Contacts of the helix formed by residues 8 - 25 (chain A) in PDB entry 2IVB
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 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLN* 6.2 0.2 - - - -
7A ASN* 1.3 75.7 + - - +
9A ASN* 1.3 73.9 + - - +
10A ILE 3.2 0.9 + - - -
11A ARG* 3.3 7.8 + - - +
12A LEU* 3.0 43.7 + - + +
50A GLN* 6.0 0.2 - - - +
80A LEU* 3.5 39.9 - - + +
82A GLY* 3.0 29.3 + - - +
83A CYS 4.3 1.2 - - - -
84A ILE 2.9 23.4 + - - +
85A ASP* 3.0 31.2 + - - +
85I ASP* 4.2 24.6 + - + +
90I THR* 4.9 12.1 - - - +
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Residues in contact with ASN 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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7A ASN* 2.8 24.0 + - - +
8A ARG* 1.3 89.4 + - - +
10A ILE* 1.3 67.5 + - + +
12A LEU* 4.3 10.7 - - - +
13A ASP* 2.8 38.4 + - - +
85I ASP* 5.9 1.0 + - - -
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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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5A GLN* 3.4 27.1 - - - +
7A ASN* 3.5 6.8 + - - +
8A ARG 3.2 0.6 - - - -
9A ASN* 1.3 82.6 - - + +
11A ARG* 1.3 61.8 + - + +
13A ASP* 3.6 8.0 - - - +
14A LEU* 3.2 17.5 + - - +
74A LEU* 3.8 33.4 - - + +
16I ASP* 3.9 37.7 - - + +
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Residues in contact with ARG 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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5A GLN* 4.2 22.4 - - + -
7A ASN 4.7 0.8 + - - +
8A ARG* 3.3 7.5 + - - +
10A ILE* 1.3 77.0 - - + +
12A LEU* 1.3 62.4 + - + +
14A LEU* 3.5 11.3 + - - +
15A ALA* 2.9 25.6 + - - +
46A ALA 2.8 26.5 + - - -
47A LEU 4.6 1.6 + - - +
49A GLY* 3.7 27.7 - - - +
51A GLN 2.9 20.4 + - - -
74A LEU* 3.0 38.7 + - - -
75A LEU* 3.8 21.8 + - - +
77A MET* 3.0 29.1 + - - +
79A PRO* 4.2 11.0 - - + +
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Residues in contact with LEU 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 ARG* 3.0 56.7 + - + +
9A ASN* 4.1 11.2 - - - +
11A ARG* 1.3 74.0 - - + +
13A ASP* 1.3 67.6 + - - +
15A ALA* 3.1 13.3 + - - +
16A ASP* 3.1 19.0 + - - +
48A LEU 3.5 24.2 - - - +
49A GLY* 4.8 1.6 - - - +
50A GLN* 3.8 14.6 - - - +
82A GLY 4.5 4.5 - - - +
83A CYS* 5.3 8.3 - - + +
6B ILE* 4.9 11.9 - - + +
7B ASN* 6.5 1.8 - - + -
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Residues in contact with ASP 13 (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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9A ASN* 2.8 30.5 + - - +
10A ILE* 3.6 8.6 - - - +
12A LEU* 1.3 78.1 - - - +
14A LEU* 1.3 61.1 - - - +
16A ASP* 3.1 22.9 + - - +
17A ALA* 3.2 12.9 + - - +
7B ASN* 5.4 2.3 + - - -
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Residues in contact with LEU 14 (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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10A ILE 3.2 11.3 + - - +
11A ARG* 3.6 15.7 - - - +
13A ASP* 1.3 75.2 - - - +
15A ALA* 1.3 61.4 + - - +
17A ALA* 3.2 12.0 + - + -
18A ILE* 2.8 45.5 + - + +
47A LEU 5.5 0.4 - - - +
67A LEU* 5.0 4.3 - - + -
71A SER* 3.6 49.1 - - - +
74A LEU* 3.9 23.8 - - + -
75A LEU* 4.0 21.3 - - + -
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Residues in contact with ALA 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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11A ARG 2.9 14.1 + - - +
12A LEU* 3.1 11.8 + - - +
14A LEU* 1.3 77.5 - - - +
16A ASP* 1.3 56.3 + - - +
18A ILE* 3.3 4.2 + - - +
19A LEU* 2.9 32.4 + - - +
47A LEU 3.3 26.0 - - - +
48A LEU* 3.8 17.8 - - + +
6B ILE* 3.9 17.9 - - + -
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Residues in contact with ASP 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 LEU 3.1 18.0 + - - +
13A ASP* 3.1 15.0 + - - +
15A ALA* 1.3 74.8 - - - +
17A ALA* 1.3 58.3 + - - +
19A LEU* 3.2 10.3 + - - +
20A LEU* 3.0 28.1 + - - +
5B GLN* 5.1 2.2 + - - +
6B ILE* 4.1 12.1 - - - +
7B ASN* 2.9 42.9 + - - +
