Contacts of the helix formed by residues 30 - 40 (chain E) in PDB entry 3DAB
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 30 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28E ARG* 3.5 1.3 + - - +
29E PRO* 1.3 73.6 - - - +
31E LEU* 1.3 68.1 + - - +
32E PRO* 3.4 6.5 - - + -
33E LEU* 3.0 7.0 + - - +
34E LEU 2.9 18.1 + - - -
104E LYS 3.6 16.7 + - - +
105E ASN* 2.8 32.4 + - - +
107E VAL* 3.0 34.4 - - - +
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Residues in contact with LEU 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E PRO 3.9 0.6 + - - -
30E LYS* 1.3 72.1 - - - +
32E PRO* 1.3 73.2 - - + +
34E LEU* 3.1 12.9 + - + +
35E LYS* 2.9 52.5 + - + +
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Residues in contact with PRO 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E LYS* 3.6 7.4 - - + -
31E LEU* 1.3 97.6 - - + +
33E LEU* 1.3 62.1 + - - +
35E LYS* 3.3 18.0 - - + +
36E ILE* 3.2 19.1 + - - +
80E LEU* 3.5 20.9 - - + +
84E LEU* 3.4 36.8 - - + -
105E ASN* 3.9 9.9 - - - +
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Residues in contact with LEU 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E PRO* 4.1 8.5 - - + -
30E LYS 3.0 7.9 + - - +
32E PRO* 1.3 79.7 - - - +
34E LEU* 1.3 58.8 + - - +
36E ILE* 3.2 20.0 + - + +
37E LEU* 2.9 50.7 + - + +
52E VAL* 4.6 3.4 - - + -
56E LEU* 4.8 7.2 - - + -
84E LEU* 3.9 6.8 - - + +
101E MET* 4.8 9.2 - - + -
102E LEU* 3.9 24.2 - - + -
105E ASN* 3.9 28.5 - - + +
106E LEU* 3.5 31.9 - - + -
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Residues in contact with LEU 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E PRO* 4.1 23.4 - - + +
30E LYS 2.9 12.0 + - - +
31E LEU* 3.5 15.5 - - + +
33E LEU* 1.3 75.8 - - - +
35E LYS* 1.3 57.0 + - - +
37E LEU* 3.3 2.8 + - + +
38E HIS* 2.8 60.2 + - + +
44E GLY 3.8 8.3 - - - +
45E GLU* 4.1 25.4 - - + +
47E PHE* 3.7 31.0 - - + -
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Residues in contact with LYS 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LEU* 2.9 51.0 + - + +
32E PRO* 3.3 11.9 - - + +
34E LEU* 1.3 77.0 - - - +
36E ILE* 1.3 56.9 + - - +
38E HIS* 3.4 6.2 + - - +
39E ALA* 2.9 30.6 + - - +
80E LEU* 4.0 22.5 - - + +
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Residues in contact with ILE 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E PRO 3.2 6.3 + - - +
33E LEU* 3.2 17.4 + - + +
35E LYS* 1.3 76.3 - - - +
37E LEU* 1.3 69.5 + - + +
39E ALA* 3.3 2.1 + - - -
40E ALA* 3.2 16.1 + - - +
56E LEU* 4.1 15.9 - - + -
59E TYR* 3.3 56.0 - - + +
80E LEU* 4.0 11.2 - - + -
81E LEU* 3.9 34.5 - - + +
84E LEU* 3.6 30.5 - - + -
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Residues in contact with LEU 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E PRO* 3.7 31.0 - - + -
33E LEU* 2.9 35.7 + - + +
34E LEU* 3.9 4.3 - - - +
36E ILE* 1.3 76.9 - - + +
38E HIS* 1.3 58.8 + - - +
40E ALA* 2.9 20.5 + - - +
41E GLY 3.2 0.5 + - - -
42E ALA* 3.0 30.5 + - + +
47E PHE* 4.2 15.7 - - + -
52E VAL* 3.7 40.4 - - + +
55E TYR* 3.8 15.3 - - + -
56E LEU* 3.9 10.1 - - + +
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Residues in contact with HIS 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LEU* 2.8 46.7 + - + +
35E LYS* 3.7 6.1 - - - +
37E LEU* 1.3 75.1 - - - +
39E ALA* 1.3 59.2 + - - +
41E GLY* 2.9 20.4 + - - -
42E ALA* 2.9 27.5 + - - +
43E GLN* 4.3 0.7 - - - -
44E GLY* 2.9 36.5 + - - -
45E GLU* 5.3 1.8 + - - +
47E PHE* 4.5 1.6 - + - -
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Residues in contact with ALA 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LYS 2.9 14.7 + - - +
36E ILE* 3.5 9.6 - - - +
38E HIS* 1.3 75.7 - - - +
40E ALA* 1.3 58.7 + - - +
41E GLY 3.3 0.9 + - - -
59E TYR* 3.8 20.4 - - + -
62E VAL* 4.7 9.7 - - + +
63E LYS* 5.9 2.9 - - + +
30G LYS* 4.5 13.5 + - - -
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Residues in contact with ALA 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ILE 3.2 4.3 + - - +
37E LEU 2.9 12.0 + - - +
39E ALA* 1.3 74.0 - - - +
41E GLY* 1.3 57.4 + - - +
42E ALA 3.6 0.7 - - - -
55E TYR* 3.1 42.8 - - + +
58E GLN* 4.1 10.9 - - + +
59E TYR* 3.5 25.4 - - + +
62E VAL* 5.0 4.3 - - - -
30G LYS* 5.9 2.0 - - - -
104G LYS* 6.0 1.4 - - - -
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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