Contacts of the helix formed by residues 16 - 29 (chain F) in PDB entry 1O94
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 PRO 16 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LEU* 3.7 5.8 - - + +
15F ARG* 1.3 92.3 - - + +
17F VAL* 1.3 62.5 + - - +
18F SER 3.1 1.4 + - - -
19F LEU* 3.3 20.0 + - + +
20F GLU* 3.5 20.0 + - - +
162F PRO* 5.7 0.3 - - - +
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Residues in contact with VAL 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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8F GLU* 4.6 4.9 - - + -
15F ARG* 3.0 31.4 + - + +
16F PRO* 1.3 81.2 - - - +
18F SER* 1.3 65.9 + - - +
20F GLU* 3.1 28.2 + - + +
21F LEU* 3.0 29.7 + - + +
94F PRO* 3.7 39.0 - - + -
155F ILE* 4.9 2.0 - - + +
156F ARG 5.4 0.4 - - - -
157F PRO* 4.1 23.8 - - + -
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Residues in contact with SER 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F VAL* 4.3 2.5 - - - +
7F ALA* 3.9 21.1 - - - +
8F GLU* 2.9 28.3 + - - +
14F LEU* 3.4 16.7 - - - +
15F ARG 2.9 16.1 + - - -
17F VAL* 1.3 80.3 - - - +
19F LEU* 1.3 58.2 + - - +
21F LEU* 3.2 14.5 + - - +
22F ILE* 3.1 29.2 + - - +
52F LEU* 4.5 5.2 - - - -
94F PRO* 6.3 0.2 - - - -
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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
----------------------------------------------------------
14F LEU* 4.5 15.0 - - + -
16F PRO* 3.3 12.4 + - + +
18F SER* 1.3 74.7 - - - +
20F GLU* 1.3 65.1 + - - +
22F ILE* 3.4 24.4 + - + +
23F GLY 3.0 17.2 + - - -
51F ALA 4.0 15.0 - - - +
52F LEU* 4.5 1.8 - - + -
54F VAL* 4.0 22.7 - - + -
162F PRO* 3.4 28.6 - - + +
163F LEU 4.4 4.7 + - - +
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Residues in contact with GLU 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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16F PRO* 3.5 15.4 + - - +
17F VAL* 3.1 27.3 + - + +
19F LEU* 1.3 76.8 - - - +
21F LEU* 1.3 59.4 + - + +
23F GLY* 3.1 2.8 + - - -
24F ALA* 2.8 27.5 + - - +
155F ILE* 6.0 2.2 - - + +
156F ARG 4.6 0.7 - - - +
157F PRO* 3.5 10.3 - - - +
158F SER* 2.7 42.3 + - - -
159F VAL 4.3 1.2 + - - -
160F PHE* 3.4 30.8 + - + +
162F PRO* 4.4 16.4 - - + -
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Residues in contact with LEU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F VAL* 3.6 20.1 - - + +
6F ILE 3.6 13.5 - - - +
17F VAL* 3.0 23.4 + - + +
18F SER* 3.5 9.4 - - - +
19F LEU 3.2 0.2 - - - -
20F GLU* 1.3 74.8 - - - +
22F ILE* 1.3 55.2 + - - +
24F ALA* 3.3 6.4 + - - +
25F ALA* 2.8 35.5 + - - +
92F LEU* 3.9 11.6 - - + +
93F LEU 3.8 9.9 - - - +
94F PRO* 3.5 36.3 - - + -
155F ILE* 3.4 43.3 - - + -
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Residues in contact with ILE 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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5F VAL* 4.5 5.2 - - + -
18F SER* 3.1 18.1 + - - +
19F LEU* 3.6 30.5 - - + +
20F GLU 3.3 0.2 - - - -
21F LEU* 1.3 74.5 - - - +
23F GLY* 1.3 63.7 + - - +
25F ALA* 3.3 5.9 + - - +
26F ASN* 3.0 41.6 + - - +
36F VAL* 5.1 1.3 - - + -
38F VAL* 3.8 24.9 - - + -
52F LEU* 4.3 11.7 - - + -
54F VAL* 4.1 3.8 - - + -
55F ASN 3.6 23.8 - - - +
56F GLY 4.1 1.3 - - - +
57F VAL* 3.7 24.7 - - + -
163F LEU* 4.9 4.7 - - + +
