Contacts of the helix formed by residues 13 - 24 (chain B) in PDB entry 1O69
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 ASN 13 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B GLY* 1.3 80.4 - - - +
14B GLU* 1.3 54.6 + - - +
15B LEU 3.4 1.3 - - - -
16B LYS* 3.1 26.7 + - + +
17B TYR* 2.8 65.5 + - + -
240B ALA* 3.9 7.1 - - + +
243B GLU* 2.8 24.9 + - - +
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 4.1 25.8 - - + -
12B GLY* 3.3 25.8 + - - +
13B ASN* 1.3 74.9 + - - +
15B LEU* 1.3 59.0 + - + +
17B TYR* 3.3 3.6 + - - +
18B ILE* 2.8 35.1 + - - +
236B ALA* 4.9 2.4 - - - +
237B ILE* 4.1 24.7 - - + +
240B ALA* 3.6 22.7 - - + +
241B GLN* 4.3 14.0 + - - +
248B ARG* 4.4 11.1 + - - -
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.8 9.1 - - + +
18A ILE* 3.9 25.4 - - + -
19A GLU* 3.4 41.3 - - + +
22A PHE* 3.7 22.7 - - + -
23A LYS* 6.4 1.6 - - + -
12B GLY 4.6 3.2 + - - +
13B ASN 3.4 0.2 - - - -
14B GLU* 1.3 78.7 - - + +
16B LYS* 1.3 67.5 + - - +
18B ILE* 3.7 3.4 - - + +
19B GLU* 2.8 26.6 + - - +
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY 5.2 0.8 + - - +
13B ASN* 3.1 31.0 + - - +
15B LEU* 1.3 81.1 - - - +
17B TYR* 1.3 79.9 + - + +
19B GLU* 3.3 9.7 + - - +
20B GLU* 3.1 48.0 + - + +
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Residues in contact with TYR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ASN* 2.8 43.6 + - + +
14B GLU 3.8 1.8 - - - +
16B LYS* 1.3 104.3 + - + +
18B ILE* 1.3 63.3 + - - +
20B GLU* 3.3 14.5 + - - +
21B VAL* 3.0 24.8 + - - +
33B PHE* 3.6 24.8 - + + -
36B ARG* 3.6 20.1 + - - -
236B ALA* 3.6 29.4 - - + +
239B VAL* 3.6 15.5 - - + -
240B ALA* 4.1 4.9 - - + -
243B GLU* 2.5 32.5 + - - -
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 3.9 6.5 - - + -
18A ILE* 3.7 32.1 - - + -
22A PHE* 3.8 23.1 - - + -
233A VAL* 4.8 0.4 - - + -
14B GLU 2.8 21.1 + - - +
15B LEU* 3.2 5.6 + - + +
17B TYR* 1.3 72.8 - - - +
19B GLU* 1.3 66.6 + - - +
21B VAL* 3.1 8.5 + - - +
22B PHE* 3.0 37.8 + - + -
233B VAL* 4.1 26.2 - - + +
236B ALA* 4.1 5.8 - - + -
237B ILE* 3.7 27.4 - - + -
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.1 31.9 - - + +
15B LEU 2.8 17.9 + - - +
16B LYS* 3.5 8.8 - - - +
18B ILE* 1.3 76.0 - - - +
20B GLU* 1.3 59.9 + - + +
22B PHE* 3.1 4.9 + - - +
23B LYS* 2.9 29.1 + - + +
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LYS* 3.1 42.9 + - + +
17B TYR* 3.6 15.8 - - - +
18B ILE 3.3 0.2 - - - -
19B GLU* 1.3 76.9 - - + +
21B VAL* 1.3 56.8 + - - +
23B LYS* 3.2 8.2 + - - +
24B SER* 2.8 31.4 + - - +
32B GLU* 4.8 3.1 - - - +
33B PHE* 3.4 24.3 - - + -
36B ARG* 4.5 5.5 + - - -
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Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A SER* 5.3 0.9 - - - +
17B TYR 3.0 13.5 + - - +
18B ILE* 3.1 9.8 + - - +
20B GLU* 1.3 73.7 - - - +
22B PHE* 1.3 73.3 + - + +
24B SER* 2.9 23.8 + - - +
33B PHE* 3.4 29.8 - - + -
232B ASN* 3.7 35.6 + - + +
233B VAL* 3.9 20.0 - - + +
236B ALA* 4.0 6.5 - - + -
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Residues in contact with PHE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 3.7 25.1 - - + -
15A LEU* 3.3 42.8 - - + -
18A ILE* 3.5 25.6 - - + -
189A SER* 6.0 0.2 - - - -
237A ILE* 3.9 15.9 - - + -
18B ILE* 3.0 15.0 + - + -
19B GLU* 3.1 9.2 + - - +
21B VAL* 1.3 76.9 - - + +
23B LYS* 1.3 59.8 + - - +
24B SER* 3.1 6.7 - - - -
233B VAL* 3.6 23.8 - - + -
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU* 2.9 19.0 + - + +
20B GLU* 3.2 8.0 + - - +
22B PHE* 1.3 75.0 - - - +
24B SER* 1.3 67.9 + - - +
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Residues in contact with SER 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLU 2.8 13.4 + - - +
21B VAL* 2.9 18.3 + - - -
22B PHE 3.1 2.0 - - - -
23B LYS* 1.3 84.8 - - - +
32B GLU* 4.6 12.0 - - - +
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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