Contacts of the helix formed by residues 9 - 21 (chain O) in PDB entry 3J0S
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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7O VAL* 3.5 16.0 - - - +
8O SER* 1.3 78.2 - - - +
10O GLY* 1.3 62.0 + - - +
11O VAL 3.4 2.2 - - - +
12O ILE* 3.5 16.1 + - - +
13O LYS* 3.2 25.7 + - - +
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Residues in contact with GLY 10 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O SER* 3.1 15.9 + - - -
9O ASP* 1.3 78.1 - - - +
11O VAL* 1.3 60.5 + - - +
13O LYS* 3.3 11.2 + - - +
14O VAL* 3.2 23.5 + - - +
48O ILE* 4.5 12.6 - - - -
49O LEU* 4.4 14.7 - - - +
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Residues in contact with VAL 11 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7O VAL* 5.8 2.2 - - + -
8O SER 6.1 0.2 - - - +
9O ASP 3.4 1.2 - - - +
10O GLY* 1.3 75.3 - - - +
12O ILE* 1.3 61.0 + - + +
14O VAL* 3.1 8.6 - - - +
15O PHE* 2.8 33.5 + - + +
38O PHE* 3.5 31.2 - - + -
47O ILE* 3.5 43.3 + - + +
48O ILE* 4.2 2.4 - - - +
84O LEU* 5.7 0.7 - - + -
101O PHE* 6.2 1.1 - - + -
127O LYS* 3.1 35.0 - - + +
128O LEU* 5.3 6.5 - - + -
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Residues in contact with ILE 12 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7O VAL* 4.2 24.0 - - + -
9O ASP* 3.5 17.2 + - - +
10O GLY 3.3 0.4 - - - -
11O VAL* 1.3 79.0 - - + +
13O LYS* 1.3 58.3 + - - +
15O PHE* 3.8 8.3 - - + +
16O ASN* 2.8 34.5 + - + +
127O LYS* 5.2 16.8 - - + +
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Residues in contact with LYS 13 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O ASP* 3.2 18.6 + - - +
10O GLY* 3.4 13.7 - - - +
12O ILE* 1.3 78.9 - - - +
14O VAL* 1.3 62.1 + - - +
16O ASN* 3.6 7.5 + - - +
17O ASP* 3.4 18.5 + - - +
49O LEU* 6.4 1.8 - - + -
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Residues in contact with VAL 14 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O GLY 3.2 9.3 + - - +
11O VAL* 3.1 15.7 - - - +
13O LYS* 1.3 77.5 - - - +
15O PHE* 1.3 64.5 + - - +
17O ASP* 3.2 20.9 + - + +
18O MET* 3.2 8.3 + - - +
33O LYS* 3.7 26.8 - - + -
36O VAL* 4.3 13.7 - - + -
38O PHE* 3.2 28.3 - - + -
49O LEU* 3.9 31.2 - - + -
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Residues in contact with PHE 15 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11O VAL* 2.8 27.6 + - + +
12O ILE* 3.8 7.4 - - + +
14O VAL* 1.3 74.9 - - - +
16O ASN* 1.3 66.4 + - - +
18O MET* 3.2 24.9 + - + +
19O LYS* 3.0 39.5 + - + -
38O PHE* 5.3 0.2 - - - -
84O LEU* 3.5 33.0 - - + -
99O LEU* 4.3 17.5 - - + -
128O LEU* 4.7 23.1 - - + -
131O ILE* 5.1 6.3 - - + -
132O LYS* 5.0 7.4 - - - -
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Residues in contact with ASN 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O ILE* 2.8 23.2 + - + +
13O LYS* 3.7 7.8 + - - +
15O PHE* 1.3 80.3 - - + +
17O ASP* 1.3 64.4 + - - +
19O LYS* 3.3 19.8 + - - +
20O VAL* 3.3 28.8 + - - +
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Residues in contact with ASP 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13O LYS 3.4 10.9 + - - +
14O VAL* 3.2 14.9 + - - +
15O PHE 3.2 0.2 - - - -
16O ASN* 1.3 82.8 - - - +
18O MET* 1.3 56.9 + - - +
20O VAL* 4.0 0.8 - - - +
21O ARG* 3.0 29.5 + - - +
22O LYS* 3.2 38.0 + - + +
33O LYS* 3.2 23.7 + - - +
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Residues in contact with MET 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O VAL 3.2 7.6 + - - +
15O PHE* 3.2 33.1 + - + +
17O ASP* 1.3 79.9 + - - +
19O LYS* 1.3 63.1 + - - +
21O ARG* 3.3 16.1 + - - +
32O ARG* 5.5 7.5 - - + -
33O LYS* 4.0 22.8 - - - +
34O LYS 5.5 0.4 - - - +
36O VAL* 5.4 6.5 - - + -
84O LEU* 4.0 27.8 - - + +
85O TYR 5.6 0.4 - - - -
86O ASP* 3.3 33.4 - - - +
99O LEU* 3.6 32.1 - - + -
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Residues in contact with LYS 19 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O PHE* 3.0 35.2 + - + +
16O ASN* 3.3 18.6 + - - +
18O MET* 1.3 78.9 - - - +
20O VAL* 1.3 65.5 + - + +
21O ARG* 5.2 1.6 - - - +
99O LEU* 5.1 11.9 - - + -
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Residues in contact with VAL 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O ASN* 3.3 30.5 + - - +
17O ASP* 4.6 0.9 - - - +
19O LYS* 1.3 84.7 - - + +
21O ARG* 1.3 72.8 + - - +
22O LYS* 3.1 15.1 + - + +
23O SER 4.7 1.0 + - - +
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Residues in contact with ARG 21 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O ASP* 3.0 14.9 + - - +
18O MET* 3.3 10.9 + - - +
19O LYS 5.2 1.8 - - - +
20O VAL* 1.3 83.3 + - - +
22O LYS* 1.3 69.2 + - - +
23O SER* 3.1 42.3 + - - +
24O SER* 5.9 0.2 - - - +
29O VAL* 5.1 7.5 - - - +
32O ARG* 4.0 44.0 - - - +
33O LYS* 5.5 0.3 + - - -
97O GLU* 6.1 0.9 - - - -
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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