Contacts of the helix formed by residues 8 - 25 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ASP* 4.1 24.1 + - + -
90B THR* 4.9 13.0 - - - +
5E GLN* 6.2 0.4 - - - -
7E ASN* 1.3 72.9 + - - +
9E ASN* 1.3 73.9 + - - +
10E ILE 3.2 0.9 + - - -
11E ARG* 3.3 7.5 + - - +
12E LEU* 3.0 42.6 + - + +
50E GLN* 6.1 0.4 - - - +
80E LEU* 3.6 40.1 - - + +
82E GLY* 3.0 28.3 + - - +
83E CYS 4.4 1.2 - - - -
84E ILE 2.9 24.5 + - - -
85E ASP* 2.9 33.6 + - - +
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Residues in contact with ASN 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ASP* 5.9 0.6 + - - -
7E ASN* 2.9 26.5 + - - +
8E ARG* 1.3 90.3 + - - +
10E ILE* 1.3 57.8 + - + +
12E LEU* 4.3 11.8 - - - +
13E ASP* 2.8 43.7 + - - +
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Residues in contact with ILE 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP* 3.8 40.8 - - + +
5E GLN* 3.4 24.0 - - - +
7E ASN* 3.5 5.0 + - - +
8E ARG 3.3 1.0 - - - -
9E ASN* 1.3 81.5 - - + +
11E ARG* 1.3 61.9 + - - +
13E ASP* 3.5 9.0 + - - +
14E LEU* 3.2 19.1 + - - +
74E LEU* 3.9 31.5 - - + +
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Residues in contact with ARG 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E GLN* 4.3 20.8 - - + +
8E ARG* 3.3 8.4 + - - +
10E ILE* 1.3 76.9 - - + +
12E LEU* 1.3 62.3 + - + +
14E LEU* 3.6 10.5 - - - +
15E ALA* 2.8 27.5 + - - +
46E ALA 2.9 23.0 + - - -
47E LEU 4.7 1.3 + - - +
49E GLY* 3.8 25.9 - - - +
51E GLN 2.8 25.3 + - - -
74E LEU* 2.9 45.2 + - - -
75E LEU* 3.9 17.4 + - - +
77E MET* 3.0 25.7 + - - +
79E PRO* 4.1 12.4 - - + +
80E LEU 6.1 0.2 - - - +
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Residues in contact with LEU 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ARG* 3.0 53.4 + - + +
9E ASN* 4.0 12.1 - - - +
11E ARG* 1.3 73.0 - - - +
13E ASP* 1.3 66.4 + - - +
15E ALA* 3.2 5.3 + - - +
16E ASP* 3.1 27.9 + - - +
48E LEU 3.4 25.6 - - - +
49E GLY* 4.8 1.6 - - - -
50E GLN* 3.9 15.5 - - - +
82E GLY 4.7 3.8 - - - +
83E CYS* 5.2 9.2 - - + +
6H ILE* 4.6 12.9 - - + +
7H ASN* 5.9 4.0 - - + +
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Residues in contact with ASP 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ASN* 2.8 34.2 + - - +
10E ILE* 3.7 9.3 - - - +
12E LEU* 1.3 70.5 - - - +
14E LEU* 1.3 64.2 + - - +
16E ASP* 3.3 14.8 + - - +
17E ALA* 3.2 20.1 + - - +
7H ASN* 5.5 1.6 + - - -
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Residues in contact with LEU 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ILE 3.2 14.5 + - - +
11E ARG* 3.6 16.2 - - - +
12E LEU 3.3 0.2 - - - -
13E ASP* 1.3 74.5 - - - +
15E ALA* 1.4 59.5 + - - +
17E ALA* 3.1 12.9 + - + +
18E ILE* 2.9 43.0 + - + +
47E LEU 5.6 0.4 - - - +
67E LEU* 4.9 4.5 - - + -
71E SER* 3.5 50.3 - - - +
74E LEU* 3.8 24.7 - - + -
75E LEU* 3.9 22.4 - - + -
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Residues in contact with ALA 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ARG 2.8 13.8 + - - +
12E LEU* 3.2 11.2 + - - +
14E LEU* 1.4 74.8 - - - +
16E ASP* 1.3 56.8 + - - +
18E ILE* 3.2 5.6 + - - +
19E LEU* 2.8 34.3 + - - +
47E LEU 3.2 26.0 + - - +
48E LEU* 3.8 18.8 - - + -
6H ILE* 3.8 17.5 - - + -
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Residues in contact with ASP 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LEU 3.1 16.5 + - - +
13E ASP* 3.3 14.0 + - - +
14E LEU 3.3 0.4 - - - -
15E ALA* 1.3 74.7 - - - +
17E ALA* 1.3 62.9 + - - +
19E LEU* 3.4 9.0 + - - +
20E LEU* 3.1 22.9 + - - +
5H GLN* 5.0 5.9 + - - +
6H ILE* 4.0 13.5 - - - +
7H ASN* 3.0 42.5 + - - +
10H ILE* 4.1 24.6 - - + +
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Residues in contact with ALA 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ASP 3.2 11.2 + - - +
