Contacts of the helix formed by residues 9 - 27 (chain A) in PDB entry 1O4X
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 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A PRO 3.4 2.8 + - - +
8A SER* 1.3 75.9 + - - +
10A LEU* 1.3 62.9 + - - +
11A GLU* 3.0 23.7 + - - +
12A GLU* 2.6 46.0 + - - +
13A LEU* 2.9 18.5 + - - +
61A PHE* 4.1 7.4 - - - -
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Residues in contact with LEU 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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9A ASP* 1.3 75.3 - - - +
11A GLU* 1.3 68.2 + - + +
13A LEU* 3.3 7.1 + - + +
14A GLU* 3.0 51.5 + - + +
57A LEU* 5.0 6.5 - - + -
61A PHE* 4.1 20.6 - - + -
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Residues in contact with GLU 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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9A ASP* 3.0 17.1 + - - +
10A LEU* 1.3 79.4 - - + +
12A GLU* 1.3 63.7 + - + +
14A GLU* 3.4 17.3 + - - +
15A GLN* 3.1 20.4 + - - +
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Residues in contact with GLU 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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6A GLU 5.5 0.2 - - - +
7A PRO 4.1 2.6 - - - +
8A SER* 2.8 26.4 - - - +
9A ASP* 2.6 55.0 + - - +
11A GLU* 1.3 72.9 - - + +
13A LEU* 1.3 57.8 + - - +
15A GLN* 3.1 8.3 + - - +
16A PHE* 2.9 28.4 + - - +
68A LYS* 5.1 0.9 - - - -
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Residues in contact with LEU 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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8A SER* 3.1 16.4 + - - +
9A ASP 2.9 13.4 + - - +
10A LEU* 3.3 6.5 + - - +
12A GLU* 1.3 73.1 - - - +
14A GLU* 1.3 61.3 + - - +
16A PHE* 3.3 3.4 + - + +
17A ALA* 2.9 31.0 + - - +
54A PHE* 5.4 0.7 - - + -
57A LEU* 4.5 9.5 - - + +
61A PHE* 4.0 26.0 - - + -
64A MET* 3.3 48.7 - - + +
65A ALA* 4.1 4.0 - - - +
68A LYS* 2.9 41.7 - - + -
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Residues in contact with GLU 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 LEU* 3.0 40.2 + - + +
11A GLU* 3.5 17.2 - - - +
12A GLU 3.2 0.2 - - - -
13A LEU* 1.3 76.4 - - - +
15A GLN* 1.3 57.0 + - - +
17A ALA* 3.6 2.3 - - - +
18A LYS* 3.0 36.6 + - + +
57A LEU* 3.5 32.5 - - + +
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Residues in contact with GLN 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 GLU 3.1 12.2 + - - +
12A GLU* 3.1 12.4 + - - +
14A GLU* 1.3 76.0 - - - +
16A PHE* 1.3 60.7 + - - +
18A LYS* 3.2 15.8 + - - +
19A THR* 2.9 42.8 + - - +
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Residues in contact with PHE 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 GLU 2.9 15.2 + - - +
13A LEU 3.3 4.5 + - - +
15A GLN* 1.3 76.8 - - - +
17A ALA* 1.3 55.1 + - - +
19A THR* 3.2 7.6 + - + -
20A PHE* 2.7 54.3 + + + +
54A PHE* 3.7 35.2 - + - -
68A LYS* 3.7 48.2 - - + -
71A LEU* 4.2 4.9 - - + -
72A GLU* 3.9 39.3 - - + -
75A LEU* 4.1 17.0 - - + -
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Residues in contact with ALA 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 LEU 2.9 16.4 + - - +
14A GLU 3.6 5.4 - - - +
15A GLN 3.2 0.2 - - - -
16A PHE* 1.3 82.6 - - - +
18A LYS* 1.3 63.1 + - + +
20A PHE* 3.8 2.4 - - - +
21A LYS* 3.1 25.6 + - - +
54A PHE* 4.2 21.1 - - + +
55A GLU* 4.1 16.6 - - - +
57A LEU* 3.7 24.5 - - + -
64A MET* 5.0 0.9 - - + -
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Residues in contact with LYS 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 GLU* 3.0 22.8 + - - +
15A GLN* 3.3 22.2 - - - +
17A ALA* 1.3 79.9 - - + +
19A THR* 1.3 63.1 + - - +
21A LYS* 3.3 4.0 + - - +
22A GLN* 3.0 31.5 + - + +
57A LEU* 6.4 1.6 - - - -
273B PRO 4.5 14.1 + - - -
