Contacts of the helix formed by residues 3 - 21 (chain A) in PDB entry 1ON2
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 THR 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A THR* 1.3 82.3 - - - +
4A PRO* 1.3 77.7 - - - +
5A SER* 3.5 7.8 + - - -
6A MET* 3.0 36.1 + - - +
7A GLU* 2.9 27.4 + - - +
42A MET* 5.1 0.2 - - - +
45A LYS* 5.1 7.9 - - - +
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Residues in contact with PRO 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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3A THR* 1.3 88.7 - - - +
5A SER* 1.3 57.9 + - - +
7A GLU* 3.2 2.4 + - + +
8A MET* 2.8 30.0 + - + +
103A HIS* 3.6 47.6 + - + +
104A HIS* 4.1 18.2 - - + +
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Residues in contact with SER 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 3.2 6.6 + - - -
4A PRO* 1.3 82.5 - - - +
6A MET* 1.3 61.9 + - - +
8A MET* 3.2 11.7 + - - +
9A TYR* 3.1 39.3 + - - -
42A MET* 3.2 18.9 - - - +
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Residues in contact with MET 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A THR* 3.9 24.0 - - + -
3A THR* 3.0 34.9 + - - +
5A SER* 1.3 76.3 - - - +
7A GLU* 1.3 57.9 - - - +
9A TYR* 3.4 2.3 + - - +
10A ILE* 2.9 36.5 + - + +
42A MET* 3.9 26.5 - - + -
45A LYS* 4.2 20.2 - - + +
46A LEU* 3.7 22.2 - - + +
49A ASP* 3.3 24.5 - - - +
51A TYR* 4.0 18.6 - - + -
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Residues in contact with GLU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A THR* 3.0 29.1 + - + +
3A THR 2.9 20.4 + - - +
4A PRO* 3.6 4.7 - - - +
6A MET* 1.3 76.3 - - - +
8A MET* 1.3 65.5 + - - +
10A ILE* 4.4 2.2 - - + -
11A GLU* 2.9 26.9 + - - +
69A ILE* 5.6 2.7 - - + +
73A LEU* 3.5 27.2 - - + +
76A ARG* 2.9 31.5 + - - +
103A HIS* 3.5 20.0 - - + +
107A TRP* 5.4 3.3 + - - -
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Residues in contact with MET 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 PRO 2.8 16.6 + - - +
5A SER* 3.2 12.8 + - - +
7A GLU* 1.3 76.9 - - - +
9A TYR* 1.3 62.6 - - - +
11A GLU* 3.7 5.7 - - - +
12A GLN* 3.1 26.7 + - - +
15A MET* 5.2 0.3 - - - +
32A LEU* 4.0 31.2 - - + -
99A GLU* 5.5 14.6 - - + +
103A HIS* 3.6 26.0 + - + +
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Residues in contact with TYR 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A SER* 3.1 35.7 + - - +
6A MET 3.7 4.0 - - - +
8A MET* 1.3 84.8 - - + +
10A ILE* 1.3 60.5 + - - +
12A GLN* 3.2 4.7 + - - +
13A ILE* 2.8 41.3 + - + +
28A ILE* 4.0 17.0 - - + -
32A LEU* 3.5 27.1 - - + -
34A VAL* 3.9 21.3 - - - +
38A SER* 3.8 16.5 + - - -
39A VAL* 3.9 22.1 - - + -
42A MET* 3.4 37.5 - - + -
43A VAL* 5.6 1.6 - - + -
46A LEU* 4.2 7.6 - - + -
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Residues in contact with ILE 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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2A THR* 4.6 9.4 - - + -
6A MET 2.9 30.8 + - - +
7A GLU* 4.5 3.1 - - - -
9A TYR* 1.3 76.0 - - - +
11A GLU* 1.3 63.8 + - - +
13A ILE* 3.8 7.7 - - + +
14A TYR* 2.9 23.8 + - + +
46A LEU* 3.9 25.8 - - + -
51A TYR* 3.7 34.5 - - + -
62A LEU* 5.0 10.6 - - + +
66A GLY* 4.1 9.6 - - - +
69A ILE* 4.8 5.4 - - + -
70A GLY* 3.8 27.1 - - - +
73A LEU* 3.8 12.3 - - + -
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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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7A GLU 2.9 18.6 + - - +
8A MET* 3.7 6.6 - - - +
10A ILE* 1.3 78.6 - - - +
12A GLN* 1.3 56.2 + - - +
14A TYR* 3.4 5.3 + - - +
15A MET* 3.0 56.2 + - + +
70A GLY 4.9 1.6 - - - -
73A LEU* 3.7 31.6 - - + +
74A VAL* 4.2 13.1 - - + +
76A ARG* 5.1 1.2 + - - -
77A HIS* 3.2 12.4 + - - +
102A GLU* 3.0 10.6 - - - +
103A HIS* 4.7 4.5 + - - -
150A MN 2.3 36.4 + - - -
