Contacts of the helix formed by residues 2 - 23 (chain A) in PDB entry 2O7T
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 ARG 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 1.3 75.8 - - - +
3A ALA* 1.3 67.6 + - - +
4A ASP* 3.2 37.2 - - - +
5A ALA* 2.9 28.3 + - + +
6A LEU* 3.0 11.3 + - - +
8A ARG* 5.0 3.8 - - - -
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Residues in contact with ALA 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 3.5 3.5 + - - -
2A ARG* 1.3 72.5 - - - +
4A ASP* 1.3 57.0 + - - +
6A LEU* 3.4 11.1 + - - +
7A LYS* 3.0 36.2 + - + +
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Residues in contact with ASP 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ARG* 3.2 38.7 - - - +
3A ALA* 1.3 77.2 + - - +
5A ALA* 1.3 60.7 + - - +
7A LYS* 3.9 7.4 - - - +
8A ARG* 3.1 52.7 + - - +
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Residues in contact with ALA 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 3.7 28.7 - - + +
2A ARG* 2.9 29.2 + - + +
4A ASP* 1.3 78.3 - - - +
6A LEU* 1.3 60.5 + - - +
8A ARG* 3.4 15.2 + - - +
9A ARG* 3.0 28.6 + - - +
47A ASN* 4.6 2.4 + - - +
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Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 3.9 28.0 - - + +
2A ARG 3.0 10.9 + - - +
3A ALA* 3.6 13.7 - - - +
5A ALA* 1.3 79.7 - - - +
7A LYS* 1.3 59.9 + - + +
9A ARG* 3.5 10.6 + - - +
10A GLU* 3.1 40.9 + - + +
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Residues in contact with LYS 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 ALA* 3.0 26.1 + - + +
4A ASP* 3.9 7.9 - - - +
6A LEU* 1.3 72.7 - - + +
8A ARG* 1.3 60.5 + - - +
10A GLU* 3.3 7.9 + - - +
11A HIS* 2.9 29.5 + - - +
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Residues in contact with ARG 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ARG* 5.0 3.4 - - - -
4A ASP* 3.1 51.5 + - - +
5A ALA* 3.6 18.8 - - - +
6A LEU 3.3 0.2 - - - -
7A LYS* 1.3 80.9 - - - +
9A ARG* 1.3 61.8 + - - +
11A HIS* 3.2 8.2 + - + +
12A ILE* 3.0 29.8 + - + +
39A VAL* 3.9 23.3 - - + -
43A THR* 3.6 29.6 - - + +
47A ASN* 5.4 2.0 - - - +
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Residues in contact with ARG 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 4.4 16.6 - - - +
5A ALA 3.0 16.8 + - - +
6A LEU* 3.6 13.9 - - - +
8A ARG* 1.3 77.2 - - - +
10A GLU* 1.3 63.0 + - + +
12A ILE* 3.3 12.6 + - - +
13A ILE* 3.2 32.0 + - + +
47A ASN* 3.0 52.6 + - - +
48A PHE* 3.7 26.8 - - + -
53A THR* 6.3 0.8 - - - +
57A ALA* 4.3 10.7 - - - +
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.1 31.1 + - + +
7A LYS* 3.7 7.4 - - - +
9A ARG* 1.3 78.3 - - + +
11A HIS* 1.3 58.1 + - - +
13A ILE* 3.4 11.3 + - + +
14A THR* 3.0 32.5 + - - +
61A TYR* 6.5 0.9 - - + -
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Residues in contact with HIS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS 2.9 16.8 + - - +
8A ARG* 3.2 8.3 + - + +
10A GLU* 1.3 75.4 - - - +
12A ILE* 1.3 57.8 + - - +
14A THR* 3.9 8.0 - - - +
15A THR* 2.7 54.9 + - - -
36A GLN 4.8 1.4 + - - -
37A ALA* 3.1 34.9 + - + -
39A VAL* 5.1 4.7 - - + -
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Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 3.0 18.9 + - + +
9A ARG 3.3 5.8 + - - +
11A HIS* 1.3 76.6 - - + +
13A ILE* 1.3 55.1 + - - +
15A THR* 3.7 2.1 - - - -
16A THR* 2.8 43.1 + - - +
33A ILE* 4.4 6.0 - - + +
37A ALA* 4.2 13.0 - - + -
39A VAL* 4.1 33.7 - - + -
43A THR* 4.9 0.7 - - + -
44A LEU* 3.4 37.0 - - + +
47A ASN* 4.2 21.5 - - - +
48A PHE* 3.8 17.0 - - + -
54A LEU* 4.3 3.1 - - + -
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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 ARG* 3.2 27.4 + - + +
10A GLU* 3.6 12.3 - - + +
11A HIS 3.2 0.2 - - - -
12A ILE* 1.3 75.3 - - - +
14A THR* 1.3 60.1 + - - +
16A THR* 3.3 3.3 + - - -
17A CYS* 3.0 29.1 + - - -
48A PHE* 3.7 23.3 - - + -
54A LEU* 4.7 1.1 - - + -
57A ALA* 4.2 20.9 - - + +
58A CYS* 4.0 21.5 - - - -