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Residues in contact with GLY 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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19F LEU 3.0 12.9 + - - -
20F GLU 3.1 4.2 + - - -
22F ILE* 1.3 77.8 - - - +
24F ALA* 1.3 63.7 + - - +
26F ASN* 3.3 1.9 + - - +
27F GLY* 3.0 20.4 + - - -
160F PHE* 5.0 0.9 - - - -
161F LYS 3.5 22.2 - - - -
163F LEU* 4.3 19.4 - - - +
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Residues in contact with ALA 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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20F GLU 2.8 15.4 + - - +
21F LEU* 3.3 11.6 + - - +
23F GLY* 1.3 73.4 - - - +
25F ALA* 1.3 55.6 + - - +
27F GLY* 3.3 2.3 + - - -
28F LEU* 2.9 31.4 + - - +
92F LEU* 4.0 14.6 - - + -
121F VAL* 5.3 4.6 - - + +
155F ILE* 5.1 7.2 - - + -
160F PHE* 3.7 40.7 - - + +
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Residues in contact with ALA 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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3F ILE* 3.7 30.2 - - + +
5F VAL* 3.8 16.4 - - + -
21F LEU 2.8 20.0 + - - +
22F ILE 3.7 3.8 - - - +
24F ALA* 1.3 72.8 - - - +
26F ASN* 1.3 62.4 + - - +
28F LEU* 3.3 3.2 + - - -
29F LYS* 3.1 27.4 + - - +
36F VAL* 3.9 14.8 - - + +
92F LEU* 3.8 8.7 - - + +
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Residues in contact with ASN 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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22F ILE* 3.0 28.1 + - - +
23F GLY 3.9 2.9 - - - +
25F ALA* 1.3 77.1 - - - +
27F GLY* 1.3 60.9 + - - +
29F LYS* 3.4 42.6 + - - +
36F VAL* 3.9 7.1 - - - +
56F GLY* 2.9 44.9 + - - +
58F ASP* 5.2 1.4 + - - -
163F LEU* 3.9 18.9 - - + +
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Residues in contact with GLY 27 (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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23F GLY 3.0 13.9 + - - -
24F ALA* 3.7 3.4 - - - -
26F ASN* 1.3 76.7 - - - +
28F LEU* 1.3 59.6 + - - +
29F LYS 3.5 2.6 - - - +
163F LEU* 6.2 0.2 - - - +
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Residues in contact with LEU 28 (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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3F ILE* 4.4 7.6 - - + -
24F ALA 2.9 17.3 + - - +
25F ALA 3.3 4.0 + - - +
26F ASN 3.3 0.2 - - - -
27F GLY* 1.3 79.2 - - - +
29F LYS* 1.3 66.2 + - - +
30F LYS* 3.5 2.3 + - - -
90F VAL* 4.1 25.4 - - + -
92F LEU* 4.9 9.2 - - + -
121F VAL* 3.8 47.6 - - + +
122F GLU* 3.9 13.7 - - - +
123F TYR* 3.6 20.7 - - + +
128F LEU* 3.8 26.5 - - + -
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Residues in contact with LYS 29 (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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3F ILE* 3.8 18.6 - - + +
25F ALA 3.1 19.6 + - - +
26F ASN* 3.4 38.2 - - - +
27F GLY 3.5 4.2 - - - +
28F LEU* 1.3 79.0 - - - +
30F LYS* 1.3 65.0 + - - +
31F SER* 3.5 15.3 + - - +
32F GLY* 3.4 21.2 + - - -
34F ASP* 3.1 43.1 + - + +
35F LYS 6.1 0.2 - - - +
36F VAL* 4.2 10.1 - - + -
58F ASP* 5.0 2.9 + - - -
123F TYR* 5.3 1.1 - - - -
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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
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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