Contacts of the helix formed by residues 12 - 25 (chain S) in PDB entry 1IBL
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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1317A C 5.2 2.9 - - - +
10S PHE* 3.0 32.6 - - - -
11S VAL* 1.3 73.0 - - - +
13S ASP* 1.3 66.8 + - - +
14S HIS* 2.6 35.3 + - + +
15S LEU* 3.0 23.3 - - + +
16S LEU* 3.5 2.3 + - - +
35S SER* 3.2 26.9 + - - +
37S ARG* 4.6 3.3 - - - +
38S SER* 3.5 10.8 - - - -
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Residues in contact with ASP 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S VAL 3.9 7.6 - - - +
12S ASP* 1.3 71.2 - - - +
14S HIS* 1.3 78.0 + - + +
16S LEU* 2.7 21.7 + - - +
17S GLU* 2.9 31.8 + - - +
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Residues in contact with HIS 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014A A 3.8 54.2 + - - +
1015A A 4.3 8.4 + - - -
12S ASP* 2.6 40.5 + - + -
13S ASP* 1.3 82.1 + - + +
15S LEU* 1.3 63.3 + - + +
17S GLU* 3.3 8.0 + - - +
18S LYS* 2.9 35.0 + - - +
33S THR* 4.4 9.4 - - + -
35S SER* 3.9 17.0 - - - -
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Residues in contact with LEU 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S VAL* 3.7 19.3 - - + -
12S ASP* 3.0 21.1 - - + +
13S ASP 3.3 0.2 + - - -
14S HIS* 1.3 81.0 - - + +
16S LEU* 1.3 71.4 + - - +
18S LYS* 3.7 13.0 - - - +
19S VAL* 2.3 44.5 + - + +
31S ILE* 5.1 7.6 - - + -
33S THR* 3.9 28.7 - - + +
38S SER* 3.5 23.8 - - - +
44S MET* 4.4 14.1 - - + -
49S ILE* 4.6 11.9 - - + -
71S LEU* 3.8 18.8 - - + -
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Residues in contact with LEU 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S VAL* 4.0 33.2 - - + +
12S ASP 3.6 9.0 - - - +
13S ASP* 2.7 21.3 + - - +
15S LEU* 1.3 78.9 - - - +
17S GLU* 1.3 56.9 + - + +
18S LYS 2.7 13.9 + - - -
19S VAL* 2.8 26.9 + - + +
20S LEU* 2.9 20.4 + - + +
41S VAL* 4.9 12.3 - - + -
43S GLU* 5.1 7.4 - - + -
44S MET* 5.4 0.2 - - + -
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Residues in contact with GLU 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13S ASP* 2.9 35.1 + - - +
14S HIS* 3.7 7.0 + - - +
16S LEU* 1.3 78.5 - - + +
18S LYS* 1.3 55.4 + - + +
20S LEU* 3.4 22.2 - - + +
21S GLU* 2.9 29.0 - - - +
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Residues in contact with LYS 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014A A 3.1 35.7 + - - -
14S HIS* 2.9 35.1 + - - +
15S LEU* 3.5 6.2 - - - +
16S LEU 2.7 2.4 + - - -
17S GLU* 1.3 80.0 - - + +
19S VAL* 1.3 59.4 + - - +
21S GLU* 3.7 12.6 - - - +
22S LEU* 2.8 32.5 + - + +
28S LYS* 5.8 4.5 - - - +
31S ILE* 4.1 24.9 - - + +
32S LYS 5.1 4.0 + - - -
33S THR* 4.9 8.7 + - - +
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Residues in contact with VAL 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S LEU* 2.3 32.4 + - + +
16S LEU* 2.8 37.8 + - + +
18S LYS* 1.3 68.9 - - - +
20S LEU* 1.3 71.8 + - + +
21S GLU 2.9 1.3 - - - -
22S LEU* 2.7 32.8 + - + +
23S ASN* 3.3 4.9 + - - -
31S ILE* 6.3 1.8 - - + -
43S GLU* 3.4 32.8 - - + +
44S MET* 4.3 20.0 - - + -
47S HIS* 3.5 19.5 - - + +
49S ILE* 5.9 3.4 - - + -
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Residues in contact with LEU 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S LEU* 2.9 23.5 + - + +
17S GLU* 3.4 33.4 - - + +
19S VAL* 1.3 85.0 - - + +
21S GLU* 1.3 91.0 + - + +
23S ASN* 3.2 29.5 + - - +
24S ALA* 3.4 4.5 + - - +
43S GLU* 5.3 4.9 - - + -
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Residues in contact with GLU 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S GLU 2.9 29.1 - - - +
18S LYS* 3.7 17.2 - - - +
19S VAL 2.8 1.4 + - - -
20S LEU* 1.3 90.3 - - + +
22S LEU* 1.3 54.6 + - + +
23S ASN 2.6 1.0 + - - -
24S ALA* 2.4 41.1 + - - +
25S LYS* 3.3 24.6 + - - +
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Residues in contact with LEU 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S LYS* 2.8 27.1 - - + +
19S VAL* 2.7 26.5 + - + +
21S GLU* 1.3 71.7 - - + +
23S ASN* 1.3 58.5 + - - +
25S LYS* 3.4 22.1 + - + +
26S GLY 3.1 5.1 + - - -
27S GLU* 3.1 24.6 + - - -
28S LYS* 3.3 44.4 - - + +
31S ILE* 3.6 32.8 - - + -
47S HIS* 3.9 19.3 - - + +
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Residues in contact with ASN 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19S VAL 3.6 4.2 + - - -
20S LEU* 3.2 30.1 - - - +
21S GLU 2.6 4.4 + - - -
22S LEU* 1.3 71.6 - - - +
24S ALA* 1.3 56.9 + - - +
26S GLY* 2.5 34.3 + - - +
27S GLU* 2.9 21.1 - - - +
43S GLU* 3.7 27.3 + - - +
47S HIS* 3.3 10.0 + - - -
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Residues in contact with ALA 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20S LEU 3.4 3.9 + - - +
21S GLU* 2.4 31.5 + - - +
23S ASN* 1.3 71.4 - - - +
25S LYS* 1.3 59.2 + - + +
26S GLY 3.0 4.2 + - - -
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Residues in contact with LYS 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21S GLU* 3.3 34.3 + - - +
22S LEU* 3.6 21.2 - - - +
23S ASN 3.2 1.0 - - - -
24S ALA* 1.3 76.4 - - + +
26S GLY* 1.3 58.2 + - - +
27S GLU 3.3 12.3 + - - +
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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