Contacts of the helix formed by residues 15 - 27 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLN 3.8 1.2 + - - -
14A LEU* 1.3 75.9 - - - +
16A SER* 1.3 80.9 + - - +
17A GLU* 2.8 22.8 + - + +
18A ASP* 3.0 24.1 + - - +
19A LEU* 2.9 27.5 + - - +
71A ARG* 5.1 1.3 - - - +
133G LEU 4.9 8.1 - - - +
134G ASP* 5.8 2.8 - - - +
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Residues in contact with SER 16 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LEU 4.2 0.2 + - - -
15A ASP* 1.3 85.8 + - - +
17A GLU* 1.3 55.1 + - - +
19A LEU* 3.5 12.0 + - - +
20A ALA* 3.0 26.9 + - - +
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Residues in contact with GLU 17 (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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15A ASP* 2.8 16.5 + - + +
16A SER* 1.3 76.9 + - - +
18A ASP* 1.3 62.1 + - - +
20A ALA* 3.3 9.7 + - - +
21A SER* 2.9 41.1 + - - +
110A GLU* 5.8 1.3 - - - +
138A ASN* 3.6 10.9 + - - -
33H ARG* 2.7 43.8 + - - +
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Residues in contact with ASP 18 (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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14A LEU* 4.2 14.4 - - + -
15A ASP* 3.0 26.5 + - - +
17A GLU* 1.3 80.4 - - - +
19A LEU* 1.3 56.8 + - - +
21A SER* 3.2 8.7 + - - -
22A LEU* 2.8 34.3 + - - +
69A ILE* 4.3 13.6 - - + +
71A ARG* 2.7 48.6 + - - +
106A TYR* 5.7 0.5 + - - -
34H LYS* 5.8 2.3 + - - -
50H GLU* 5.1 1.0 - - - +
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Residues in contact with LEU 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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14A LEU* 5.5 2.7 - - + +
15A ASP 2.9 12.8 + - - +
16A SER* 3.6 13.2 - - - +
17A GLU 3.3 0.2 - - - -
18A ASP* 1.3 75.7 - - - +
20A ALA* 1.3 57.0 + - - +
22A LEU* 3.1 11.0 + - + +
23A LYS* 2.8 48.6 + - + +
38A ILE* 3.9 23.3 - - + +
39A LYS* 3.5 35.7 - - - +
40A ASP* 3.7 15.0 - - - +
41A ALA* 4.4 3.4 - - + +
44A LEU* 4.2 19.7 - - + -
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Residues in contact with ALA 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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16A SER 3.0 14.9 + - - +
17A GLU* 3.3 17.5 + - - +
19A LEU* 1.3 75.5 - - - +
21A SER* 1.3 62.8 + - - +
23A LYS* 3.3 15.4 + - - +
24A PHE* 3.1 20.4 + - - +
138A ASN* 5.6 6.5 - - + +
140A LEU* 5.1 2.2 - - - +
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Residues in contact with SER 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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17A GLU* 2.9 25.5 + - - +
18A ASP* 3.4 11.4 - - - -
20A ALA* 1.3 77.2 - - - +
22A LEU* 1.3 61.8 + - - +
24A PHE* 3.3 4.9 + - - +
25A LEU* 3.1 27.2 + - - +
69A ILE* 4.3 8.7 - - - -
106A TYR* 3.5 32.2 + - - -
110A GLU* 4.7 2.3 + - - -
138A ASN* 5.8 0.2 + - - -
140A LEU* 4.4 14.2 - - - +
33H ARG* 5.6 0.2 + - - -
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Residues in contact with LEU 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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14A LEU* 4.3 23.8 - - + -
18A ASP 2.8 26.7 + - - +
19A LEU* 3.4 11.4 - - + +
21A SER* 1.3 69.7 - - - +
23A LYS* 1.3 59.8 + - - +
25A LEU* 3.2 5.7 + - - +
26A SER* 2.8 32.4 + - - -
41A ALA* 6.0 0.2 - - + -
44A LEU* 4.0 29.4 - - + -
45A PHE* 6.1 0.7 - - + -
62A LEU* 5.8 5.2 - - + -
65A LEU* 3.7 42.3 - - + +
66A LEU* 5.7 2.9 - - + -
69A ILE* 3.9 28.0 - - + -
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Residues in contact with LYS 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 LEU* 2.8 36.3 + - + +
20A ALA* 3.4 15.5 - - + +
21A SER 3.3 0.2 - - - -
22A LEU* 1.3 71.1 - - - +
24A PHE* 1.3 62.9 + - - +
26A SER* 2.6 25.7 + - - +
27A LEU* 3.3 3.6 + - - +
35A GLN* 2.9 54.0 + - + +
36A GLU* 3.9 19.8 + - - +
38A ILE* 2.9 44.3 + - + -
44A LEU* 5.3 2.7 - - + +
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Residues in contact with PHE 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 ALA 3.1 8.2 + - - +
21A SER 3.3 7.6 + - - +
23A LYS* 1.3 79.0 - - - +
25A LEU* 1.3 72.8 + - + +
27A LEU* 3.1 42.5 + - + +
35A GLN* 4.9 0.2 - - - +
102A ARG* 3.4 62.0 - - - -
105A LEU* 3.8 19.1 - - + -
106A TYR* 4.4 2.2 - - + -
140A LEU* 3.7 64.6 - - + -
143A PHE* 4.3 6.3 - - + -
144A ILE* 4.2 10.1 - - + -
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Residues in contact with LEU 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 SER 3.1 14.8 + - - +
22A LEU* 3.2 7.6 + - - +
24A PHE* 1.3 84.8 - - + +
26A SER* 1.3 59.3 + - - +
27A LEU 3.2 1.4 + - - -
28A ASP* 4.0 8.8 + - - +
29A TYR* 5.4 0.2 - - - -
61A PHE* 5.1 0.5 - - - -
65A LEU* 3.9 22.9 - - + -
68A ARG* 4.0 21.3 - - + +
69A ILE* 3.6 31.6 - - + -
98A ILE* 3.8 33.5 - - + +
102A ARG* 3.9 31.8 - - + +
103A VAL* 4.5 4.5 - - - +
106A TYR* 4.6 13.5 - - + -
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Residues in contact with SER 26 (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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22A LEU 2.8 13.9 + - - -
23A LYS* 2.6 25.0 + - - -
25A LEU* 1.3 73.1 - - - +
27A LEU* 1.3 59.9 + - - +
28A ASP 3.1 3.8 - - - -
29A TYR* 3.0 7.0 + - - +
30A ILE* 2.8 49.7 + - - +
35A GLN* 3.5 7.6 + - - +
44A LEU* 4.6 9.6 - - - +
48A LEU* 5.1 7.2 - - - -
61A PHE* 5.0 12.3 - - - -
65A LEU* 5.7 2.9 - - - -
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Residues in contact with LEU 27 (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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23A LYS 3.3 6.1 + - - +
24A PHE* 3.1 45.2 + - + +
25A LEU 3.2 0.4 - - - -
26A SER* 1.3 77.9 - - - +
28A ASP* 1.3 60.9 + - - +
29A TYR 3.1 1.3 + - - -
30A ILE 3.3 14.3 - - - +
31A PRO* 5.4 0.3 - - - +
32A GLN* 3.9 31.3 - - + +
35A GLN* 3.4 28.9 - - - +
102A ARG* 4.2 24.3 + - - +
144A ILE* 3.8 22.2 - - + -
147A GLU* 5.2 1.3 - - - +
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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