Contacts of the helix formed by residues 33 - 47 (chain R) in PDB entry 5L4K
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 GLY 33 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29R PRO* 4.9 8.9 - - - +
32R ARG* 1.3 76.5 - - - +
34R ASP* 1.3 81.1 + - - +
37R VAL* 3.5 21.5 + - - +
63R TRP* 4.7 15.3 - - - -
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Residues in contact with ASP 34 (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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32R ARG* 3.1 40.5 + - - +
33R GLY* 1.3 90.7 + - - +
35R ALA* 1.3 62.0 + - - +
37R VAL* 3.8 2.3 + - - +
38R ARG* 3.7 21.7 + - - +
63R TRP* 4.4 3.6 - - - -
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Residues in contact with ALA 35 (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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32R ARG* 4.6 0.4 - - - +
34R ASP* 1.3 72.3 - - - +
36R ALA* 1.3 65.2 + - - +
37R VAL 3.2 2.5 - - - -
38R ARG* 3.8 16.6 - - + -
39R ASP* 3.0 26.2 + - - +
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Residues in contact with ALA 36 (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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32R ARG* 3.4 37.4 - - + +
34R ASP 3.3 0.6 - - - -
35R ALA* 1.3 77.7 - - - +
37R VAL* 1.3 61.6 + - + +
39R ASP* 4.1 5.0 - - - +
40R GLU* 3.9 18.5 + - - +
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Residues in contact with VAL 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R ARG 4.3 1.8 - - - +
26R LEU* 3.4 28.0 - - + +
27R SER* 2.9 28.7 - - - +
32R ARG* 3.8 13.9 - - + +
33R GLY* 3.5 20.2 - - - +
34R ASP 3.8 1.7 + - - +
35R ALA 3.2 0.2 - - - -
36R ALA* 1.3 75.1 - - - +
38R ARG* 1.3 68.8 + - - +
39R ASP 2.8 3.3 + - - -
40R GLU* 2.8 25.8 + - - +
41R LEU* 3.1 22.4 + - + -
63R TRP* 4.7 11.7 - - + -
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Residues in contact with ARG 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34R ASP* 3.7 12.1 + - - +
35R ALA* 3.4 17.4 + - + +
37R VAL* 1.3 79.6 - - - +
39R ASP* 1.3 56.6 + - - +
41R LEU* 3.2 9.4 + - - +
42R MET* 2.9 34.7 + - + +
63R TRP* 3.4 59.6 - - + +
64R GLN* 5.6 7.9 - - - +
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Residues in contact with ASP 39 (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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35R ALA 3.0 17.2 + - - +
36R ALA* 4.1 7.0 - - - +
37R VAL 2.8 1.0 + - - -
38R ARG* 1.3 73.8 - - - +
40R GLU* 1.3 69.0 + - - +
42R MET* 2.7 21.9 + - - +
43R ALA* 3.1 9.7 + - - +
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Residues in contact with GLU 40 (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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19R ILE* 3.8 25.6 - - + +
22R LEU* 4.5 4.7 - - - +
23R ARG* 3.1 47.2 + - + +
26R LEU* 5.3 5.9 - - - +
36R ALA 3.9 11.6 - - - +
37R VAL* 2.8 21.4 + - - +
39R ASP* 1.3 77.4 + - - +
41R LEU* 1.3 64.1 + - - +
43R ALA* 3.1 20.4 + - - +
44R ALA* 3.6 4.7 + - - +
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Residues in contact with LEU 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R ARG* 3.6 44.6 - - + +
27R SER* 4.1 10.1 - - - +
37R VAL* 3.1 25.0 + - + +
38R ARG* 3.6 9.4 - - - +
39R ASP 3.1 1.0 - - - -
40R GLU* 1.3 80.6 - - - +
42R MET* 1.3 59.0 + - - +
44R ALA* 2.9 20.5 + - - +
45R VAL* 2.9 17.0 + - + +
49R ASN* 5.4 0.2 - - - +
57R LEU* 4.2 20.2 - - + -
63R TRP* 3.8 33.2 - - + +
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Residues in contact with MET 42 (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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38R ARG* 2.9 19.6 + - + +
39R ASP* 2.7 20.5 + - - +
41R LEU* 1.3 69.0 - - - +
43R ALA* 1.3 60.7 + - - +
45R VAL* 2.8 35.3 + - + +
46R ARG* 2.9 65.9 + - - +
69R LEU* 4.8 13.5 - - + -
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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
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19R ILE* 6.2 3.4 - - + -
39R ASP 3.1 7.2 + - - +
40R GLU* 3.1 13.8 + - - +
42R MET* 1.3 76.5 - - - +
44R ALA* 1.3 56.0 + - - +
46R ARG* 3.2 22.4 + - - +
47R ASP* 3.5 13.7 + - - +
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Residues in contact with ALA 44 (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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16R ASP* 5.9 3.1 - - - +
20R ALA* 6.2 0.2 - - + -
23R ARG* 4.0 33.7 - - - +
40R GLU 3.6 2.9 + - - +
41R LEU 2.9 12.7 + - - +
43R ALA* 1.3 75.4 - - - +
45R VAL* 1.3 56.2 + - - +
46R ARG 3.4 0.2 - - - -
47R ASP* 2.7 28.2 - - - +
49R ASN* 3.2 20.9 - - - +
54R TYR* 5.0 5.6 + - - +
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Residues in contact with VAL 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 LEU* 2.9 19.9 + - + +
42R MET* 2.8 28.1 + - + +
44R ALA* 1.3 79.4 - - - +
46R ARG* 1.3 84.9 + - - +
47R ASP 3.7 3.5 - - - +
49R ASN* 3.7 17.9 - - + +
69R LEU* 3.9 21.1 - - + -
73R MET* 3.7 41.0 - - + +
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Residues in contact with ARG 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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42R MET* 2.9 50.6 + - - +
43R ALA* 3.2 10.3 + - - +
45R VAL* 1.3 94.0 + - - +
47R ASP* 1.3 66.8 + - - +
48R ASN* 3.3 9.0 + - - +
69R LEU* 4.5 7.9 - - - +
73R MET* 4.7 6.0 - - - +
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Residues in contact with ASP 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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16R ASP* 6.0 1.2 - - - -
43R ALA 3.5 10.4 + - - +
44R ALA* 2.7 26.3 - - - +
45R VAL 3.7 0.2 - - - +
46R ARG* 1.3 78.1 - - - +
48R ASN* 1.3 70.2 + - - +
49R ASN 3.2 0.4 + - - -
54R TYR* 5.4 0.5 + - - -
113R ARG* 3.4 50.8 + - - +
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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