Contacts of the helix formed by residues 8 - 26 (chain F) in PDB entry 2IUO
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5F GLN* 6.2 0.2 - - - -
7F ASN* 1.3 75.1 + - - +
9F ASN* 1.3 70.8 + - - +
10F ILE 3.1 0.5 + - - -
11F ARG* 3.3 8.2 + - - +
12F LEU* 2.9 47.6 + - + +
50F GLN* 6.1 0.4 - - - +
80F LEU* 3.6 40.7 - - + +
82F GLY* 2.9 30.5 + - - +
83F CYS 4.4 1.0 - - - -
84F ILE 2.9 21.4 + - - -
85F ASP* 2.9 32.8 + - - +
85G ASP* 4.2 22.2 + - - -
90G THR* 4.9 12.2 - - - +
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Residues in contact with ASN 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ASN* 2.9 23.4 + - - +
8F ARG* 1.3 91.6 + - - +
10F ILE* 1.3 63.4 + - + +
12F LEU* 3.7 12.6 - - - +
13F ASP* 3.0 36.5 + - - +
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Residues in contact with ILE 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F GLN* 3.3 28.3 - - - +
7F ASN* 3.3 7.6 + - - +
8F ARG 3.1 1.4 + - - -
9F ASN* 1.3 79.3 - - + +
11F ARG* 1.3 62.5 + - + +
13F ASP* 3.7 7.2 - - - +
14F LEU* 3.2 20.8 + - - +
74F LEU* 4.0 31.7 - - + +
16G ASP* 3.9 35.0 - - + +
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Residues in contact with ARG 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F GLN* 4.4 20.6 - - + +
7F ASN 4.6 0.8 + - - +
8F ARG* 3.3 7.8 + - - +
10F ILE* 1.3 78.1 - - + +
12F LEU* 1.3 63.3 + - + +
14F LEU* 3.4 10.6 + - - +
15F ALA* 2.9 25.8 + - - +
46F ALA 2.8 21.6 + - - -
47F LEU 4.8 1.5 + - - +
49F GLY* 3.8 26.8 - - - +
51F GLN 2.8 24.9 + - - -
74F LEU* 2.9 44.9 + - + -
75F LEU* 3.9 22.8 + - - +
77F MET* 3.0 23.4 + - - +
79F PRO* 4.1 12.1 - - + +
80F LEU 6.3 0.2 - - - +
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Residues in contact with LEU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 4.8 11.4 - - + +
7D ASN* 6.4 1.3 - - + -
8F ARG* 2.9 54.6 + - + +
9F ASN* 4.1 12.1 - - - +
10F ILE 3.3 0.2 - - - -
11F ARG* 1.3 74.8 - - + +
13F ASP* 1.3 69.0 + - - +
15F ALA* 3.1 5.5 + - - +
16F ASP* 3.1 26.4 + - - +
48F LEU 3.4 24.9 - - - +
49F GLY* 4.7 1.8 - - - +
50F GLN* 3.9 13.9 - - - +
82F GLY 4.5 5.8 - - - +
83F CYS* 5.3 8.5 - - + +
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Residues in contact with ASP 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ASN* 5.2 2.9 + - - -
9F ASN* 3.0 28.2 + - - +
10F ILE* 3.7 7.8 - - - +
12F LEU* 1.3 77.0 - - - +
14F LEU* 1.3 63.7 + - - +
16F ASP* 3.1 16.6 + - - +
17F ALA* 3.1 20.7 + - - +
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Residues in contact with LEU 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ILE 3.2 11.5 + - - +
11F ARG* 3.5 16.8 - - - +
13F ASP* 1.3 76.6 - - - +
15F ALA* 1.3 64.7 + - - +
17F ALA* 3.2 12.1 + - + +
18F ILE* 2.9 36.5 + - + +
47F LEU 5.6 0.4 - - - +
67F LEU* 5.0 2.9 - - + -
71F SER* 3.5 48.2 - - - +
74F LEU* 4.0 23.6 - - + -
75F LEU* 3.9 22.4 - - + -
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Residues in contact with ALA 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 3.8 26.7 - - + -
11F ARG 2.9 13.8 + - - +
12F LEU* 3.1 14.3 + - - +
14F LEU* 1.3 76.3 - - - +
16F ASP* 1.3 55.7 + - - +
18F ILE* 3.3 4.7 + - - +
19F LEU* 2.9 34.7 + - - +
47F LEU 3.5 24.4 + - - +
48F LEU* 3.9 7.8 - - + +
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Residues in contact with ASP 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GLN* 5.2 4.2 + - - +
6D ILE* 4.2 11.8 - - - +
7D ASN* 2.8 45.6 + - - +
10D ILE* 4.0 25.3 - - + +
12F LEU* 3.1 16.5 + - - +
13F ASP* 3.1 15.0 + - - +
15F ALA* 1.3 72.9 - - - +
17F ALA* 1.3 66.1 + - - +
19F LEU* 3.3 9.3 + - - +
20F LEU* 3.0 23.7 + - - +
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Residues in contact with ALA 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ASP 3.1 12.0 + - - +
