Contacts of the helix formed by residues 2 - 21 (chain A) in PDB entry 1M12
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 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A SER* 1.3 73.1 - - - +
3A VAL* 1.3 59.5 + - - +
4A TYR* 2.9 32.1 + - - +
5A CYS* 3.0 47.0 + - + +
6A GLU* 3.8 6.2 + - - +
77A LEU 4.1 4.3 - - - +
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Residues in contact with VAL 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SER 2.9 11.4 + - - +
2A ASP* 1.3 72.7 + - - +
4A TYR* 1.3 73.8 + - + +
6A GLU* 3.6 11.4 - - - +
7A VAL* 3.4 24.8 + - + +
43A LEU* 4.8 13.0 - - + -
46A GLU* 3.9 38.6 - - + +
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Residues in contact with TYR 4 (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 ASP* 2.9 24.1 + - - +
3A VAL* 1.3 84.7 - - + +
5A CYS* 1.3 67.4 + - - +
7A VAL* 3.1 5.2 + - + +
8A CYS* 3.0 23.1 + - - +
46A GLU* 4.0 26.8 - - + +
49A GLU* 4.8 12.9 - - + +
50A VAL* 3.6 32.7 - - + +
77A LEU* 4.4 22.7 - - + +
78A CYS* 5.0 0.2 - - - -
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Residues in contact with CYS 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASP* 3.0 33.4 + - + +
4A TYR* 1.3 76.1 - - - +
6A GLU* 1.3 63.6 + - - +
8A CYS* 3.9 2.2 - - - +
9A GLU* 3.1 28.5 + - + +
77A LEU 3.9 0.4 - - - -
78A CYS* 2.0 58.9 - - - -
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Residues in contact with GLU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASP 3.8 3.5 + - - +
3A VAL* 3.6 14.6 + - - +
4A TYR 3.2 0.6 - - - -
5A CYS* 1.3 81.1 - - - +
7A VAL* 1.3 86.0 + - - +
9A GLU* 3.6 5.1 + - - +
10A PHE* 3.1 29.5 + - - +
39A LEU* 4.8 6.2 - - - +
43A LEU* 3.3 26.7 - - + +
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Residues in contact with VAL 7 (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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3A VAL* 3.4 12.1 + - + +
4A TYR* 3.1 8.8 + - - +
6A GLU* 1.3 102.4 - - - +
8A CYS* 1.3 67.0 + - - +
10A PHE* 3.0 3.4 + - + +
11A LEU* 2.9 44.0 + - + +
39A LEU* 4.9 9.4 - - + -
43A LEU* 4.6 17.5 - - + +
46A GLU* 5.0 11.4 - - + -
47A CYS* 4.2 23.1 - - + -
50A VAL* 4.5 10.3 - - + -
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Residues in contact with CYS 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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4A TYR 3.0 16.5 + - - +
5A CYS* 3.3 4.5 + - - +
7A VAL* 1.3 76.2 - - - +
9A GLU* 1.3 59.8 + - - +
11A LEU* 3.6 8.6 + - - +
12A VAL* 3.0 30.6 + - - +
50A VAL* 5.0 5.3 - - + +
58A ILE* 4.8 9.2 - - - -
71A VAL* 4.1 11.9 - - - -
72A CYS* 2.0 56.8 - - + -
75A LEU* 5.6 0.7 - - - -
77A LEU* 4.9 17.3 - - + -
78A CYS* 5.1 1.1 - - - -
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Residues in contact with GLU 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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5A CYS* 3.1 18.6 + - + +
6A GLU* 4.0 4.7 - - - +
8A CYS* 1.3 76.4 - - - +
10A PHE* 1.3 60.9 + - - +
12A VAL* 3.8 8.7 - - - +
13A LYS* 2.9 32.5 + - - +
68A PRO 3.9 5.9 - - - +
69A GLU* 2.8 44.1 - - - +
72A CYS* 3.9 10.9 - - + -
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Residues in contact with PHE 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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6A GLU* 3.1 25.1 + - - +
7A VAL* 3.0 9.0 + - - +
9A GLU* 1.3 78.1 - - - +
11A LEU* 1.3 75.7 + - + +
13A LYS* 3.2 28.2 + - - +
14A GLU* 2.9 43.6 + - + +
35A MET* 5.1 10.8 - - + -
38A LYS* 4.7 16.2 - - + -
39A LEU* 3.8 41.7 - - + -
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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
----------------------------------------------------------
7A VAL* 2.9 36.8 + - + +
8A CYS* 4.1 3.4 - - - +
10A PHE* 1.3 84.0 - - + +
12A VAL* 1.3 52.9 + - - +
14A GLU* 3.8 2.6 - - - +
15A VAL* 2.6 46.5 + - + +
