Contacts of the helix formed by residues 11 - 29 (chain A) in PDB entry 1PA8
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 GLY 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A MET 4.3 0.2 + - - -
10A TYR* 1.3 76.3 - - - +
12A VAL* 1.3 67.5 + - - -
13A GLY 3.0 3.8 + - - -
14A VAL* 3.0 27.9 + - - +
15A ASP* 4.8 0.9 - - - +
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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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11A GLY* 1.3 71.2 - - - -
13A GLY* 1.3 59.2 + - - +
15A ASP* 2.7 45.3 + - + +
16A MET* 3.3 13.8 + - + -
100A PRO 5.8 2.0 - - - +
105A THR* 4.1 33.0 - - + +
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Residues in contact with GLY 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY* 3.0 2.8 - - - -
12A VAL* 1.3 87.0 - - - +
14A VAL* 1.3 62.3 + - - +
16A MET* 3.0 6.5 + - - -
17A TRP 2.9 19.1 + - - -
100A PRO* 4.8 9.2 + - - -
103A ARG* 3.3 38.7 + - - -
104A ILE 5.5 0.4 - - - -
105A THR* 5.9 0.2 - - - -
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Residues in contact with VAL 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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2A GLU* 3.9 20.4 - - + +
3A LEU* 5.5 10.1 - - + -
9A MET 5.8 0.2 - - - +
10A TYR* 4.3 27.6 - - + -
11A GLY 3.0 31.6 + - - +
13A GLY* 1.3 76.3 - - - +
15A ASP* 1.3 77.9 + - - +
17A TRP* 3.3 15.1 + - - +
18A ALA* 3.4 11.1 + - - +
103A ARG* 4.4 4.3 - - - +
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Residues in contact with ASP 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 GLY 4.8 0.4 - - - +
12A VAL* 2.7 32.1 + - + +
14A VAL* 1.3 88.3 - - - +
16A MET* 1.3 62.6 + - + +
18A ALA* 3.2 16.4 + - - +
19A VAL* 3.3 18.8 + - + +
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Residues in contact with MET 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* 3.3 17.4 + - + +
13A GLY* 3.0 9.4 + - - +
15A ASP* 1.3 78.3 - - + +
17A TRP* 1.3 65.2 + - - +
19A VAL* 3.2 13.5 + - + +
20A GLY* 2.9 19.2 + - - -
95A LEU* 3.0 48.6 - - + +
103A ARG* 4.5 5.6 - - - -
104A ILE* 2.9 39.9 - - + +
105A THR* 3.5 20.0 - - - +
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Residues in contact with TRP 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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1A PRO* 3.5 42.0 - - + +
2A GLU* 5.6 0.4 - - - +
13A GLY 2.9 12.6 + - - +
14A VAL* 3.4 11.7 - - - +
15A ASP 3.2 0.2 - - - -
16A MET* 1.3 75.5 - - - +
18A ALA* 1.3 65.2 + - - +
20A GLY* 3.1 10.9 + - - -
21A CYS* 3.1 29.6 + - - -
45A ILE* 3.7 37.0 - - + +
49A LEU* 4.4 2.5 - - + -
95A LEU 4.0 11.6 + - - -
96A PHE* 3.2 60.2 - + - -
98A PHE* 5.2 1.3 - + - -
103A ARG* 3.9 20.0 - - - +
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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 VAL 3.4 6.7 + - - +
15A ASP* 3.2 11.9 + - - +
17A TRP* 1.3 84.9 - - + +
19A VAL* 1.3 64.8 + - + +
21A CYS* 3.2 7.9 + - - +
22A ILE* 3.0 29.8 + - + +
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Residues in contact with VAL 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 ASP* 3.3 17.7 - - + +
16A MET* 3.2 18.8 + - + +
18A ALA* 1.3 74.8 - - + +
20A GLY* 1.3 66.1 + - - +
22A ILE* 2.9 37.0 - - + +
23A LEU* 2.9 10.3 + - + +
95A LEU* 4.4 10.8 - - + -
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Residues in contact with GLY 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 MET 2.9 11.5 + - - -
