Contacts of the helix formed by residues 39 - 52 (chain R) 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 39 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38R LYS* 1.3 72.0 - - - +
40R ALA* 1.3 66.5 + - - +
41R GLY* 3.3 8.3 - - - +
42R GLU* 2.6 51.1 + - + +
43R ALA* 2.7 10.8 + - - -
107R GLU* 2.7 26.7 - - + +
108R ALA* 3.7 12.9 + - - -
109R MET 3.2 10.9 + - - -
110R THR* 4.5 3.5 + - - +
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Residues in contact with ALA 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R LYS 3.6 2.8 + - - -
39R THR* 1.3 68.7 - - - +
41R GLY* 1.3 58.4 + - - +
43R ALA* 2.9 22.9 - - - +
44R VAL* 3.1 13.3 + - - +
92R LEU* 4.0 14.5 - - + +
96R VAL* 3.8 21.8 - - + -
106R GLY 3.5 15.3 - - - +
107R GLU* 3.5 10.3 - - - +
109R MET 2.8 11.2 + - - +
111R ILE* 4.3 5.2 - - - +
147R LEU* 4.0 15.5 - - + -
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Residues in contact with GLY 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R THR* 2.8 13.5 + - - +
40R ALA* 1.3 73.6 - - - +
42R GLU* 1.3 64.8 + - - +
43R ALA 3.0 1.8 - - - -
44R VAL* 2.9 9.5 + - - +
45R ASP* 2.9 33.4 + - - +
107R GLU* 3.4 22.7 + - - +
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Residues in contact with GLU 42 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R LYS* 3.5 18.4 - - + +
39R THR* 2.6 54.2 + - + +
41R GLY* 1.3 71.7 - - - +
43R ALA* 1.3 51.6 + - - +
45R ASP* 3.4 10.2 + - - +
46R TYR* 2.7 36.8 + - - +
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Residues in contact with ALA 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35R ILE* 4.6 8.7 - - + -
38R LYS* 4.4 7.8 - - + +
39R THR 2.7 9.1 + - - +
40R ALA 2.9 15.5 - - - +
42R GLU* 1.3 74.6 - - - +
44R VAL* 1.3 63.1 + - - +
46R TYR* 3.0 9.1 + - - +
47R LEU* 2.8 28.4 + - - +
92R LEU* 3.6 17.5 - - + -
111R ILE* 3.7 23.6 - - + -
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Residues in contact with VAL 44 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R ALA 3.1 11.9 + - - +
41R GLY* 2.9 11.1 + - - +
43R ALA* 1.3 77.1 - - - +
45R ASP* 1.3 69.0 + - - +
47R LEU* 2.8 15.2 + - - +
48R GLU* 2.8 39.7 + - + +
89R LEU* 3.7 25.8 - - + +
92R LEU* 4.0 18.6 - - + +
96R VAL* 6.1 2.5 - - + -
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Residues in contact with ASP 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41R GLY* 2.9 28.3 + - - +
42R GLU* 3.6 10.2 - - - +
44R VAL* 1.3 76.3 - - - +
46R TYR* 1.3 62.6 + - - +
48R GLU* 3.4 18.9 + - - +
49R ALA* 3.1 21.7 + - - +
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Residues in contact with TYR 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31R ILE* 5.6 0.4 - - + -
34R GLU* 3.3 34.7 + - + +
35R ILE* 4.0 10.1 - - + -
38R LYS* 3.2 27.4 - - + +
42R GLU 2.7 19.0 + - - +
43R ALA* 3.1 11.4 - - - +
44R VAL 2.8 0.8 + - - -
45R ASP* 1.3 73.8 - - - +
47R LEU* 1.3 83.2 + - + +
49R ALA* 3.1 15.9 + - - +
50R VAL* 3.1 34.2 + - + +
55R GLN* 3.6 27.8 - - + -
56R PRO 2.8 22.5 + - - -
57R VAL* 3.6 12.2 - - + +
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Residues in contact with LEU 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31R ILE* 3.9 13.0 - - + -
35R ILE* 3.8 17.7 - - + -
43R ALA 2.8 15.7 + - - +
44R VAL 2.8 8.1 + - - +
46R TYR* 1.3 90.5 - - + +
48R GLU* 1.3 60.9 + - - +
50R VAL* 3.0 7.1 + - + +
51R ILE* 2.8 36.1 + - - +
57R VAL* 5.8 0.4 - - + -
85R SER* 3.2 33.4 - - - +
88R PHE* 3.4 23.1 - - + -
89R LEU* 3.7 24.7 - - + +
92R LEU* 4.3 8.1 - - + -
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Residues in contact with GLU 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44R VAL* 2.8 41.4 + - + +
45R ASP* 3.5 18.6 - - - +
47R LEU* 1.3 78.2 - - - +
49R ALA* 1.3 56.6 + - - +
51R ILE* 3.2 9.4 + - - +
52R GLU* 2.8 32.9 + - - +
89R LEU* 4.6 11.7 - - + +
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Residues in contact with ALA 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45R ASP 3.1 9.6 + - - +
46R TYR* 3.1 12.5 + - - +
48R GLU* 1.3 78.8 - - - +
50R VAL* 1.3 56.4 + - - +
52R GLU* 3.5 5.4 + - - -
53R GLY 2.9 5.9 + - - -
54R ASP* 2.6 40.2 + - + +
55R GLN* 3.2 24.2 + - + +
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Residues in contact with VAL 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46R TYR* 3.1 44.2 - - + +
47R LEU* 3.4 9.0 - - + +
49R ALA* 1.3 74.5 - - - +
51R ILE* 1.3 61.6 + - - +
52R GLU 3.0 1.3 - - - -
53R GLY 2.9 14.1 + - - +
55R GLN* 3.2 20.9 - - + +
57R VAL* 3.4 24.0 - - + -
79R ARG 4.6 0.2 - - - +
80R TYR* 3.4 36.1 - - - +
81R PRO 4.3 0.2 - - - -
85R SER* 3.7 16.8 - - - +
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Residues in contact with ILE 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47R LEU 2.8 21.5 + - - +
48R GLU* 3.7 6.3 - - - +
50R VAL* 1.3 72.6 - - - +
52R GLU* 1.3 60.0 + - - +
53R GLY 3.6 0.2 + - - -
82R GLU* 4.0 22.2 - - + +
85R SER* 3.6 16.8 - - - -
86R LYS* 3.3 51.6 - - + +
89R LEU* 3.7 28.5 - - + -
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Residues in contact with GLU 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48R GLU 2.8 18.1 + - - +
49R ALA* 3.8 3.6 - - - +
51R ILE* 1.3 78.6 - - - +
53R GLY* 1.3 61.3 + - - +
54R ASP* 3.3 25.0 - - - +
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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