32A PHE* 5.4 6.3 - - + -
35A MET* 4.1 25.8 - - + -
36A CYS* 6.1 2.0 - - - +
39A LEU* 6.1 2.2 - - + -
47A CYS* 5.8 1.8 - - + -
50A VAL* 3.9 18.8 - - + -
51A VAL* 3.6 35.2 - - + -
58A ILE* 4.7 14.8 - - + -
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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
----------------------------------------------------------
8A CYS* 3.0 25.0 + - - +
9A GLU* 3.8 12.6 - - - +
11A LEU* 1.3 76.8 - - - +
13A LYS* 1.3 58.4 + - - +
15A VAL* 4.3 4.9 - - - -
16A THR* 2.8 38.7 + - + +
58A ILE* 4.4 12.8 - - + -
62A LEU* 4.7 5.6 - - + -
68A PRO* 3.2 44.2 - - + +
71A VAL* 3.9 29.8 - - + -
72A CYS* 4.5 1.1 - - - -
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Residues in contact with LYS 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU* 2.9 18.1 + - - +
10A PHE* 3.6 36.1 + - - +
12A VAL* 1.3 80.5 - - - +
14A GLU* 1.3 63.9 + - - +
16A THR* 3.5 7.4 + - - -
17A LYS* 3.3 20.3 + - + +
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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
----------------------------------------------------------
10A PHE* 2.9 42.8 + - + +
11A LEU 3.8 2.5 - - - +
13A LYS* 1.3 79.8 - - - +
15A VAL* 1.3 63.0 + - - +
17A LYS* 3.5 9.6 + - - +
18A LEU* 3.1 37.6 + - - +
35A MET* 3.1 39.5 - - + +
38A LYS* 5.5 10.6 - - + +
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 2.6 31.2 + - + +
12A VAL* 3.8 4.0 - - - +
14A GLU* 1.3 72.9 - - - +
16A THR* 1.3 62.6 + - - +
18A LEU* 2.8 9.3 + - - +
19A ILE* 2.7 37.9 + - + +
28A ILE* 4.1 15.5 - - + -
32A PHE* 4.1 29.8 - - + -
35A MET* 4.5 5.8 - - + -
58A ILE* 5.5 4.7 - - + -
59A LEU* 4.7 4.9 - - + -
62A LEU* 3.5 28.7 - - + -
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Residues in contact with THR 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* 2.8 43.0 + - + +
13A LYS* 3.5 9.3 + - - -
15A VAL* 1.3 72.9 - - - +
17A LYS* 1.3 53.2 + - - +
19A ILE* 2.9 12.4 + - - +
20A ASP* 2.6 52.4 + - - +
62A LEU* 3.9 22.4 - - + -
68A PRO* 4.1 14.4 - - + -
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Residues in contact with LYS 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 LYS* 3.3 12.5 + - + +
14A GLU* 3.9 10.3 - - - +
15A VAL 3.2 0.8 - - - -
16A THR* 1.3 81.9 + - - +
18A LEU* 1.3 69.4 + - + +
20A ASP* 3.2 12.4 + - + +
21A ASN* 2.8 31.9 + - + +
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Residues in contact with LEU 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* 3.1 44.0 - - - +
15A VAL* 2.8 13.8 + - - +
17A LYS* 1.3 89.7 - - + +
19A ILE* 1.3 58.6 + - - +
21A ASN* 3.3 6.6 + - + -
23A LYS* 3.2 54.9 + - + +
27A GLU 5.7 0.7 - - - +
28A ILE* 4.2 20.9 - - + -
31A ALA* 4.7 12.6 - - + -
35A MET* 4.0 14.4 - - + -
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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 VAL* 2.7 36.5 + - + +
16A THR* 3.4 13.0 - - - +
18A LEU* 1.3 77.4 - - - +
20A ASP* 1.3 67.5 + - - +
22A ASN* 3.4 11.8 + - - -
23A LYS 4.6 5.1 + - - +
28A ILE* 4.1 13.2 - - + -
59A LEU* 5.2 1.3 - - + -
62A LEU* 3.9 29.2 - - + +
63A LEU* 4.5 17.5 - - + -
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Residues in contact with ASP 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 THR* 2.6 45.8 + - - +
17A LYS* 3.4 11.5 - - + +
19A ILE* 1.3 81.9 - - - +
21A ASN* 1.3 58.1 + - - +
22A ASN* 3.2 2.8 + - - +
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Residues in contact with ASN 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 LYS* 2.8 21.6 + - + +
18A LEU* 3.3 6.7 + - + +
19A ILE 3.2 0.8 - - - -
20A ASP* 1.3 76.7 - - - +
22A ASN* 1.3 71.7 + - - +
23A LYS* 3.0 32.8 - - - +
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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
------------------------------------------------------------
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