10B ILE* 3.4 31.9 - - + +
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Residues in contact with ALA 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 ASP 3.2 10.3 + - - +
14A LEU* 3.5 18.6 - - + +
16A ASP* 1.3 76.7 - - - +
18A ILE* 1.3 62.6 + - - +
20A LEU* 3.2 10.4 + - - +
21A SER* 3.1 22.1 + - - -
67A LEU* 5.5 3.6 - - + -
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Residues in contact with ILE 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 LEU* 2.8 38.2 + - + +
15A ALA 3.5 8.5 - - - +
17A ALA* 1.3 71.3 - - - +
19A LEU* 1.3 64.5 + - + +
21A SER* 3.3 7.7 + - - -
22A LYS* 2.9 30.8 + - + +
47A LEU* 4.0 37.5 - - + +
65A LEU* 3.8 20.8 - - + +
67A LEU* 4.0 33.8 - - + +
75A LEU* 3.9 22.4 - - + -
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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 ALA 2.9 21.7 + - - +
16A ASP* 3.2 12.1 + - - +
18A ILE* 1.3 76.9 - - + +
20A LEU* 1.3 57.1 + - - +
22A LYS* 3.7 10.8 - - + +
23A ALA* 2.9 28.2 + - - +
29A PHE* 3.9 30.5 - - + -
48A LEU* 4.1 13.0 - - + -
3B GLN* 4.8 0.7 - - - +
4B SER 3.5 24.7 - - - +
5B GLN* 4.3 13.2 - - - +
6B ILE* 3.8 38.6 - - + +
77B MET* 4.7 5.6 - - + +
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Residues in contact with LEU 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 ASP 3.0 12.7 + - - +
17A ALA* 3.2 11.4 + - - +
19A LEU* 1.3 75.9 - - - +
21A SER* 1.3 57.6 + - - +
23A ALA* 3.0 7.1 + - + +
24A LYS* 2.8 56.9 + - + +
5B GLN* 5.5 0.8 + - - -
70B ASP* 4.1 24.9 - - + +
73B LEU* 4.7 10.5 - - + -
74B LEU* 4.5 25.4 - - + -
77B MET* 5.6 2.0 - - - -
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Residues in contact with SER 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 ALA 3.1 12.5 + - - -
18A ILE* 3.7 8.1 - - - -
20A LEU* 1.3 75.5 - - - +
22A LYS* 1.3 53.9 + - - +
24A LYS* 3.2 10.4 + - - +
25A LYS* 2.8 56.2 + - - +
65A LEU* 2.6 38.7 + - - -
67A LEU* 5.2 2.9 - - - -
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Residues in contact with LYS 22 (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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18A ILE* 2.9 18.8 + - + +
19A LEU* 3.7 12.3 - - + +
21A SER* 1.3 75.5 - - - +
23A ALA* 1.3 56.1 + - - +
25A LYS 3.6 0.3 + - - -
26A ASP* 2.9 21.8 + - - -
27A LEU* 3.0 35.4 + - + +
28A SER 3.8 2.2 - - - -
29A PHE* 3.5 60.8 - - + +
32A ILE* 3.6 14.8 - - + -
47A LEU* 5.6 0.7 - - + -
65A LEU* 3.8 18.0 - - + +
2B ILE 3.9 9.1 + - - -
3B GLN* 2.7 33.0 + - - +
4B SER 5.1 1.0 - - - +
114D GLU* 4.4 3.0 + - - -
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Residues in contact with ALA 23 (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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19A LEU 2.9 18.1 + - - +
20A LEU* 3.0 6.0 + - + +
22A LYS* 1.3 74.4 - - - +
24A LYS* 1.3 64.7 + - - +
26A ASP* 3.0 16.6 + - - +
3B GLN* 3.7 27.7 - - + +
73B LEU* 3.9 29.1 - - + +
77B MET* 4.1 17.7 - - - -
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Residues in contact with LYS 24 (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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20A LEU* 2.8 42.3 + - + +
21A SER* 3.2 8.7 + - - +
23A ALA* 1.3 74.0 - - - +
25A LYS* 1.3 66.8 + - + +
26A ASP* 3.6 1.9 + - - +
70B ASP* 3.1 39.8 + - - -
73B LEU* 3.9 16.8 - - + -
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Residues in contact with LYS 25 (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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21A SER* 2.8 40.5 + - - +
22A LYS 4.1 0.4 - - - +
24A LYS* 1.3 79.1 - - + +
26A ASP* 1.3 70.1 + - - +
27A LEU* 3.3 28.4 + - + +
63A ALA 5.6 0.2 - - - -
64A LYS 3.2 28.3 - - - +
65A LEU* 3.6 10.6 + - - -
66A ASP* 3.8 14.4 + - - +
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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
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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