14E LEU* 3.1 18.0 + - + +
16E ASP* 1.3 74.5 - - - +
18E ILE* 1.3 63.6 + - - +
20E LEU* 3.3 7.5 + - - +
21E SER* 3.1 23.8 + - - -
67E LEU* 5.6 3.8 - - + -
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Residues in contact with ILE 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E LEU* 2.9 36.3 + - + +
15E ALA* 3.2 8.7 + - - +
17E ALA* 1.3 71.1 - - - +
19E LEU* 1.3 67.6 + - + +
21E SER* 3.2 6.1 + - - -
22E LYS* 2.9 30.7 + - + +
47E LEU* 4.0 45.3 - - + +
48E LEU* 6.1 0.4 - - + -
65E LEU* 4.0 22.0 - - + +
67E LEU* 4.0 30.5 - - + -
75E LEU* 4.0 17.9 - - + -
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Residues in contact with LEU 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ALA 2.8 23.7 + - - +
16E ASP* 3.8 8.5 - - - +
17E ALA 3.3 0.2 - - - -
18E ILE* 1.3 75.9 - - + +
20E LEU* 1.3 57.4 + - - +
22E LYS* 3.6 11.6 + - + +
23E ALA* 3.0 28.8 + - - +
29E PHE* 3.7 33.0 - - + -
48E LEU* 4.1 13.0 - - + -
3H GLN* 4.8 0.7 - - - +
4H SER 3.6 25.1 - - - +
5H GLN* 4.3 11.9 - - - +
6H ILE* 3.9 39.9 - - + +
77H MET* 4.8 6.3 - - + +
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Residues in contact with LEU 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ASP 3.1 14.6 + - - +
17E ALA* 3.3 9.1 + - - +
19E LEU* 1.3 77.3 - - - +
21E SER* 1.3 61.6 + - - +
23E ALA* 3.3 6.1 + - + +
24E LYS* 3.1 49.8 + - - +
5H GLN* 5.5 0.8 + - - -
70H ASP* 3.7 26.5 - - + +
73H LEU* 4.6 13.9 - - + -
74H LEU* 4.3 29.2 - - + -
77H MET* 5.5 2.5 - - - -
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Residues in contact with SER 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ALA 3.1 12.7 + - - -
18E ILE* 3.7 9.0 - - - -
20E LEU* 1.3 73.3 - - - +
22E LYS* 1.3 60.0 + - - +
24E LYS* 3.3 11.8 + - - +
25E LYS* 3.0 41.7 + - - +
65E LEU* 2.7 37.4 + - - -
66E ASP* 4.9 0.2 - - - +
67E LEU* 5.3 3.1 - - - -
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Residues in contact with LYS 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E ILE* 2.9 18.8 + - + +
19E LEU* 3.7 12.7 - - + +
21E SER* 1.3 77.2 + - - +
23E ALA* 1.3 56.1 + - - +
25E LYS 3.4 1.0 + - - -
26E ASP 2.9 22.9 + - - -
27E LEU* 3.0 41.0 + - + +
28E SER 3.8 1.6 - - - -
29E PHE* 3.5 62.1 - - + +
32E ILE* 3.6 11.9 - - + -
65E LEU* 3.7 17.6 - - + +
114G GLU* 4.4 3.0 + - - -
2H ILE 4.1 9.1 + - - -
3H GLN* 2.9 30.1 + - - +
4H SER 5.2 1.6 - - - +
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Residues in contact with ALA 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E LEU 3.0 17.6 + - - +
20E LEU* 3.7 5.8 - - - +
21E SER 3.3 0.4 - - - -
22E LYS* 1.3 75.0 - - - +
24E LYS* 1.3 63.9 + - - +
26E ASP* 3.0 15.9 + - - +
3H GLN* 3.5 30.3 + - + +
73H LEU* 4.0 28.4 - - + +
77H MET* 4.1 17.5 - - - -
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Residues in contact with LYS 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 3.1 38.8 + - - +
21E SER* 3.3 11.0 + - - +
23E ALA* 1.3 75.8 - - - +
25E LYS* 1.3 61.7 + - + +
26E ASP* 3.6 1.2 + - - +
70H ASP* 3.5 32.4 + - - -
73H LEU* 3.8 17.3 - - + -
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Residues in contact with LYS 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E SER* 3.0 33.1 + - - +
22E LYS 4.0 0.4 - - - +
24E LYS* 1.3 77.0 - - + +
26E ASP* 1.3 70.2 + - - +
27E LEU* 2.9 35.5 - - + +
63E ALA 5.7 0.4 + - - -
64E LYS 3.3 26.0 + - - +
65E LEU* 3.9 9.6 - - - -
66E ASP* 4.1 13.2 - - - +
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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) + - + + + + + -
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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