
24C LEU* 4.4 16.0 - - + +
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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