Contacts of the helix formed by residues 6 - 21 (chain F) in PDB entry 5O6I
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 ASN 6 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C C 4.7 17.7 + - - +
20C G 4.5 15.0 - - - +
5F GLU* 1.3 77.8 - - - +
7F VAL* 1.3 58.9 + - - -
8F SER* 3.1 4.9 + - - +
9F GLY* 3.3 4.9 + - - +
10F ILE* 3.1 35.0 + - - +
58F PHE* 4.1 21.0 - - - -
104F ARG* 4.3 17.0 - - - +
183F ASN* 4.6 23.5 + - - +
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Residues in contact with VAL 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F GLU* 2.5 37.4 + - + +
6F ASN* 1.3 74.7 + - - +
8F SER* 1.3 55.3 + - - +
10F ILE* 4.3 5.3 - - + +
11F SER* 2.6 37.5 + - - +
58F PHE* 4.6 14.4 - - + -
59F LEU* 3.7 25.6 - - + -
62F GLU* 4.4 26.2 - - + +
63F LEU* 4.7 6.3 - - + -
90F TYR* 5.0 4.7 - - - +
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Residues in contact with SER 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F GLU* 3.5 27.8 + - - +
6F ASN 3.8 3.4 + - - +
7F VAL* 1.3 80.7 - - - +
9F GLY* 1.3 60.9 + - - +
11F SER* 3.4 6.5 + - - -
12F ALA* 2.9 30.0 + - - +
90F TYR* 5.3 1.6 - - - -
94F MET* 4.2 0.9 - - - +
102F ASN* 5.0 3.4 + - - -
104F ARG* 4.2 8.3 - - - +
105F GLU* 3.5 32.7 - - - +
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Residues in contact with GLY 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ASN* 3.3 9.1 + - - +
8F SER* 1.3 80.5 + - - +
10F ILE* 1.3 59.2 + - - +
12F ALA* 3.4 1.5 + - - -
13F TYR* 3.0 24.6 + - - +
104F ARG* 4.5 15.7 - - - +
105F GLU* 5.0 1.1 - - - -
108F ALA* 3.2 20.6 - - - +
183F ASN* 3.9 17.0 - - - -
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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
----------------------------------------------------------
6F ASN* 3.1 23.6 + - - +
7F VAL* 4.3 5.4 - - + +
9F GLY* 1.3 73.3 - - - +
11F SER* 1.3 60.7 + - - +
13F TYR* 3.7 5.0 - - - +
14F LEU* 2.9 38.3 + - + +
55F LEU* 4.0 48.9 - - + +
58F PHE* 3.8 32.8 - - + -
59F LEU* 5.0 4.9 - - + -
183F ASN* 4.3 21.5 - - + +
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Residues in contact with SER 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL 2.6 21.6 + - - -
8F SER* 3.6 6.1 - - - -
10F ILE* 1.3 78.4 - - - +
12F ALA* 1.3 56.5 + - - +
14F LEU* 3.4 0.4 + - - -
15F LEU* 2.9 30.1 + - - +
59F LEU* 3.4 16.7 - - - +
90F TYR* 2.6 33.8 + - - -
91F PHE* 3.6 10.5 - - - -
94F MET* 3.8 17.9 - - - -
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Residues in contact with ALA 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F SER 2.9 17.8 + - - +
9F GLY 3.4 4.5 + - - +
11F SER* 1.3 75.8 - - - +
13F TYR* 1.3 63.1 + - - +
15F LEU* 3.3 5.5 + - - +
16F GLY 3.0 17.5 + - - -
94F MET* 3.5 12.3 - - + +
101F CYS* 5.7 0.7 - - - -
105F GLU* 3.3 42.0 - - + +
108F ALA* 3.8 2.0 - - + -
109F PHE* 3.4 17.1 - - + +
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Residues in contact with TYR 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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9F GLY 3.0 17.7 + - - +
10F ILE* 3.7 7.9 - - - +
11F SER 3.3 0.2 - - - -
12F ALA* 1.3 77.4 - - - +
14F LEU* 1.3 65.4 + - + +
16F GLY* 3.1 11.4 + - - -
17F LEU* 3.2 34.3 + - + +
52F PHE* 4.1 15.7 - + - -
55F LEU* 3.7 32.3 - - + -
108F ALA* 3.3 16.7 - - + +
111F LYS* 3.8 29.7 + - + -
112F GLY* 3.4 32.6 - - - -
115F VAL* 3.9 16.2 - - + +
183F ASN* 4.4 10.8 - - - +
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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
----------------------------------------------------------
