Contacts of the helix formed by residues 9 - 21 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7M VAL* 3.5 14.7 - - - +
8M SER* 1.3 78.8 - - - +
10M GLY* 1.3 62.2 + - - +
11M VAL 3.4 2.4 - - - +
12M ILE* 3.5 16.1 + - - +
13M LYS* 3.2 24.3 + - - +
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Residues in contact with GLY 10 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M SER* 3.1 15.7 + - - -
9M ASP* 1.3 76.9 - - - +
11M VAL* 1.3 62.0 + - - +
13M LYS* 3.3 11.5 + - - +
14M VAL* 3.2 23.4 + - - +
48M ILE* 4.5 12.3 - - - -
49M LEU* 4.4 15.3 - - - +
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Residues in contact with VAL 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M VAL* 5.8 2.2 - - + -
9M ASP 3.4 1.2 - - - +
10M GLY* 1.3 74.4 - - - +
12M ILE* 1.3 60.3 + - + +
14M VAL* 3.1 9.1 - - - +
15M PHE* 2.8 33.7 + - + +
38M PHE* 3.5 31.4 - - + -
47M ILE* 3.5 42.8 + - + +
48M ILE 4.2 2.0 - - - +
84M LEU* 5.7 1.1 - - + -
101M PHE* 6.2 1.1 - - + -
127M LYS* 3.1 35.4 - - + +
128M LEU* 5.3 5.8 - - + -
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Residues in contact with ILE 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M VAL* 4.2 24.0 - - + -
9M ASP* 3.5 16.9 + - - +
10M GLY 3.3 0.2 - - - -
11M VAL* 1.3 80.5 - - + +
13M LYS* 1.3 58.3 + - - +
15M PHE* 3.8 7.1 - - + +
16M ASN* 2.8 34.1 + - + +
127M LYS* 5.2 17.7 - - + +
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Residues in contact with LYS 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M ASP* 3.2 18.8 + - - +
10M GLY* 3.4 13.2 - - - +
11M VAL 3.2 0.2 - - - -
12M ILE* 1.3 79.9 - - - +
14M VAL* 1.3 61.8 + - - +
16M ASN* 3.7 6.7 + - - +
17M ASP* 3.4 19.2 + - - +
49M LEU* 6.4 2.0 - - + -
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Residues in contact with VAL 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M GLY 3.2 8.8 + - - +
11M VAL* 3.1 15.3 - - - +
13M LYS* 1.3 78.1 - - - +
15M PHE* 1.3 65.0 + - - +
17M ASP* 3.2 21.3 + - + +
18M MET* 3.2 8.5 + - - +
33M LYS* 3.7 26.8 - - + -
36M VAL* 4.3 14.6 - - + -
38M PHE* 3.2 29.6 - - + -
49M LEU* 3.9 30.5 - - + -
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Residues in contact with PHE 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M VAL* 2.8 27.8 + - + +
12M ILE* 3.8 7.6 - - + +
14M VAL* 1.3 75.0 - - - +
16M ASN* 1.3 67.1 + - - +
18M MET* 3.2 26.1 + - + +
19M LYS* 3.0 38.8 + - + +
36M VAL* 6.5 0.2 - - - -
84M LEU* 3.5 32.8 - - + -
99M LEU* 4.3 17.0 - - + -
128M LEU* 4.7 24.2 - - + -
131M ILE* 5.1 6.3 - - + -
132M LYS* 5.0 7.0 - - - -
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Residues in contact with ASN 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M ILE* 2.8 24.6 + - + +
13M LYS* 3.7 8.1 + - - +
15M PHE* 1.3 79.3 - - - +
17M ASP* 1.3 63.9 + - - +
19M LYS* 3.3 20.0 + - - +
20M VAL* 3.3 28.0 + - - +
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Residues in contact with ASP 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M LYS 3.4 10.1 + - - +
14M VAL* 3.2 14.8 + - - +
16M ASN* 1.3 81.4 - - - +
18M MET* 1.3 56.2 + - - +
20M VAL* 3.6 1.0 + - - -
21M ARG* 3.0 30.8 + - - +
22M LYS* 3.2 38.1 + - + +
33M LYS* 3.2 24.0 + - - +
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Residues in contact with MET 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M VAL 3.2 7.4 + - - +
15M PHE* 3.2 33.3 + - + +
17M ASP* 1.3 79.7 + - - +
19M LYS* 1.3 62.2 + - - +
21M ARG* 3.3 16.5 + - - +
32M ARG* 5.5 7.6 - - + -
33M LYS* 4.0 24.1 - - - +
34M LYS 5.5 0.4 - - - +
36M VAL* 5.4 6.5 - - + -
84M LEU* 4.0 27.1 - - + -
85M TYR 5.6 0.2 - - - -
86M ASP* 3.3 33.9 - - - +
99M LEU* 3.6 32.8 - - + -
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Residues in contact with LYS 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M PHE* 3.0 35.6 + - + +
16M ASN* 3.3 18.8 + - - +
18M MET* 1.3 79.5 - - - +
20M VAL* 1.3 64.1 + - + +
21M ARG* 5.2 1.4 - - - +
99M LEU* 5.1 11.9 - - + -
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Residues in contact with VAL 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M ASN* 3.3 30.2 + - - +
17M ASP* 4.6 0.7 - - - +
19M LYS* 1.3 83.7 - - + +
21M ARG* 1.3 72.6 + - - +
22M LYS* 3.1 15.5 + - + +
23M SER 4.7 1.2 + - - +
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Residues in contact with ARG 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M ASP* 3.0 15.0 + - - +
18M MET* 3.3 12.7 + - - +
19M LYS 5.2 1.3 - - - +
20M VAL* 1.3 82.8 + - - +
22M LYS* 1.3 69.0 + - - +
23M SER* 3.1 41.5 + - - +
24M SER* 5.9 0.6 - - - +
29M VAL* 5.1 7.1 - - - +
32M ARG* 4.0 43.6 - - - +
97M 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