Contacts of the helix formed by residues 15 - 26 (chain I) in PDB entry 5L08
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 15 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I GLN 3.2 5.6 + - - +
14I LEU* 1.3 76.8 - - - +
16I SER* 1.3 60.0 + - - +
17I GLU* 2.7 34.9 + - - +
18I ASP* 2.9 23.1 + - - +
19I LEU* 2.8 32.7 + - - +
71I ARG* 3.8 11.7 - - - +
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Residues in contact with SER 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I LEU 3.8 2.4 + - - -
15I ASP* 1.3 78.9 + - - +
17I GLU* 1.3 60.0 + - - +
19I LEU* 3.5 15.3 - - - +
20I ALA* 2.9 25.6 + - - +
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Residues in contact with GLU 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I ASP* 2.7 22.3 + - - +
16I SER* 1.3 73.1 + - - +
18I ASP* 1.3 63.5 + - - +
20I ALA* 3.2 10.2 + - - +
21I SER* 2.9 33.8 + - - +
138I ASN* 2.9 32.2 + - - +
140I LEU* 5.6 0.5 - - - +
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Residues in contact with ASP 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I LEU* 3.6 17.7 - - + -
15I ASP* 2.9 16.5 + - - +
17I GLU* 1.3 78.8 - - - +
19I LEU* 1.3 59.5 + - - +
21I SER* 3.2 11.5 + - - -
22I LEU* 2.9 30.7 + - - +
69I ILE* 4.0 18.7 - - + +
71I ARG* 2.8 39.8 + - - -
106I TYR* 5.4 2.8 + - - -
110I GLU* 5.8 0.3 - - - +
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Residues in contact with LEU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I LEU* 4.1 19.4 - - + +
15I ASP 2.8 12.2 + - - +
16I SER* 3.5 16.2 - - - +
18I ASP* 1.3 73.6 - - - +
20I ALA* 1.3 59.7 - - - +
22I LEU* 3.0 10.6 + - + +
23I LYS* 2.8 40.7 + - + +
38I ILE* 4.4 7.6 - - + +
39I LYS 3.9 8.1 - - - +
40I ASP* 3.5 44.6 - - - +
41I ALA 4.2 0.7 - - - +
44I LEU* 4.0 29.2 - - + -
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Residues in contact with ALA 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I SER 2.9 14.2 + - - +
17I GLU* 3.2 21.7 + - - +
19I LEU* 1.3 75.8 - - - +
21I SER* 1.3 57.2 + - - +
23I LYS* 3.2 17.2 + - + +
24I PHE* 3.0 26.0 + - - +
138I ASN* 5.3 7.0 - - - +
140I LEU* 4.9 3.1 - - - +
141I ASP* 5.8 3.4 - - - +
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Residues in contact with SER 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I GLU* 2.9 19.8 + - - +
18I ASP* 3.3 14.7 + - - -
20I ALA* 1.3 77.8 - - - +
22I LEU* 1.3 56.0 + - - +
24I PHE* 3.2 4.5 + - - +
25I LEU* 3.0 33.2 + - - +
69I ILE* 3.8 8.3 - - - -
106I TYR* 3.6 31.6 + - - -
110I GLU* 5.4 0.2 + - - -
140I LEU* 3.7 19.0 - - - +
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Residues in contact with LEU 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I LEU* 4.0 22.0 - - + -
18I ASP 2.9 16.5 + - - +
19I LEU* 3.0 8.7 + - - +
21I SER* 1.3 71.0 - - - +
23I LYS* 1.3 60.6 + - - +
25I LEU* 3.2 7.6 + - + +
26I SER* 2.8 32.3 + - - -
44I LEU* 3.9 31.4 - - + -
62I LEU* 6.1 2.2 - - + -
65I LEU* 3.6 48.2 - - + +
66I LEU* 4.5 8.7 - - + +
69I ILE* 3.7 25.8 - - + -
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Residues in contact with LYS 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I LEU* 2.8 26.4 + - + +
20I ALA* 3.2 20.2 + - + +
22I LEU* 1.3 75.2 - - - +
24I PHE* 1.3 63.2 + - - +
26I SER* 2.7 15.3 + - - +
27I LEU* 3.1 3.5 + - - +
35I GLN* 2.7 53.9 + - + +
36I GLU* 4.2 9.0 + - - +
38I ILE* 2.8 51.5 + - + -
39I LYS* 5.8 0.2 - - - +
44I LEU* 5.6 2.9 - - + -
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Residues in contact with PHE 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I ALA 3.0 13.4 + - - +
21I SER 3.4 8.1 - - - +
23I LYS* 1.3 75.7 - - - +
25I LEU* 1.3 70.7 + - + +
27I LEU* 3.0 39.8 - - + +
102I ARG* 3.5 57.9 - - - -
105I LEU* 3.7 30.1 - - + -
106I TYR* 5.0 2.2 - + + -
140I LEU* 3.5 59.2 - - + -
143I PHE* 3.9 11.7 - + + -
144I ILE* 4.2 8.9 - - + +
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Residues in contact with LEU 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I SER 3.0 17.9 + - - +
22I LEU* 3.6 7.4 - - - +
24I PHE* 1.3 80.8 - - + +
26I SER* 1.3 59.6 + - - +
27I LEU 3.2 1.6 + - - -
28I ASP* 4.2 6.1 + - - +
29I TYR* 4.7 5.2 - - - -
65I LEU* 3.5 31.1 - - + +
68I ARG* 3.4 39.3 - - + -
69I ILE* 4.1 12.1 - - + -
98I ILE* 4.0 37.8 - - + +
102I ARG* 4.2 26.8 - - + +
103I VAL* 5.0 0.2 - - - -
106I TYR* 4.7 11.9 - - + -
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Residues in contact with SER 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I LEU 2.8 14.3 + - - -
23I LYS* 2.7 8.4 + - - -
25I LEU* 1.3 74.2 - - - +
27I LEU* 1.3 53.9 + - - +
28I ASP 3.1 6.3 - - - -
29I TYR* 2.9 13.9 + - - +
30I ILE* 2.8 56.0 + - - +
35I GLN* 2.6 29.7 + - - +
44I LEU* 4.6 6.5 - - - +
48I LEU* 5.6 1.1 - - - -
61I PHE* 5.3 2.5 - - - -
65I LEU* 5.1 9.6 - - - -
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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