Contacts of the helix formed by residues 36 - 46 (chain P) in PDB entry 3CME
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 THR 36 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15010 A 3.3 23.1 - - - +
9P LEU* 5.0 0.7 - - - -
35P ILE* 1.3 90.1 - - + +
37P ARG* 1.3 60.0 + - - +
38P GLU* 3.1 10.9 + - - +
39P ASP* 2.8 44.2 + - - +
40P VAL* 3.0 20.2 - - - +
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Residues in contact with ARG 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15000 U 3.2 55.3 + - - +
15010 A 2.9 27.3 + - - +
15020 A 2.4 44.0 + - - -
8P ARG* 4.5 2.2 - - - +
9P LEU* 4.0 27.0 + - + +
12P ASP* 3.1 38.0 + - - +
13P VAL* 5.0 9.8 - - + +
36P THR* 1.3 70.6 - - - +
38P GLU* 1.3 61.7 + - - +
40P VAL* 2.8 12.1 + - + +
41P ARG* 2.8 39.5 + - - +
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Residues in contact with GLU 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15000 U 4.5 3.0 + - - +
36P THR* 3.1 9.9 + - - +
37P ARG* 1.3 78.5 - - - +
39P ASP* 1.3 63.3 + - - +
41P ARG* 2.7 50.8 + - - +
42P GLU* 3.0 32.3 + - - +
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Residues in contact with ASP 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P ASP 3.6 4.9 - - - +
34P ALA* 3.6 19.7 - - + -
35P ILE* 3.0 19.6 + - - +
36P THR* 2.8 44.7 + - - +
38P GLU* 1.3 79.3 - - - +
40P VAL* 1.3 61.0 + - - +
42P GLU* 3.5 11.0 - - - +
43P LEU* 3.3 27.5 + - - +
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Residues in contact with VAL 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P GLN* 5.0 6.1 - - + +
9P LEU* 4.1 21.5 - - + -
10P ALA* 3.8 16.2 - - + +
13P VAL* 3.7 27.6 - - + -
34P ALA* 4.8 10.3 - - + -
36P THR 3.0 19.1 - - - +
37P ARG* 2.8 13.9 + - - +
39P ASP* 1.3 75.8 - - + +
41P ARG* 1.3 65.2 + - - +
43P LEU* 3.2 5.6 + - - +
44P VAL* 2.9 27.3 + - + +
49P ILE* 3.8 19.5 - - + +
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Residues in contact with ARG 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14990 U 3.2 31.0 + - - -
15000 U 2.8 43.2 + - - -
13P VAL* 3.9 23.9 - - + +
37P ARG* 2.8 21.7 + - - +
38P GLU* 2.7 63.0 + - - +
40P VAL* 1.3 71.6 - - - +
42P GLU* 1.3 65.6 + - - +
44P VAL* 2.7 20.9 + - - +
45P ASP* 2.8 22.5 + - - +
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Residues in contact with GLU 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38P GLU* 3.0 15.5 + - - +
39P ASP* 3.5 15.5 - - - +
41P ARG* 1.3 77.2 - - - +
43P LEU* 1.3 56.9 + - + +
45P ASP* 2.7 35.0 + - - +
46P GLU* 2.9 30.9 + - + +
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Residues in contact with LEU 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P ARG* 3.7 37.0 - - - +
30P ASP* 3.7 12.6 - - + +
31P ILE* 3.5 38.8 - - + +
34P ALA* 3.9 17.3 - - + -
39P ASP 3.3 7.1 + - - +
40P VAL 3.2 9.7 + - - +
42P GLU* 1.3 79.3 - - + +
44P VAL* 1.3 58.3 + - - +
46P GLU* 3.5 11.4 + - - +
47P GLY 3.3 1.9 + - - -
48P ALA* 2.9 34.9 + - + +
49P ILE* 3.3 16.7 + - + -
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Residues in contact with VAL 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P VAL* 5.1 4.7 - - + -
14P LEU* 3.9 26.5 - - + -
40P VAL* 2.9 25.1 + - + +
41P ARG* 2.7 16.9 + - - +
43P LEU* 1.3 74.0 - - - +
45P ASP* 1.3 60.9 + - - +
46P GLU 3.0 1.3 - - - -
47P GLY* 2.6 25.8 + - - -
49P ILE* 3.6 38.8 - - + +
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Residues in contact with ASP 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P ARG* 2.8 25.6 + - - +
42P GLU* 2.7 15.0 + - - +
44P VAL* 1.3 77.8 - - - +
46P GLU* 1.3 62.3 + - + +
47P GLY* 3.2 1.2 + - - -
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Residues in contact with GLU 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P ARG* 2.6 45.7 + - - +
42P GLU* 2.9 41.0 + - + +
43P LEU* 3.7 15.8 + - - +
44P VAL 3.0 0.4 - - - -
45P ASP* 1.3 77.5 - - + +
47P GLY* 1.3 61.4 + - - +
48P ALA 3.4 0.7 + - - -
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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