61A TYR* 3.9 40.2 - - + -
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Residues in contact with THR 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 3.0 18.4 + - - +
11A HIS* 3.9 10.0 - - + +
12A ILE 3.5 0.2 - - - -
13A ILE* 1.3 74.6 - - - +
15A THR* 1.3 65.9 + - - +
17A CYS* 3.4 6.8 + - - +
18A ASN* 3.0 42.9 + - - +
21A ARG* 6.1 0.2 - - - +
61A TYR* 4.7 16.6 + - + +
199A UNL 5.5 7.0 - - - +
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Residues in contact with THR 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A HIS* 2.7 49.2 + - - -
12A ILE 3.7 4.5 - - - +
14A THR* 1.3 76.7 - - - +
16A THR* 1.3 58.2 + - - +
18A ASN* 3.4 10.0 + - - +
19A LEU* 2.8 35.7 + - + +
33A ILE* 4.5 2.2 - - + +
36A GLN* 3.9 17.7 + - + +
37A ALA* 3.7 29.8 - - + +
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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
----------------------------------------------------------
12A ILE 2.8 21.8 + - - -
13A ILE 3.3 4.7 + - - -
15A THR* 1.3 77.2 - - - +
17A CYS* 1.3 63.0 + - - +
19A LEU* 3.0 11.8 + - + +
20A TYR* 2.9 48.9 + - + +
28A LEU* 6.0 1.1 - - + -
33A ILE* 3.2 28.4 - - + +
54A LEU* 3.8 20.5 - - + +
55A ASP* 4.6 0.2 - - - +
58A CYS* 3.8 17.5 - - - -
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Residues in contact with CYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.0 27.3 + - - +
14A THR* 3.7 7.4 - - - +
16A THR* 1.3 74.6 - - - +
18A ASN* 1.3 62.4 + - - +
20A TYR* 3.3 11.0 + - - -
21A ARG* 3.3 31.8 + - - +
58A CYS* 4.0 18.2 - - - -
61A TYR* 4.5 4.0 - - + -
62A LEU* 3.8 37.0 - - + -
100A LEU* 3.5 18.1 - - + +
104A LEU* 5.4 0.7 - - - -
199A UNL 5.2 3.1 - - - +
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Residues in contact with ASN 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 THR* 3.0 36.0 + - - +
15A THR* 3.6 7.7 - - - +
17A CYS* 1.3 73.8 - - - +
19A LEU* 1.3 65.2 + - + +
21A ARG* 2.8 39.4 + - - +
22A THR* 3.1 21.3 + - + +
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Residues in contact with LEU 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 THR* 2.8 30.1 + - + +
16A THR* 3.5 9.2 - - - +
18A ASN* 1.3 72.8 - - - +
20A TYR* 1.3 57.5 + - - +
22A THR* 3.7 3.4 - - - +
23A HIS* 2.7 72.0 + - + +
28A LEU* 4.0 21.5 - - + +
33A ILE* 4.0 27.1 - - + -
36A GLN* 3.9 39.3 - - + +
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Residues in contact with TYR 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* 2.9 43.3 + - + -
17A CYS* 3.6 10.8 - - - +
18A ASN 3.2 0.2 - - - -
19A LEU* 1.3 77.3 - - - +
21A ARG* 1.3 60.4 + - - +
22A THR 3.8 0.2 + - - -
23A HIS 3.8 2.3 - - - +
25A HIS* 2.9 45.5 + + + -
28A LEU* 4.1 13.2 - - + -
51A ARG* 3.1 26.7 + - - -
55A ASP* 2.4 29.9 + - - -
58A CYS* 5.0 1.3 - - - -
99A SER* 4.0 6.0 - - - +
100A LEU* 3.8 14.4 - - + -
103A ALA* 3.4 30.9 + - + -
104A LEU* 3.4 28.7 - - + -
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Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A THR* 4.9 0.8 + - - +
17A CYS* 3.3 18.6 + - - +
18A ASN* 2.8 49.3 + - - +
20A TYR* 1.3 78.8 - - - +
22A THR* 1.3 63.3 + - + +
23A HIS 5.1 0.2 - - - -
62A LEU* 4.9 1.0 - - - +
95A ARG* 3.0 29.6 + - - +
96A GLY* 4.6 7.2 - - - -
99A SER* 4.3 17.9 + - - -
100A LEU* 3.6 26.8 - - + +
199A UNL 3.0 43.3 + - - -
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Residues in contact with THR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASN* 3.2 18.6 + - + +
19A LEU* 3.1 3.0 + - - +
21A ARG* 1.3 85.5 - - + +
23A HIS* 1.3 90.0 + - - +
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Residues in contact with HIS 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 2.7 46.3 + - + +
20A TYR* 3.8 2.4 - - - +
21A ARG 5.1 0.2 - - - -
22A THR* 1.3 106.2 + - - +
24A HIS* 1.3 65.2 + - - +
25A HIS* 3.2 18.4 + - - -
27A SER* 4.2 4.3 - - - +
28A LEU* 4.1 22.6 - - + +
36A GLN* 4.7 11.4 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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