Contacts of the helix formed by residues 35 - 47 (chain R) in PDB entry 2D3O
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 LYS 35 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13550 A 5.2 5.6 + - - -
13560 G 3.5 14.5 + - - -
16130 G 5.2 1.2 + - - +
16140 C 3.0 49.9 + - - +
16150 C 2.9 40.6 + - - +
34R THR* 1.3 75.0 - - - +
36R THR* 1.3 59.8 + - - +
38R ILE* 3.2 17.3 - - - +
39R LYS* 3.2 18.0 - - - +
53R ILE* 2.9 46.8 + - + +
54R SER* 4.4 11.2 - - - +
55R THR* 4.8 2.5 - - + +
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Residues in contact with THR 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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16130 G 5.0 13.0 - - - +
16140 C 3.2 31.4 + - - -
34R THR* 3.5 3.8 + - - -
35R LYS* 1.3 75.8 - - - +
37R GLU* 1.3 65.9 - - - +
39R LYS* 3.7 14.2 + - - +
40R ASP* 3.4 13.0 + - - +
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Residues in contact with GLU 37 (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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1370 A 6.3 3.4 - - - -
1380 G 5.5 4.9 + - - +
2R SER 4.7 0.5 - - - +
6R ILE* 4.0 14.9 - - + +
33R ALA* 5.3 2.4 - - - -
34R THR* 2.8 42.1 + - - +
36R THR* 1.3 78.9 - - - +
38R ILE* 1.3 59.2 + - - +
40R ASP* 2.7 30.6 - - - +
41R ALA* 3.6 6.2 - - - +
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Residues in contact with ILE 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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6R ILE* 3.9 25.1 - - + +
29R VAL* 3.8 17.7 - - + -
33R ALA* 5.4 0.7 - - + -
34R THR 2.8 28.0 + - - +
35R LYS 3.2 13.5 - - - +
37R GLU* 1.3 75.1 - - - +
39R LYS* 1.3 65.2 + - - +
40R ASP 3.1 2.7 - - - -
41R ALA* 2.8 20.5 + - + +
42R ILE* 3.2 18.0 + - + +
53R ILE* 3.2 30.7 - - + -
55R THR* 4.8 3.8 - - - -
78R ALA* 3.5 24.5 - - + -
80R VAL* 6.2 0.7 - - + -
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Residues in contact with LYS 39 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16120 U 4.2 18.4 + - - +
16130 G 2.7 42.5 + - - +
35R LYS 3.2 15.9 + - - +
36R THR* 3.7 9.2 - - + +
37R GLU 3.3 0.2 - - - -
38R ILE* 1.3 84.0 - - - +
40R ASP* 1.3 56.5 + - + +
42R ILE* 3.5 9.7 - - + +
43R GLN* 2.9 45.5 + - - +
50R VAL* 3.7 23.9 + - + -
51R ILE* 3.6 19.4 + - - +
53R ILE* 4.6 16.9 - - + +
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Residues in contact with ASP 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1360 A 5.2 7.6 + - - -
2R SER 3.3 12.0 - - - +
3R HIS* 3.3 25.8 + - + -
36R THR 3.4 14.5 + - - +
37R GLU* 2.7 21.1 - - - +
39R LYS* 1.3 77.4 - - + +
41R ALA* 1.3 56.6 + - - +
42R ILE 3.6 0.9 - - - -
43R GLN* 4.6 8.1 - - - +
44R GLN* 3.7 9.8 - - + +
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Residues in contact with ALA 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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2R SER 3.7 13.9 - - - +
3R HIS* 2.7 31.1 - - - +
5R ASP 4.4 8.4 - - - +
6R ILE* 4.1 14.4 - - + +
37R GLU 3.6 12.6 - - - +
38R ILE* 2.8 16.0 + - + +
40R ASP* 1.3 79.1 - - - +
42R ILE* 1.3 61.4 + - - +
45R ALA* 3.1 11.3 - - - +
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Residues in contact with ILE 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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27R PHE* 3.9 33.7 - - + -
38R ILE* 3.3 23.1 - - + +
39R LYS* 3.5 14.1 - - - +
41R ALA* 1.3 81.7 - - - +
43R GLN* 1.3 63.4 + - - +
44R GLN 3.5 0.7 - - - -
45R ALA* 3.9 2.2 - - - -
46R PHE* 3.6 34.9 + - + +
47R GLY 4.6 0.2 + - - -
48R VAL* 4.6 4.1 - - + +
50R VAL* 3.9 19.4 - - + +
53R ILE* 5.4 3.8 - - + -
80R VAL* 3.9 26.5 - - + -
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Residues in contact with GLN 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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16120 U 5.7 2.0 + - - -
39R LYS* 2.9 46.0 + - - +
40R ASP* 5.0 3.2 - - - +
42R ILE* 1.3 77.1 - - - +
44R GLN* 1.3 58.5 + - + +
45R ALA 3.2 4.3 - - - -
47R GLY* 2.9 30.8 + - - -
48R VAL 3.2 16.7 + - - +
49R ARG* 2.7 17.5 - - - +
50R VAL* 2.6 47.5 + - + +
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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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3R HIS* 2.9 55.2 + - + +
4R TYR* 4.4 5.2 + - - -
40R ASP* 3.7 12.0 + - + +
42R ILE 4.3 0.2 - - - +
43R GLN* 1.3 78.7 - - + +
45R ALA* 1.3 61.4 + - - +
47R GLY* 4.7 2.5 - - - +
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Residues in contact with ALA 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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3R HIS 3.3 10.5 - - - +
4R TYR* 3.7 30.1 + - + -
41R ALA 3.1 26.5 + - - +
42R ILE* 3.9 3.1 - - - +
43R GLN 3.2 0.4 - - - -
44R GLN* 1.3 81.0 - - - +
46R PHE* 1.3 83.0 + - + +
26W MET* 5.9 2.2 - - + -
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Residues in contact with PHE 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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27R PHE* 4.4 21.5 - + - -
42R ILE* 3.6 27.1 + - + +
44R GLN 5.0 0.2 - - - -
45R ALA* 1.3 101.0 - - + +
47R GLY* 1.3 59.3 + - - +
48R VAL* 4.9 9.9 - - + -
88R ILE* 3.8 25.6 - - + -
89R GLU* 3.2 37.5 - - - +
91R LEU* 5.3 7.0 - - + -
26W MET* 5.1 10.1 - - + -
27W GLU* 4.8 13.9 - - - -
30W PHE* 5.0 10.8 - + - -
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Residues in contact with GLY 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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43R GLN 2.9 15.1 + - - -
44R GLN* 4.7 1.3 - - - -
45R ALA 3.9 0.2 - - - -
46R PHE* 1.3 81.5 - - - +
48R VAL* 1.3 62.6 + - - +
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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