17A TRP 3.1 3.7 + - - -
19A VAL* 1.3 76.1 - - - +
21A CYS* 1.3 61.4 + - - +
23A LEU* 3.2 8.1 + - - +
24A ALA* 3.1 18.9 + - - +
92A ILE* 4.6 4.6 - - - +
95A LEU* 3.7 29.6 - - - +
96A PHE* 3.6 16.2 - - - -
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Residues in contact with CYS 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 TRP* 3.1 45.7 + - - -
18A ALA* 3.4 9.0 - - - +
19A VAL 3.1 0.2 - - - -
20A GLY* 1.3 77.9 - - - +
22A ILE* 1.3 64.1 + - + +
24A ALA* 3.3 4.7 + - - +
25A GLU* 3.0 21.0 + - - +
32A PHE* 4.3 19.5 + - + +
33A LEU* 5.9 0.9 - - - -
45A ILE* 6.1 0.7 - - - -
96A PHE* 3.6 20.6 - - - -
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Residues in contact with ILE 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* 3.0 14.9 + - + +
19A VAL* 2.9 34.7 + - + +
21A CYS* 1.3 77.3 - - + +
23A LEU* 1.3 86.6 + - + +
25A GLU* 3.0 13.1 + - - +
26A LEU* 3.0 24.7 + - + +
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Residues in contact with LEU 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 VAL* 2.9 12.4 + - + +
20A GLY* 3.2 13.0 + - - +
22A ILE* 1.3 88.8 - - + +
24A ALA* 1.3 61.5 + - - +
26A LEU* 3.2 10.0 + - + +
27A LEU* 2.7 68.2 + - + +
88A LEU* 5.5 8.5 - - + +
91A LEU* 6.5 0.4 - - + -
92A ILE* 5.0 17.5 - - + -
95A LEU* 6.1 1.3 - - + -
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Residues in contact with ALA 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 GLY 3.1 12.4 + - - +
21A CYS 3.6 7.4 - - - +
23A LEU* 1.3 82.7 - - - +
25A GLU* 1.3 53.4 + - - +
27A LEU* 3.1 3.5 + - - -
28A LEU* 2.7 55.1 + - + +
30A VAL 4.7 0.2 - - - -
32A PHE* 4.0 27.8 - - + -
80A ILE* 4.6 3.8 - - + -
81A PHE* 5.6 1.1 - - + -
92A ILE* 5.1 8.7 - - + -
96A PHE* 5.1 0.9 - - + -
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Residues in contact with GLU 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 CYS 3.0 13.7 + - - +
22A ILE* 3.0 16.4 + - - +
24A ALA* 1.3 77.9 - - - +
26A LEU* 1.3 55.3 + - - +
29A ARG* 2.6 33.7 + - - -
30A VAL* 3.3 28.7 - - - +
31A PRO* 4.1 22.9 - - + +
32A PHE 5.0 0.9 - - - +
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Residues in contact with LEU 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 ILE* 3.0 13.2 + - + +
23A LEU* 3.6 15.0 - - + +
25A GLU* 1.3 79.4 - - - +
27A LEU* 1.3 73.5 + - + +
29A ARG* 3.8 11.4 + - - +
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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 LEU* 2.7 54.3 - - + +
24A ALA* 3.1 6.9 + - - +
26A LEU* 1.3 93.6 - - + +
28A LEU* 1.3 59.1 + - - +
29A ARG* 4.3 4.3 - - - +
81A PHE* 2.9 60.8 - - + -
84A ALA* 4.0 10.3 - - + -
88A LEU* 5.0 7.9 - - + +
92A ILE* 6.4 0.2 - - + -
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Residues in contact with LEU 28 (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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24A ALA* 2.7 44.0 + - + +
27A LEU* 1.3 74.5 - - - +
29A ARG* 1.3 71.6 + - - +
30A VAL* 3.3 38.1 + - + +
31A PRO 5.4 1.3 - - - +
32A PHE* 5.1 6.1 - - + -
80A ILE* 3.2 29.2 - - + +
81A PHE* 2.9 46.9 - - + -
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Residues in contact with ARG 29 (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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25A GLU* 2.6 23.5 + - - -
26A LEU 4.2 10.3 - - - +
27A LEU 3.5 4.0 - - - +
28A LEU* 1.3 77.7 + - - +
30A VAL* 1.4 62.3 + - + +
31A PRO* 4.6 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