14F LEU* 3.5 19.3 - - + +
16F ASP* 1.3 74.5 - - - +
18F ILE* 1.3 63.6 + - + +
20F LEU* 3.3 8.9 + - - +
21F SER* 3.0 23.3 + - - -
67F LEU* 5.5 4.5 - - + -
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Residues in contact with ILE 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LEU* 2.9 34.0 + - + +
15F ALA* 3.6 7.2 - - - +
17F ALA* 1.3 78.4 - - - +
19F LEU* 1.3 65.2 + - + +
21F SER* 3.3 6.8 + - - -
22F LYS* 2.8 30.1 + - + +
47F LEU* 4.0 40.4 - - + +
65F LEU* 3.8 21.3 - - + +
67F LEU* 3.9 34.1 - - + -
75F LEU* 4.0 17.0 - - + -
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Residues in contact with LEU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLN* 4.6 0.7 - - - +
4D SER 3.4 25.8 - - - +
5D GLN* 4.2 12.6 - - - +
6D ILE* 3.9 39.3 - - + +
77D MET* 4.4 6.4 - - + +
15F ALA 2.9 20.0 + - - +
16F ASP* 3.3 9.8 + - - +
18F ILE* 1.3 77.6 - - + +
20F LEU* 1.3 61.0 + - - +
22F LYS* 3.8 10.6 - - + +
23F ALA* 2.9 29.5 + - - +
29F PHE* 3.8 31.2 - - + -
48F LEU* 4.0 12.3 - - + -
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Residues in contact with LEU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GLN* 5.4 1.2 + - - -
70D ASP* 4.5 16.2 - - + +
73D LEU* 4.8 11.0 - - + -
74D LEU* 4.3 26.7 - - + -
77D MET* 5.6 2.2 - - - -
16F ASP 3.0 17.3 + - - +
17F ALA* 3.7 7.9 - - - +
19F LEU* 1.3 77.0 - - - +
21F SER* 1.3 51.6 + - - +
23F ALA* 3.1 6.1 + - + +
24F LYS* 2.8 65.4 + - + +
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Residues in contact with SER 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F ALA 3.0 16.5 + - - -
18F ILE* 3.7 6.5 - - - -
20F LEU* 1.3 74.8 - - - +
22F LYS* 1.3 58.8 + - - +
24F LYS* 3.3 8.6 + - - +
25F LYS* 2.8 55.4 + - - +
65F LEU* 2.7 35.8 + - - -
67F LEU* 5.1 3.1 - - - -
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Residues in contact with LYS 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLU* 4.3 1.0 + - - -
2D ILE 3.9 8.5 + - - -
3D GLN* 2.8 31.5 + - - +
4D SER 5.1 0.8 - - - +
18F ILE* 2.8 19.3 + - + +
19F LEU* 3.8 12.3 - - + +
21F SER* 1.3 77.8 + - - +
23F ALA* 1.3 56.5 + - - +
25F LYS 3.3 0.7 + - - -
26F ASP* 2.9 23.0 + - - -
27F LEU* 3.1 41.7 + - + +
28F SER* 3.7 3.3 - - - +
29F PHE* 3.5 63.4 - - + +
32F ILE* 3.5 12.8 - - + -
65F LEU* 3.7 16.9 - - + +
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Residues in contact with ALA 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLN* 3.5 33.1 + - + +
73D LEU* 3.9 27.4 - - + +
77D MET* 4.3 14.8 - - + -
19F LEU 2.9 19.5 + - - +
20F LEU* 3.1 6.5 + - + +
22F LYS* 1.3 71.3 - - - +
24F LYS* 1.3 67.3 + - - +
26F ASP* 3.1 14.2 + - - +
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Residues in contact with LYS 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ASP* 3.4 32.6 + - - +
73D LEU* 3.9 17.9 - - + -
20F LEU* 2.8 40.6 + - + +
21F SER* 3.6 8.7 - - - +
23F ALA* 1.3 80.6 - - - +
25F LYS* 1.3 66.9 + - + +
26F ASP* 3.5 1.9 + - - +
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Residues in contact with LYS 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F SER* 2.8 44.7 + - - +
24F LYS* 1.3 82.7 - - + +
26F ASP* 1.3 69.3 + - - +
27F LEU* 3.2 30.2 - - + +
64F LYS 3.5 18.4 - - - +
65F LEU* 3.8 5.8 + - - -
66F ASP* 3.1 37.0 + - - +
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Residues in contact with ASP 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 2.8 47.8 + - - +
3D GLN* 3.7 4.4 + - - +
22F LYS 2.9 7.5 + - - -
23F ALA 3.1 12.5 + - - +
24F LYS 4.8 1.8 - - - +
25F LYS* 1.3 79.7 - - - +
27F LEU* 1.3 61.1 + - - +
31F GLU* 3.9 4.7 - - - +
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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
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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