Contacts of the helix formed by residues 21 - 32 (chain A) in PDB entry 4O6M
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 LEU 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.4 20.6 - - + +
12A TYR* 3.3 22.8 + - + +
14A GLU* 3.1 24.4 + - + +
16A LEU* 3.8 36.6 - - + -
20A THR* 1.3 73.4 - - - +
22A ARG* 1.3 60.9 + - - +
24A ARG* 3.7 6.4 - - - +
25A ILE* 3.1 25.3 + - - +
57A VAL 5.2 1.3 - - - +
58A LEU* 4.3 16.3 - - + +
118A LEU* 3.9 30.1 - - + -
123A LEU* 4.3 19.3 - - + -
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Residues in contact with ARG 22 (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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8A ASN* 3.5 12.5 + - - +
12A TYR* 2.9 31.5 + - + +
13A GLY* 5.5 0.9 - - - -
20A THR* 3.6 7.0 - - - +
21A LEU* 1.3 75.5 - - - +
23A GLU* 1.3 61.2 + - + +
25A ILE* 3.3 8.8 - - - +
26A GLU* 3.0 36.0 + - - +
38A PHE* 3.2 67.9 - - + +
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Residues in contact with GLU 23 (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 GLY 4.9 0.2 - - - +
19A LEU* 3.6 26.9 - - + +
20A THR* 3.0 46.1 + - - +
22A ARG* 1.3 78.0 - - + +
24A ARG* 1.3 57.9 + - - +
26A GLU* 3.5 11.0 + - - +
27A LYS* 2.9 45.0 + - - +
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Residues in contact with ARG 24 (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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16A LEU* 2.8 20.4 + - - -
17A LEU 2.8 29.1 + - - -
19A LEU* 4.0 19.9 + - + +
20A THR 2.9 15.9 + - - +
21A LEU* 3.7 19.3 - - - +
22A ARG 3.2 0.2 - - - -
23A GLU* 1.3 75.1 - - - +
25A ILE* 1.3 66.1 + - - +
27A LYS 4.0 0.2 - - - -
28A THR* 3.0 29.9 + - - +
58A LEU* 4.1 22.4 - - + -
130A LEU* 3.6 30.0 - - - +
222A ARG 5.2 0.2 + - - -
223A LEU* 2.8 38.0 + - - +
225A PHE* 3.9 23.7 - - + -
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Residues in contact with ILE 25 (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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6A VAL* 4.2 9.0 - - + -
12A TYR* 3.7 26.5 - - + +
21A LEU 3.1 15.9 + - - +
22A ARG* 3.3 12.6 - - - +
24A ARG* 1.3 75.7 - - - +
26A GLU* 1.3 67.2 + - - +
28A THR* 3.9 4.2 - - - -
29A LEU* 3.0 45.7 + - + +
38A PHE* 4.0 21.5 - - + -
53A ILE* 4.0 17.9 - - + -
57A VAL* 3.8 30.7 - - + +
58A LEU* 5.9 0.6 - - - +
59A ILE* 4.1 14.6 - - + +
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Residues in contact with GLU 26 (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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22A ARG* 3.0 24.9 + - - +
23A GLU* 3.6 11.6 - - - +
25A ILE* 1.3 82.3 - - - +
27A LYS* 1.3 61.5 + - + +
29A LEU 3.3 0.2 + - - -
30A GLN* 2.9 59.3 + - - +
36A VAL* 3.8 22.9 - - + +
38A PHE* 3.7 21.9 - - + -
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Residues in contact with LYS 27 (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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19A LEU* 4.7 12.6 - - + -
23A GLU* 2.9 29.5 + - - +
26A GLU* 1.3 80.2 + - + +
28A THR* 1.3 61.6 + - - +
30A GLN* 3.7 16.9 + - - +
31A ARG* 2.9 35.7 + - + +
224A LYS 5.3 1.6 - - - -
225A PHE* 3.6 48.7 + - + +
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Residues in contact with THR 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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24A ARG 3.0 19.5 + - - -
25A ILE* 3.9 5.8 - - - -
27A LYS* 1.3 78.5 - - - +
29A LEU* 1.3 63.7 + - + +
31A ARG* 3.4 6.6 + - - +
32A ALA* 3.1 21.0 + - - +
59A ILE* 3.9 42.5 + - + +
61A GLU 4.0 13.7 - - - +
62A ARG* 5.6 4.7 - - - +
64A LEU* 5.6 7.2 - - + -
225A PHE* 3.6 18.7 - - - -
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Residues in contact with LEU 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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4A ALA* 3.9 12.3 - - + -
6A VAL* 3.9 22.4 - - + -
25A ILE* 3.0 40.4 + - + +
26A GLU 3.9 2.5 - - - +
28A THR* 1.3 74.3 - - - +
30A GLN* 1.3 63.2 - - - +
32A ALA* 3.2 5.3 + - + +
33A GLY 3.2 5.0 + - - -
34A PHE* 2.9 35.0 + - + +
36A VAL* 4.0 12.3 - - + -
51A LEU* 3.7 24.9 - - + -
53A ILE* 4.0 7.2 - - + -
59A ILE* 3.9 21.3 - - + -
64A LEU* 4.6 11.0 - - + -
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Residues in contact with GLN 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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26A GLU* 2.9 46.4 + - - +
27A LYS* 3.7 20.2 + - - +
28A THR 3.3 0.2 - - - -
29A LEU* 1.3 73.9 - - - +
31A ARG* 1.3 57.0 + - + +
33A GLY* 2.7 25.3 + - - -
34A PHE 3.4 17.4 + - - +
35A ASP* 5.5 0.7 - - - -
36A VAL* 4.2 10.6 - - + +
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Residues in contact with ARG 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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27A LYS* 2.9 23.8 + - + +
28A THR* 3.5 8.3 - - - +
30A GLN* 1.3 75.7 - - - +
32A ALA* 1.3 57.4 + - - +
33A GLY* 3.3 3.8 + - - -
62A ARG 5.1 10.8 - - - +
225A PHE* 3.4 43.6 + - + +
227A GLU* 2.9 43.6 + - - +
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Residues in contact with ALA 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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2A ARG* 4.0 9.7 + - - -
28A THR 3.1 13.6 + - - +
29A LEU* 3.5 12.1 - - + +
30A GLN 3.0 0.8 - - - -
31A ARG* 1.3 75.7 - - - +
33A GLY* 1.3 57.8 + - - +
34A PHE* 3.6 21.0 - - + -
64A LEU* 4.0 40.4 - - + +
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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