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Residues in contact with GLN 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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8A MET 3.1 14.9 + - - +
9A TYR* 3.2 5.8 + - - +
11A GLU* 1.3 78.3 - - - +
13A ILE* 1.3 63.9 + - - +
15A MET* 3.0 27.9 + - + +
16A LEU* 3.1 40.7 + - + +
28A ILE* 4.5 10.1 - - + -
31A ALA* 3.4 34.6 + - + +
32A LEU* 4.3 23.0 - - + +
95A TYR* 5.8 2.0 + - - -
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Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 2.8 25.0 + - + +
10A ILE* 3.8 6.1 - - + +
12A GLN* 1.3 73.2 - - - +
14A TYR* 1.3 67.1 + - - +
16A LEU* 3.3 3.8 + - - +
17A ILE* 3.1 33.7 + - + +
23A ALA* 4.0 9.1 - - + +
28A ILE* 3.6 26.2 - - + -
43A VAL* 4.9 3.8 - - + -
46A LEU* 4.1 16.6 - - + -
52A LEU* 4.0 14.8 - - + -
60A LEU* 3.4 41.5 - - + -
62A LEU* 4.1 11.9 - - + -
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Residues in contact with TYR 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE 2.9 17.5 + - - +
11A GLU 3.6 4.7 - - - +
13A ILE* 1.3 78.1 - - - +
15A MET* 1.3 63.0 + - - +
17A ILE* 3.4 4.5 + - + +
18A GLU* 3.0 42.3 + - + +
62A LEU* 3.7 26.6 - - + +
67A LYS* 3.4 29.7 + - + +
70A GLY* 3.8 15.0 - - - +
71A LYS* 3.1 48.4 + - + +
74A VAL* 3.9 16.8 - - + -
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Residues in contact with MET 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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8A MET 5.2 0.4 - - - +
11A GLU* 3.0 53.0 + - + +
12A GLN* 3.0 44.2 - - + +
14A TYR* 1.3 77.2 - - - +
16A LEU* 1.3 56.4 + - + +
18A GLU* 3.4 14.0 + - - +
19A GLU* 2.9 30.8 + - - +
74A VAL* 4.0 20.2 - - + -
95A TYR* 6.0 2.5 - - - +
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Residues in contact with LEU 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 GLN* 3.1 36.7 + - + +
13A ILE 3.8 3.6 - - - +
15A MET* 1.3 73.9 - - - +
17A ILE* 1.3 57.5 + - - +
19A GLU* 4.4 4.0 - - + +
20A LYS* 2.6 59.7 + - + +
22A TYR 3.3 16.7 - - - +
23A ALA* 4.1 7.9 - - + -
27A ASP* 4.0 18.6 - - + +
28A ILE* 3.6 43.3 - - + +
31A ALA* 5.7 1.1 - - + -
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Residues in contact with ILE 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 ILE* 3.1 32.9 + - + +
14A TYR* 3.8 4.7 - - + +
16A LEU* 1.3 75.5 - - - +
18A GLU* 1.3 61.4 + - - +
21A GLY* 2.7 36.8 + - - +
22A TYR* 3.8 14.6 - - - +
23A ALA* 3.9 13.2 - - + +
60A LEU 3.9 17.7 - - - +
61A VAL* 4.7 0.9 - - - -
62A LEU* 4.1 26.5 - - + +
67A LYS* 6.5 1.1 - - - -
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Residues in contact with GLU 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 TYR* 3.0 36.6 + - + +
15A MET* 3.7 11.3 - - - +
17A ILE* 1.3 78.9 - - - +
19A GLU* 1.3 64.3 + - + +
21A GLY 4.9 0.2 + - - -
71A LYS* 3.5 23.4 + - - -
74A VAL* 5.1 9.2 - - - +
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Residues in contact with GLU 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 MET 2.9 18.2 + - - +
16A LEU* 3.8 4.5 - - + +
18A GLU* 1.3 83.1 - - + +
20A LYS* 1.3 72.4 + - + +
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Residues in contact with LYS 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 LEU* 2.6 36.3 + - + +
19A GLU* 1.3 87.9 - - + +
21A GLY* 1.3 55.8 + - - +
22A TYR* 3.2 48.0 + - + +
27A ASP* 2.8 34.6 + - - +
30A GLU* 5.7 2.2 + - - -
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Residues in contact with GLY 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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16A LEU 3.5 0.2 + - - -
17A ILE* 2.7 35.6 + - - +
18A GLU 4.7 0.2 - - - -
19A GLU 3.8 0.4 - - - -
20A LYS* 1.3 72.7 - - - +
22A TYR* 1.3 64.4 + - - +
58A ARG* 5.5 5.7 - - - +
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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