Contacts of the helix formed by residues 27 - 39 (chain A) in PDB entry 1O7F
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 SER 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LYS* 4.8 0.7 + - - -
25A GLU 3.7 3.4 + - - -
26A ARG* 1.3 75.5 - - - +
28A SER* 1.3 54.1 + - - +
29A GLU* 2.6 53.3 + - - +
30A ASP* 2.7 39.3 + - - +
31A VAL* 3.1 9.2 + - - +
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Residues in contact with SER 28 (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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26A ARG 3.8 1.6 + - - -
27A SER* 1.3 69.6 - - - +
29A GLU* 1.3 68.5 + - - +
31A VAL* 3.5 14.3 - - - +
32A ASP* 2.4 35.4 + - - +
53A ARG* 4.0 18.9 + - - +
57A LEU* 6.0 0.2 - - - -
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Residues in contact with GLU 29 (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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27A SER* 2.6 30.6 + - - +
28A SER* 1.3 88.2 + - - +
30A ASP* 1.3 63.3 + - - +
32A ASP* 3.2 20.9 + - - +
33A ILE* 3.5 13.8 + - + +
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Residues in contact with ASP 30 (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 CYS* 3.5 31.6 - - + -
21A LYS* 2.7 35.0 + - - -
26A ARG* 3.5 9.7 - - + -
27A SER* 2.7 43.2 + - - +
29A GLU* 1.3 69.6 - - - +
31A VAL* 1.3 57.5 + - - +
33A ILE* 2.7 29.8 + - - +
34A ILE* 3.0 16.9 + - + +
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Residues in contact with VAL 31 (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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26A ARG* 4.7 4.7 - - + +
27A SER 3.6 11.7 - - - +
28A SER* 3.5 9.9 - - - +
30A ASP* 1.3 76.2 - - - +
32A ASP* 1.3 57.3 + - - +
34A ILE* 3.9 9.4 - - + +
35A PHE* 2.9 31.5 + - - +
53A ARG* 3.0 50.9 - - - +
56A CYS* 3.9 18.5 - - + +
57A LEU* 3.4 35.9 - - + -
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Residues in contact with ASP 32 (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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28A SER* 2.4 25.0 + - - +
29A GLU* 3.3 12.3 - - - +
30A ASP 3.0 0.6 - - - -
31A VAL* 1.3 78.1 - - - +
33A ILE* 1.3 60.3 + - + +
35A PHE* 3.5 7.1 - - - +
36A THR* 3.1 27.7 + - - -
53A ARG* 3.4 15.1 + - - +
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Residues in contact with ILE 33 (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 GLU* 4.4 13.5 - - + -
15A TRP* 3.9 30.6 - - + +
18A CYS* 4.0 20.2 - - - -
29A GLU* 3.6 16.6 - - + +
30A ASP* 2.7 13.8 + - - +
32A ASP* 1.3 72.5 - - + +
34A ILE* 1.3 62.6 + - - +
36A THR* 3.7 7.9 + - - -
37A ARG* 3.5 13.9 + - - +
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Residues in contact with ILE 34 (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 TRP* 4.0 15.3 - - + +
18A CYS* 3.4 38.8 - - + +
19A LEU* 3.5 32.1 - - + -
26A ARG* 4.5 6.3 - - - -
30A ASP 3.0 12.9 + - - +
31A VAL* 3.9 6.7 - - - +
33A ILE* 1.3 73.2 - - - +
35A PHE* 1.3 66.4 + - - +
37A ARG* 3.1 4.3 + - - +
38A LEU* 2.9 50.7 + - + +
56A CYS* 3.5 27.8 - - + +
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Residues in contact with PHE 35 (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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31A VAL* 2.9 19.8 + - + +
32A ASP* 3.5 8.7 - - - +
34A ILE* 1.3 77.2 - - - +
36A THR* 1.3 60.2 + - - +
38A LEU* 3.1 2.2 + - - +
39A LYS* 2.8 49.9 + - + +
49A PRO* 3.8 27.4 - - + -
52A LEU* 3.6 37.1 - - + +
53A ARG* 4.1 20.2 - - + -
56A CYS* 3.4 17.2 - - - -
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Residues in contact with THR 36 (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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32A ASP 3.1 15.7 + - - -
33A ILE* 3.8 8.1 - - - -
34A ILE 3.3 0.2 - - - -
35A PHE* 1.3 80.2 - - - +
37A ARG* 1.3 60.5 + - - +
39A LYS* 2.9 50.0 + - - +
40A GLY 4.5 0.2 + - - -
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Residues in contact with ARG 37 (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 TRP* 3.5 66.5 - - + +
33A ILE 3.5 9.9 + - - +
34A ILE 3.1 9.2 + - - +
36A THR* 1.3 81.1 - - - +
38A LEU* 1.3 63.5 + - + +
40A GLY* 4.1 6.2 + - - -
41A VAL* 4.9 6.1 + - - +
84A LEU* 4.0 42.1 + - - +
85A ALA* 5.4 1.8 - - - +
134A GLU* 5.3 5.9 + - - -
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Residues in contact with LEU 38 (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 TRP* 5.5 1.8 - - + -
19A LEU* 5.4 2.5 - - + -
34A ILE* 2.9 40.9 + - + +
35A PHE 3.9 2.2 - - - +
37A ARG* 1.3 83.1 - - + +
39A LYS* 1.3 62.8 + - - +
40A GLY 2.9 7.6 + - - -
41A VAL* 2.9 14.8 + - + -
44A PHE* 3.4 25.1 - - + +
52A LEU* 4.0 13.2 - - + -
55A ILE* 4.8 2.5 - - + -
56A CYS* 3.8 17.3 - - - -
84A LEU* 4.0 26.5 - - + -
136A LEU* 3.8 38.1 - - + -
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Residues in contact with LYS 39 (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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35A PHE* 2.8 34.7 + - + +
36A THR* 2.9 46.7 + - - +
38A LEU* 1.3 72.3 - - - +
40A GLY* 1.3 61.3 + - - +
41A VAL 3.6 0.5 + - - -
44A PHE* 4.8 0.4 - - - -
45A GLU* 4.3 19.6 + - - +
52A LEU* 3.8 13.8 - - + +
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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