Contacts of the helix formed by residues 7 - 25 (chain A) in PDB entry 1PI8
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 ALA 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ILE* 1.3 68.8 + - - +
9A VAL* 3.1 9.4 - - + +
10A ALA* 2.9 28.9 + - + +
11A LEU* 3.0 20.3 + - - +
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Residues in contact with ILE 8 (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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7A ALA* 1.3 75.1 - - - +
9A VAL* 1.3 66.9 + - + +
11A LEU* 3.4 13.3 + - + +
12A VAL* 3.1 37.8 + - + +
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Residues in contact with VAL 9 (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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7A ALA* 3.1 6.6 - - + +
8A ILE* 1.3 78.4 - - + +
10A ALA* 1.3 59.0 + - - +
12A VAL* 3.2 8.6 + - + +
13A VAL* 2.9 46.7 + - + +
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Residues in contact with ALA 10 (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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7A ALA* 2.9 26.0 + - + +
9A VAL* 1.3 80.8 - - - +
11A LEU* 1.3 58.5 + - + +
13A VAL* 3.3 7.8 + - - +
14A ALA* 2.9 31.1 + - - +
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Residues in contact with LEU 11 (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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7A ALA 3.0 18.3 + - - +
8A ILE* 3.6 15.0 - - + +
10A ALA* 1.3 78.8 - - + +
12A VAL* 1.3 52.5 + - + +
14A ALA* 4.7 2.7 - - + -
15A ILE* 2.4 68.7 + - + +
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Residues in contact with VAL 12 (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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8A ILE* 3.1 27.0 + - + +
9A VAL* 3.4 10.1 - - - +
11A LEU* 1.3 80.6 - - + +
13A VAL* 1.3 54.6 + - + +
15A ILE* 4.2 5.8 - - + -
16A ILE* 2.6 78.6 + - + +
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Residues in contact with VAL 13 (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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9A VAL* 2.9 32.5 + - + +
10A ALA* 3.5 9.6 - - - +
12A VAL* 1.3 80.3 - - + +
14A ALA* 1.3 53.7 + - + +
16A ILE* 3.9 2.5 - - - +
17A ILE* 2.4 61.9 + - + +
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Residues in contact with ALA 14 (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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10A ALA 2.9 16.8 + - - +
11A LEU* 3.9 3.1 - - + +
13A VAL* 1.3 74.2 - - + +
15A ILE* 1.3 59.6 + - + +
17A ILE* 2.9 9.9 + - - +
18A ALA* 2.6 39.3 + - - +
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Residues in contact with ILE 15 (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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11A LEU* 2.4 75.8 + - + +
12A VAL* 4.0 5.4 - - + +
14A ALA* 1.3 69.7 - - + +
16A ILE* 1.3 57.4 + - + +
18A ALA* 4.0 3.5 - - - +
19A ILE* 2.8 60.9 + - + +
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Residues in contact with ILE 16 (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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12A VAL* 2.6 59.7 + - + +
13A VAL* 3.9 4.3 - - - +
15A ILE* 1.3 75.3 - - + +
17A ILE* 1.3 60.3 + - + +
19A ILE* 4.5 5.2 - - + -
20A VAL* 2.6 52.0 + - + +
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Residues in contact with ILE 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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13A VAL* 2.4 55.5 + - + +
14A ALA* 3.3 8.3 - - - +
16A ILE* 1.3 77.9 - - + +
18A ALA* 1.3 59.4 + - - +
20A VAL* 3.8 2.8 - - - +
21A VAL* 2.6 50.9 + - + +
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Residues in contact with ALA 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 ALA 2.6 20.4 + - - +
15A ILE* 4.0 4.5 - - - +
17A ILE* 1.3 73.0 - - - +
19A ILE* 1.3 59.0 + - + +
21A VAL* 3.0 4.4 + - - -
22A TRP* 2.5 41.9 + - + +
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Residues in contact with ILE 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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15A ILE* 2.8 47.0 + - + +
16A ILE* 4.1 5.4 - - + +
18A ALA* 1.3 79.0 - - + +
20A VAL* 1.3 62.0 + - + +
22A TRP* 3.9 9.9 - - + +
23A SER* 2.9 34.1 + - - -
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Residues in contact with VAL 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 ILE* 2.6 44.0 + - + +
17A ILE* 3.8 4.0 - - - +
19A ILE* 1.3 80.0 - - + +
21A VAL* 1.3 64.6 + - + +
23A SER* 3.3 6.9 - - - -
24A ILE* 3.0 41.9 + - + +
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Residues in contact with VAL 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 ILE* 2.6 43.4 + - + +
18A ALA* 3.5 4.7 - - - +
20A VAL* 1.3 74.9 - - + +
22A TRP* 1.3 68.8 + - - +
23A SER 2.9 1.6 - - - -
24A ILE* 2.8 33.7 + - + +
25A VAL 3.2 10.1 + - - +
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Residues in contact with TRP 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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18A ALA* 2.5 25.3 + - + +
19A ILE* 4.0 9.2 - - + +
21A VAL* 1.3 76.3 - - - +
23A SER* 1.3 70.9 + - - +
25A VAL 3.0 21.9 + - - +
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Residues in contact with SER 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 ILE* 2.9 24.5 + - - -
20A VAL* 3.3 8.5 - - - -
22A TRP* 1.3 88.2 - - - +
24A ILE* 1.3 66.7 + - - +
25A VAL* 3.3 1.2 + - - -
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Residues in contact with ILE 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 VAL* 3.0 28.8 + - + +
21A VAL* 2.8 21.4 + - + +
23A SER* 1.3 79.6 - - - +
25A VAL* 1.3 86.9 - - + +
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Residues in contact with VAL 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 VAL* 3.2 10.9 - - - +
22A TRP* 3.0 24.1 - - - +
23A SER 3.2 2.1 - - - -
24A ILE* 1.3 115.0 - - + +
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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