274B ASP* 4.6 10.7 + - - +
276B LYS* 4.7 17.3 - - - +
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Residues in contact with THR 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 GLN* 2.9 34.2 + - - +
16A PHE* 3.5 8.7 - - + -
18A LYS* 1.3 74.6 - - - +
20A PHE* 1.3 65.6 + - - +
22A GLN* 3.2 9.1 + - - +
23A ARG* 3.0 24.8 + - + +
75A LEU* 4.2 18.8 - - + -
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Residues in contact with PHE 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 PHE* 2.7 36.4 + + + +
17A ALA* 3.8 5.8 - - - +
19A THR* 1.3 74.9 - - - +
21A LYS* 1.3 59.6 + - - +
23A ARG* 3.7 1.7 - - - +
24A ARG* 2.9 35.9 + - + +
34A VAL* 3.7 27.4 - - + -
51A ILE* 4.5 7.4 - - + -
54A PHE* 4.9 5.4 - + + -
55A GLU* 3.5 29.4 - - + -
71A LEU* 3.9 42.8 - - + -
74A TRP* 3.4 27.4 - + - -
75A LEU* 4.2 15.3 - - + +
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Residues in contact with LYS 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 ALA 3.1 16.4 + - - +
18A LYS* 3.7 4.7 - - - +
20A PHE* 1.3 80.1 - - - +
22A GLN* 1.3 64.6 + - + +
24A ARG* 3.5 8.1 + - - +
25A ILE* 3.1 46.0 + - + +
55A GLU* 3.6 47.5 + - + +
269B MET* 4.7 9.8 - - + +
275B TYR 5.4 5.3 + - - -
276B LYS* 6.3 1.2 - - - +
310C C 5.9 0.7 - - - -
311C A 5.9 0.8 + - - -
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Residues in contact with GLN 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 LYS* 3.0 19.7 + - + +
19A THR* 3.2 10.5 + - - +
21A LYS* 1.3 79.1 - - - +
23A ARG* 1.3 53.2 + - - +
25A ILE* 3.8 3.9 - - - +
26A LYS* 2.8 71.8 + - - +
269B MET* 2.6 43.8 - - - +
273B PRO* 5.8 2.2 + - - +
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Residues in contact with ARG 23 (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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19A THR* 3.0 14.8 + - + +
20A PHE 3.7 0.4 - - - +
22A GLN* 1.3 73.1 - - - +
24A ARG* 1.3 66.2 + - - +
26A LYS* 4.2 20.4 - - - +
27A LEU* 2.7 55.3 + - + +
74A TRP* 5.0 1.1 - - + -
75A LEU* 3.4 24.9 - - + -
78A ALA* 5.4 0.2 - - + -
79A GLU* 2.5 53.0 + - + +
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Residues in contact with ARG 24 (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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20A PHE* 2.9 21.2 + - + +
21A LYS* 3.7 17.8 + - - +
23A ARG* 1.3 78.0 - - - +
25A ILE* 1.3 72.8 + - - +
27A LEU* 3.3 1.8 + - - +
28A GLY 3.1 4.5 + - - -
29A PHE* 3.0 47.5 + - + +
30A THR* 3.8 2.9 - - - -
31A GLN* 2.9 39.7 + - - +
34A VAL* 3.6 30.3 - - + -
51A ILE* 3.8 1.6 - - - +
55A GLU* 3.1 38.2 + - - +
74A TRP* 4.0 15.4 - - + -
265B ARG* 5.1 2.4 - - - +
310C C 3.7 19.2 + - - -
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Residues in contact with ILE 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 LYS* 3.1 34.1 + - + +
22A GLN* 3.8 3.1 - - - +
24A ARG* 1.3 88.1 - - - +
26A LYS* 1.3 70.5 + - + +
28A GLY* 3.0 15.1 + - - +
29A PHE 4.7 5.2 - - - +
262B LYS* 5.0 18.1 - - + +
265B ARG* 5.0 22.4 - - + +
266B ALA* 4.6 26.6 - - + +
269B MET* 3.2 34.3 - - + -
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Residues in contact with LYS 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 GLN* 2.8 62.2 + - - +
23A ARG* 3.3 24.9 + - - +
25A ILE* 1.3 78.4 - - + +
27A LEU* 1.3 67.5 + - + +
28A GLY* 3.4 0.7 + - - -
266B ALA* 6.3 4.0 - - + -
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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 ARG* 2.7 62.2 + - + +
24A ARG* 3.8 0.9 - - - +
26A LYS* 1.3 82.3 - - + +
28A GLY* 1.3 61.5 + - - +
29A PHE* 3.5 32.6 + - + -
74A TRP* 4.8 1.6 - - + -
78A ALA* 3.3 44.6 - - + +
79A GLU* 3.8 5.4 - - - -
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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