10F ILE* 2.9 27.0 + - + +
11F SER 3.8 3.1 - - - +
13F TYR* 1.3 80.5 - - + +
15F LEU* 1.3 58.9 + - - +
17F LEU* 3.1 15.5 + - + +
18F ILE* 2.8 36.8 + - + +
40F ILE* 4.2 12.5 - - + +
52F PHE 4.3 10.1 - - - +
55F LEU* 4.0 24.2 - - + +
56F MET* 3.9 36.1 - - + +
59F LEU* 3.8 26.2 - - + -
91F PHE* 4.0 9.2 - - + -
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Residues in contact with LEU 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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11F SER 2.9 17.6 + - - +
12F ALA 3.6 5.6 - - - +
13F TYR 3.2 0.2 - - - -
14F LEU* 1.3 75.8 - - - +
16F GLY* 1.3 56.3 + - - +
18F ILE* 4.2 8.3 - - + -
19F ILE* 2.9 45.8 + - + +
24F LEU* 4.8 3.8 - - + -
91F PHE* 3.7 37.2 - - + +
94F MET* 3.8 31.2 - - + +
95F LEU* 4.2 20.2 - - + +
98F ILE* 4.5 7.6 - - + -
101F CYS* 6.3 0.7 - - - -
109F PHE* 4.0 19.7 - - + -
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Residues in contact with GLY 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ALA 3.0 11.1 + - - -
13F TYR 3.1 4.6 + - - -
15F LEU* 1.3 77.4 - - - +
17F LEU* 1.3 55.9 + - - +
20F GLY* 3.0 24.6 + - - -
109F PHE* 3.6 22.4 - - - -
112F GLY 3.7 7.1 - - - +
113F LEU* 3.7 26.3 - - - +
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Residues in contact with LEU 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 TYR* 3.2 29.9 + - + +
14F LEU* 3.1 13.5 + - + +
16F GLY* 1.3 73.0 - - - +
18F ILE* 1.3 59.7 + - - +
21F ASP* 2.6 34.7 + - + +
22F GLY 3.5 2.6 + - - -
40F ILE* 3.9 23.7 - - + +
42F GLN* 5.9 0.4 - - - +
52F PHE* 3.5 40.2 - - + -
112F GLY* 3.2 23.1 - - - +
115F VAL* 3.7 26.0 - - + -
116F ALA* 4.2 9.2 - - + +
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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 2.8 24.8 + - - +
15F LEU* 3.8 5.2 - - + +
17F LEU* 1.3 72.1 - - - +
19F ILE* 1.3 63.0 + - + +
22F GLY 2.8 33.8 + - - -
23F GLY* 3.3 26.8 + - - +
24F LEU* 3.8 20.2 - - + -
38F VAL* 3.6 24.5 - - + -
39F VAL 3.8 9.2 - - - +
40F ILE* 3.6 18.6 - - + -
56F MET* 4.4 4.7 - - + -
91F PHE* 3.7 33.9 - - + -
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Residues in contact with ILE 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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15F LEU* 2.9 39.3 + - + +
16F GLY 4.3 1.8 - - - +
18F ILE* 1.3 74.9 - - + +
20F GLY* 1.3 63.5 + - - +
22F GLY 4.5 3.7 - - - +
23F GLY* 5.6 2.9 - - - -
24F LEU* 4.9 10.8 - - + +
95F LEU* 3.9 35.7 - - + -
109F PHE* 4.6 7.9 - - + -
113F LEU* 4.7 4.7 - - + -
117F GLU* 4.5 0.5 - - - +
129F ASN* 4.7 5.0 + - - +
131F ASN* 6.1 0.9 - - - +
134F LEU* 3.6 32.3 - - + -
202F MN 3.9 6.8 + - - -
15G G 5.1 0.3 - - - +
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Residues in contact with GLY 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F GLY 3.0 19.0 + - - -
18F ILE 3.1 0.2 - - - -
19F ILE* 1.3 78.2 - - - +
21F ASP* 1.3 64.0 + - - +
113F LEU* 4.4 2.7 - - - +
116F ALA* 3.6 11.7 - - - -
117F GLU* 3.6 16.8 - - - -
202F MN 2.4 27.9 + - - -
15G G 2.9 7.4 + - - +
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Residues in contact with ASP 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F LEU* 2.6 17.5 + - + +
20F GLY* 1.3 72.8 - - - -
22F GLY* 1.3 54.8 + - - +
40F ILE* 4.5 4.0 - - + -
41F THR* 2.5 48.1 + - - +
42F GLN* 2.8 18.0 - - - +
115F VAL 4.8 0.2 - - - -
116F ALA* 3.2 20.3 - - + +
117F GLU* 3.6 2.1 - - - +
201F MN 2.6 33.7 + - - -
14G A 3.6 14.3 - - - +
15G G 3.4 12.5 - - - +
16I C 3.3 7.1 + - - -
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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