Contacts of the helix formed by residues 33 - 46 (chain R) in PDB entry 1JJ2
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 SER 33 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16730 U 3.5 23.8 - - - -
16740 C 3.3 14.6 - - - -
31R ARG 3.8 1.2 + - - -
32R ALA* 1.3 76.1 - - - +
34R LYS* 1.3 65.2 + - - +
35R GLY* 3.5 4.1 + - - -
36R GLU* 2.8 37.6 + - - +
37R VAL* 2.9 22.4 + - - +
54R THR* 5.4 0.4 - - - -
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Residues in contact with LYS 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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14480 A 2.7 42.7 + - - +
14490 G 4.9 3.4 + - - -
16730 U 3.5 32.6 + - - +
16740 C 2.9 35.8 + - - +
33R SER* 1.3 72.2 - - - +
35R GLY* 1.3 58.4 + - - +
37R VAL* 3.2 5.1 + - - +
38R ALA* 2.8 29.7 + - - +
52R VAL* 3.3 41.4 + - + +
53R ASN* 5.4 0.4 - - - -
54R THR* 3.6 24.2 - - + +
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Residues in contact with GLY 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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16720 G 6.0 2.5 - - - -
16730 U 5.0 4.0 + - - -
33R SER* 3.1 6.5 + - - -
34R LYS* 1.3 80.6 - - - +
36R GLU* 1.3 61.9 + - - +
38R ALA* 3.3 6.6 + - - +
39R ASP* 3.0 33.1 + - - -
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Residues in contact with GLU 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2R TRP* 4.2 11.6 - - - -
4R VAL* 4.0 12.3 - - + +
31R ARG 3.5 6.2 - - - +
32R ALA* 3.1 17.4 - - + -
33R SER* 2.8 40.2 + - - +
35R GLY* 1.3 75.2 - - - +
37R VAL* 1.3 58.0 + - - +
39R ASP* 3.8 6.6 - - - +
40R ALA* 2.9 31.7 + - - +
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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
----------------------------------------------------------
4R VAL* 4.0 7.9 - - + -
26R PHE* 5.8 0.2 - - + -
28R VAL* 4.1 34.3 - - + -
32R ALA* 4.1 12.3 - - + +
33R SER 2.9 19.3 + - - +
34R LYS* 3.5 9.2 - - - +
36R GLU* 1.3 74.6 - - - +
38R ALA* 1.3 66.3 + - - +
40R ALA* 4.0 0.3 - - - +
41R VAL* 3.0 35.9 + - + +
52R VAL* 3.8 21.1 - - + -
54R THR* 5.1 3.1 - - + -
64R ALA* 3.9 11.0 - - + -
66R VAL* 3.9 18.8 - - + -
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Residues in contact with ALA 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34R LYS 2.8 16.5 + - - +
35R GLY* 3.3 8.9 + - - +
37R VAL* 1.3 78.6 - - - +
39R ASP* 1.3 65.6 + - - +
41R VAL* 4.7 0.4 - - - -
42R GLU* 3.0 31.3 + - - +
49R VAL* 3.5 27.1 - - + +
52R VAL* 3.9 11.0 - - + -
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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
----------------------------------------------------------
35R GLY 3.0 23.2 + - - +
36R GLU* 3.8 5.3 - - - +
38R ALA* 1.3 76.9 - - - +
40R ALA* 1.3 67.9 + - - +
42R GLU* 2.9 26.2 + - - +
43R GLU* 3.1 31.1 + - - +
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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
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4R VAL* 3.7 32.1 - - + -
5R ILE* 4.0 11.2 - - + -
36R GLU 2.9 19.0 + - - +
37R VAL 4.0 1.8 - - - +
39R ASP* 1.3 76.6 - - - +
41R VAL* 1.3 62.4 - - - +
43R GLU* 3.4 9.0 + - - +
44R GLN* 3.1 28.1 + - + +
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Residues in contact with VAL 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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5R ILE* 3.8 22.0 - - + -
24R LEU* 5.3 1.8 - - + -
26R PHE* 4.1 26.9 - - + -
37R VAL* 3.0 39.0 + - + +
38R ALA 3.7 3.6 - - - +
39R ASP 3.1 0.2 - - - -
40R ALA* 1.3 77.0 - - - +
42R GLU* 1.3 63.6 + - - +
45R TYR* 3.1 34.4 + - + +
47R VAL* 4.2 9.1 - - + +
49R VAL* 3.8 18.4 - - + -
66R VAL* 4.3 10.8 - - + -
68R LEU* 4.9 3.6 - - + -
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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
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38R ALA* 3.0 18.8 + - - +
39R ASP* 2.9 19.8 + - - +
41R VAL* 1.3 76.3 - - - +
43R GLU* 1.3 58.3 + - + +
46R ASP* 2.7 36.2 + - - -
47R VAL* 3.4 22.7 - - - +
48R THR* 3.5 10.0 - - - +
49R VAL* 2.7 39.8 + - + +
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Residues in contact with GLU 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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39R ASP* 3.1 31.4 + - - +
40R ALA* 3.9 7.3 + - - +
42R GLU* 1.3 76.8 - - + +
44R GLN* 1.3 66.3 + - + +
46R ASP* 4.4 2.2 + - - +
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Residues in contact with GLN 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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5R ILE* 4.3 11.7 - - + -
40R ALA* 3.1 18.2 + - + +
42R GLU 3.2 0.2 - - - -
43R GLU* 1.3 85.2 - - + +
45R TYR* 1.3 85.4 + - + +
46R ASP 3.7 0.2 - - - -
25U THR* 4.6 16.9 + - - +
28U LEU* 3.3 28.5 - - + +
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Residues in contact with TYR 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R ILE* 4.0 18.0 - - + +
8R PRO* 4.8 4.0 - - - +
24R LEU* 5.5 0.9 - - + -
26R PHE* 3.5 28.6 - + - -
41R VAL* 3.1 24.9 + - + +
44R GLN* 1.3 96.2 - - + +
46R ASP* 1.3 71.9 - - - +
47R VAL* 3.3 10.5 - - + +
77R VAL* 3.7 34.1 - - + -
80R ARG* 2.8 32.9 + - + +
81R ILE* 4.0 32.0 - - + +
28U LEU* 4.0 21.3 - - + +
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Residues in contact with ASP 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R GLU 2.7 20.7 + - - -
43R GLU 4.4 2.3 + - - +
44R GLN 3.7 1.2 - - - -
45R TYR* 1.3 77.0 - - - +
47R VAL* 1.3 58.9 + - - +
72R ASP* 4.5 3.1 - - - +
80R ARG* 4.9 2.3 + - - +
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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