Contacts of the helix formed by residues 12 - 25 (chain F) in PDB entry 6BZE
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 ASP 12 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F GLU* 2.8 45.7 + - - +
11F GLU* 1.3 79.5 - - - +
13F LEU* 1.3 66.1 + - - +
14F THR 3.2 2.7 - - - -
15F GLU* 3.1 25.7 + - - +
16F VAL* 3.5 8.0 - - - +
113F HIS* 4.1 26.7 - - + +
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Residues in contact with LEU 13 (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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10F GLU* 5.4 9.1 + - - +
11F GLU* 4.8 18.8 - - - +
12F ASP* 1.3 78.0 - - - +
14F THR* 1.3 73.2 + - - +
15F GLU 3.0 5.6 - - - -
16F VAL* 2.8 32.7 + - + +
17F LYS* 2.6 44.2 + - - +
76F PRO 5.7 0.7 - - - +
110F LYS* 5.1 16.2 - - + +
113F HIS* 5.7 0.2 + - - -
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Residues in contact with THR 14 (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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11F GLU* 3.3 32.8 - - + +
13F LEU* 1.3 84.6 - - - +
15F GLU* 1.3 78.2 + - + +
17F LYS* 3.5 24.3 - - - +
18F LYS* 4.2 8.5 - - - +
73F GLN 4.9 1.4 - - - +
75F ASN 4.0 5.9 + - - +
76F PRO* 3.2 37.7 + - + +
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Residues in contact with GLU 15 (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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11F GLU 5.3 0.4 - - - +
12F ASP* 3.3 15.0 - - - +
13F LEU 3.0 0.4 - - - -
14F THR* 1.3 93.5 + - + +
16F VAL* 1.3 66.7 + - + +
17F LYS 3.0 2.5 - - - -
18F LYS* 2.4 54.3 + - - +
19F ASP* 3.6 3.7 + - - +
73F GLN 5.4 1.0 - - - +
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Residues in contact with VAL 16 (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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12F ASP 3.5 17.0 - - - +
13F LEU* 2.8 20.1 + - - +
15F GLU* 1.3 78.2 - - + +
17F LYS* 1.3 63.1 + - - +
18F LYS 3.2 0.2 - - - -
19F ASP* 2.7 39.4 - - - +
20F ALA* 3.0 6.1 + - - +
106F LEU* 3.5 21.1 - - + -
109F ILE* 3.6 17.7 - - + -
110F LYS* 4.0 13.2 - - + -
113F HIS* 4.1 25.8 - - + +
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Residues in contact with LYS 17 (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 LEU* 2.6 64.2 + - - +
14F THR* 3.5 17.9 - - - +
15F GLU 3.0 0.4 - - - -
16F VAL* 1.3 79.2 - - - +
18F LYS* 1.3 51.8 + - + +
20F ALA* 3.5 3.9 - - - +
21F LEU* 2.7 36.6 + - - +
76F PRO 4.2 11.4 - - - +
77F LYS 4.7 10.8 - - - +
78F GLY* 5.1 13.2 - - - +
79F LEU* 5.1 6.7 - - + -
106F LEU* 3.2 41.0 - - + +
110F LYS* 5.4 1.2 - - - +
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Residues in contact with LYS 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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14F THR 4.2 4.7 - - - +
15F GLU* 2.4 73.4 + - - +
17F LYS* 1.3 77.7 - - + +
19F ASP* 1.3 50.1 + - - +
21F LEU* 2.9 6.6 + - - +
22F GLU* 2.3 54.8 + - - +
73F GLN* 3.5 51.5 + - + +
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Residues in contact with ASP 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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15F GLU 3.6 2.7 + - - +
16F VAL* 2.7 34.8 + - - +
18F LYS* 1.3 78.1 - - - +
20F ALA* 1.3 69.0 + - - +
22F GLU* 2.7 19.5 + - - +
23F ASN* 2.2 48.1 + - - +
109F ILE* 3.0 32.7 - - + +
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Residues in contact with ALA 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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16F VAL 3.0 12.7 + - - +
17F LYS* 3.5 7.0 - - - +
19F ASP* 1.3 85.4 + - - +
21F LEU* 1.3 53.3 + - - +
23F ASN* 3.1 12.6 + - - +
24F LEU* 2.5 37.0 + - - +
102F GLU* 5.0 3.1 - - + +
105F LYS* 3.6 26.8 - - + +
106F LEU* 3.6 20.4 - - + +
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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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17F LYS 2.7 19.4 + - - +
18F LYS* 3.1 10.8 - - - +
20F ALA* 1.3 69.9 - - - +
22F GLU* 1.3 54.9 + - - +
24F LEU* 3.0 18.4 - - + +
25F ARG* 2.3 41.0 + - + +
69F LEU* 3.6 53.8 - - + +
72F LEU* 4.8 8.1 - - + -
73F GLN* 3.6 28.5 - - + +
102F GLU* 4.9 8.3 - - + +
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Residues in contact with GLU 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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18F LYS* 2.3 55.6 + - - +
19F ASP* 3.2 17.6 + - - +
21F LEU* 1.3 68.4 - - - +
23F ASN* 1.3 64.1 + - - +
25F ARG* 3.3 25.7 - - - +
26F VAL* 4.6 3.5 + - - +
73F GLN* 3.4 18.8 + - - +
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Residues in contact with ASN 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 ASP* 2.2 52.6 + - - +
20F ALA* 3.3 5.8 + - - +
22F GLU* 1.3 70.1 - - - +
24F LEU* 1.3 58.6 + - - +
25F ARG 3.3 0.9 - - - -
26F VAL* 3.9 16.7 - - - +
105F LYS* 3.5 30.1 + - - +
109F ILE* 3.3 27.4 - - - +
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Residues in contact with LEU 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 ALA 2.5 18.9 + - - +
21F LEU* 2.9 16.5 + - + +
23F ASN* 1.3 71.9 - - - +
25F ARG* 1.3 66.6 + - - +
26F VAL* 2.9 2.7 - - - -
27F TYR* 2.9 43.1 + - + +
69F LEU* 4.9 4.6 - - + +
95F LEU* 6.3 2.5 - - + -
98F LYS 5.1 1.3 - - - +
101F ASP* 3.9 11.0 - - - +
102F GLU* 3.3 45.5 - - + +
105F LYS* 3.7 27.4 - - + -
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Residues in contact with ARG 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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21F LEU* 2.3 24.0 + - - +
22F GLU* 3.3 24.7 - - - +
23F ASN 3.3 0.4 - - - -
24F LEU* 1.3 71.2 - - - +
26F VAL* 1.3 63.1 + - + +
27F TYR 3.3 0.5 + - - -
28F LEU* 3.4 29.7 + - + +
66F GLY* 4.1 26.0 + - - -
69F LEU* 5.0 16.8 - - - -
70F ASP* 4.2 23.0 + - - +
73F GLN* 5.4 8.0 - - - +
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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