Contacts of the helix formed by residues 37 - 47 (chain R) in PDB entry 3K9Q
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 ASP 37 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194O GLY* 6.0 1.7 - - - -
36R THR* 1.3 85.4 + - - +
38R ASP* 1.3 64.1 - - - +
39R ASP* 3.9 16.8 - - - +
40R MET* 3.2 28.6 + - - +
41R LEU* 3.2 14.7 + - - +
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Residues in contact with ASP 38 (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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37R ASP* 1.3 72.7 - - - +
39R ASP* 1.3 59.1 + - - +
41R LEU* 3.8 8.6 - - - +
42R ALA* 2.8 37.9 + - - +
60R VAL* 3.8 23.2 - - + +
61R VAL 4.4 2.8 - - - +
63R GLY* 4.1 4.0 + - - -
64R GLY* 3.4 29.3 + - - +
65R PHE* 4.1 3.0 - - + -
74R SER* 2.3 33.7 + - - -
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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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194O GLY 5.3 1.0 - - - +
196O LYS* 2.8 40.8 + - - +
37R ASP* 3.9 16.3 - - - +
38R ASP* 1.3 77.9 - - - +
40R MET* 1.3 62.8 + - - +
42R ALA* 4.0 2.3 - - - +
43R HIS* 3.2 24.5 + - - +
60R VAL* 4.1 15.3 - - + +
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Residues in contact with MET 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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190O PRO* 4.0 5.4 - - + -
191O HIS 3.9 15.9 - - - +
194O GLY* 3.6 39.7 - - - +
195O ASP 4.1 9.9 - - - -
196O LYS* 4.1 13.9 - - + -
199O ALA* 4.0 15.3 - - - -
36R THR* 3.1 33.7 - - + +
37R ASP* 3.2 7.8 + - - +
38R ASP 3.2 0.8 - - - -
39R ASP* 1.3 78.7 + - - +
41R LEU* 1.3 65.6 + - - +
43R HIS* 3.2 6.0 + - - +
44R LEU* 3.0 50.8 + - + +
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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
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190O PRO* 5.3 2.7 - - + -
10R PHE* 3.8 37.7 - - + +
32R VAL* 4.1 11.0 - - + -
34R ASP* 4.0 12.3 - - + -
36R THR* 3.5 25.8 - - + +
37R ASP 3.2 13.1 + - - +
38R ASP* 3.8 11.2 - - - +
40R MET* 1.3 76.7 - - - +
42R ALA* 1.3 63.5 + - - +
43R HIS 3.1 0.3 + - - -
44R LEU* 3.2 7.0 + - + +
45R LEU* 3.0 23.2 + - - +
65R PHE* 4.1 17.0 - - + -
74R SER* 4.0 26.9 - - - +
75R PHE 5.3 4.5 - - - +
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Residues in contact with ALA 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 ASP 2.8 20.8 + - - +
39R ASP 4.0 2.0 - - - +
41R LEU* 1.3 72.8 - - - +
43R HIS* 1.3 56.9 + - - +
45R LEU* 3.3 5.6 + - - +
46R LYS* 2.9 38.8 + - + +
58R VAL* 3.8 25.6 - - + +
60R VAL* 3.7 22.4 - - + +
65R PHE* 4.7 11.8 - - + -
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Residues in contact with HIS 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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196O LYS* 3.6 45.5 + - + +
200O ARG* 4.2 10.7 + - - -
276P ASP* 4.7 3.3 - - + +
277P GLU 3.5 38.9 + - - -
39R ASP 3.2 17.4 + - - +
40R MET* 3.5 6.3 - - - +
41R LEU 3.1 0.6 - - - -
42R ALA* 1.3 81.4 - - - +
44R LEU* 1.3 68.4 + - + +
46R LYS* 3.4 11.1 + - - +
47R TYR* 3.0 57.1 + + - +
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Residues in contact with LEU 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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188O ASP* 4.2 23.3 - - + -
189O ALA* 3.7 9.6 - - - +
190O PRO* 3.6 34.3 - - + -
199O ALA* 4.4 8.1 - - + -
200O ARG* 4.2 18.8 - - - +
10R PHE 5.6 0.4 - - - +
15R ARG* 3.1 36.7 + - - +
19R ARG* 4.8 0.3 + - - -
40R MET* 3.0 35.8 + - + +
41R LEU* 4.0 3.8 - - + +
43R HIS* 1.3 79.5 - - + +
45R LEU* 1.3 61.8 + - - +
47R TYR 2.8 19.6 - - - +
48R ASP* 4.7 3.8 - - - +
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Residues in contact with LEU 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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10R PHE* 4.2 13.5 - - + -
15R ARG* 3.8 11.6 - - + +
18R PHE* 3.7 39.5 - - + -
19R ARG* 3.0 37.3 + - + +
41R LEU 3.0 12.1 + - - +
42R ALA* 3.5 7.2 - - - +
44R LEU* 1.3 76.1 - - - +
46R LYS* 1.4 56.8 + - - +
54R PHE* 3.2 25.3 - - + +
58R VAL* 3.9 24.9 - - + -
65R PHE* 4.0 21.8 - - + -
67R VAL* 4.0 4.3 - - + -
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Residues in contact with LYS 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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276P ASP* 3.3 32.1 + - - -
42R ALA* 2.9 26.2 + - + +
43R HIS* 3.4 12.5 + - - +
45R LEU* 1.4 75.8 - - - +
47R TYR* 1.3 80.8 + - + +
53R ARG* 3.4 5.9 - - - +
54R PHE* 2.8 37.6 + - + +
56R GLY 5.7 1.8 - - - +
58R VAL* 4.0 38.0 + - + +
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Residues in contact with TYR 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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188O ASP* 4.2 4.3 - - - +
200O ARG* 3.5 16.9 + - - +
274P THR* 4.8 2.4 + - - -
276P ASP* 2.7 32.0 + - - +
278P ILE* 3.7 20.7 - - + +
282P ASP* 3.3 28.9 - - - +
15R ARG* 5.5 0.2 + - - -
43R HIS* 3.0 40.9 + + + +
44R LEU* 2.8 28.3 - - - +
46R LYS* 1.3 102.0 - - + +
48R ASP* 1.3 58.4 + - - +
52R GLY 4.9 0.2 - - - -
53R ARG* 3.7 36.6 + - + +
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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