Contacts of the helix formed by residues 24 - 40 (chain E) in PDB entry 4DHX
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 24 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E LEU 3.3 1.4 + - - -
21E ILE 3.2 15.5 + - - -
22E GLU 3.2 0.2 - - - -
23E THR* 1.3 77.6 + - - +
25E GLU* 1.3 64.8 + - - +
26E ARG 3.1 2.9 - - - -
27E GLU* 3.2 25.0 + - - +
28E ARG* 3.3 23.0 + - - +
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Residues in contact with GLU 25 (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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20E LEU* 3.1 10.6 + - + +
23E THR* 3.2 16.3 + - - +
24E GLY* 1.3 78.6 - - - +
26E ARG* 1.3 63.1 + - - +
28E ARG* 2.6 42.8 + - - +
29E LEU* 2.9 58.8 + - + +
90E ARG* 3.7 19.6 + - - +
94E PHE* 3.5 34.7 - - + +
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Residues in contact with ARG 26 (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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1175D LEU* 4.0 26.6 - - + +
1178D ARG* 4.8 18.0 - - - +
1179D VAL* 6.2 1.2 - - - +
1182D GLU* 4.3 15.8 + - - -
17E ASN* 5.3 6.8 - - - +
20E LEU* 3.1 41.9 + - + +
21E ILE* 3.8 23.0 - - - +
25E GLU* 1.3 78.2 - - - +
27E GLU* 1.3 80.3 + - - +
29E LEU* 3.5 5.0 + - - +
30E LYS* 3.1 23.2 + - + +
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Residues in contact with GLU 27 (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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20E LEU 4.6 0.7 - - - +
21E ILE* 4.7 7.5 - - - +
24E GLY* 3.2 22.2 + - - +
26E ARG* 1.3 96.2 + - - +
28E ARG* 1.3 66.1 + - + +
30E LYS* 3.3 17.3 + - - +
31E GLU* 3.2 29.7 + - + +
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Residues in contact with ARG 28 (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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23E THR* 3.3 26.9 + - - -
24E GLY* 3.3 10.6 + - - +
25E GLU* 2.6 48.8 + - - +
27E GLU* 1.3 78.9 - - + +
29E LEU* 1.3 57.6 + - - +
31E GLU* 3.5 5.8 + - - +
32E LEU* 3.0 26.9 + - - +
90E ARG* 4.5 18.5 + - - +
94E PHE* 4.8 2.8 - - - -
98E HIS* 6.0 0.2 + - - -
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Residues in contact with LEU 29 (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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1175D LEU* 3.8 30.7 - - + -
20E LEU* 4.7 8.5 - - + -
25E GLU* 2.9 52.6 + - + +
26E ARG* 3.9 2.2 - - - +
28E ARG* 1.3 74.5 - - - +
30E LYS* 1.3 65.2 + - - +
32E LEU* 3.3 17.8 + - + +
33E LEU* 3.1 29.9 + - - +
87E LEU* 4.3 10.3 - - + -
90E ARG* 4.1 29.8 - - + +
91E ILE* 4.0 19.5 - - + -
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Residues in contact with LYS 30 (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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1175D LEU* 5.4 0.6 - - + +
1179D VAL* 3.7 35.1 - - + +
1182D GLU* 3.4 27.7 + - - +
1183D PHE* 3.6 10.2 - - + -
26E ARG* 3.1 15.2 + - + +
27E GLU* 3.3 19.7 + - - +
29E LEU* 1.3 77.0 - - - +
31E GLU* 1.3 86.9 + - - +
33E LEU* 3.2 6.4 + - - +
34E ARG* 3.0 38.7 + - - +
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Residues in contact with GLU 31 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E GLU* 3.2 17.3 + - + +
28E ARG* 4.0 5.6 - - - +
30E LYS* 1.3 104.3 + - - +
32E LEU* 1.3 60.4 + - - +
34E ARG* 2.9 33.5 + - - +
35E ALA* 2.9 30.3 + - - +
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Residues in contact with LEU 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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28E ARG 3.0 16.0 + - - +
29E LEU* 3.4 22.0 - - + +
30E LYS 3.2 0.2 - - - -
31E GLU* 1.3 78.9 - - - +
33E LEU* 1.3 61.5 + - + +
35E ALA* 3.4 5.5 + - + +
36E LYS* 3.0 60.8 + - + +
86E GLU* 4.4 19.1 - - + +
87E LEU* 4.9 9.0 - - + -
90E ARG* 3.7 47.8 - - + +
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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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1175D LEU* 4.9 2.7 - - + -
1176D MET* 4.0 29.4 - - + +
1179D VAL* 4.0 34.1 - - + -
1183D PHE* 4.3 1.3 - - + -
29E LEU 3.1 15.9 + - - +
30E LYS 3.5 6.7 - - - +
32E LEU* 1.3 78.8 - - + +
34E ARG* 1.3 60.4 + - - +
36E LYS* 4.0 2.9 - - + +
37E LEU* 2.8 41.9 + - + +
83E VAL* 3.6 27.8 - - + +
87E LEU* 4.1 32.5 - - + -
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Residues in contact with ARG 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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1182D GLU* 5.9 0.2 + - - -
1183D PHE* 3.3 45.0 - - + -
1186D GLU* 3.1 37.7 + - - -
30E LYS* 3.0 29.2 + - - +
31E GLU* 2.9 32.7 + - - +
33E LEU* 1.3 77.4 - - - +
35E ALA* 1.3 56.6 + - - +
37E LEU* 3.8 1.4 - - - +
38E ILE* 2.9 55.4 + - + +
43E LYS* 4.9 7.4 - - + +
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Residues in contact with ALA 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 GLU 2.9 16.2 + - - +
32E LEU* 3.7 7.6 - - + +
34E ARG* 1.3 78.1 - - - +
36E LYS* 1.3 59.3 + - + +
38E ILE* 3.7 7.4 - - - +
39E GLU* 3.0 44.5 + - - +
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Residues in contact with LYS 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 LEU* 3.0 36.8 + - + +
33E LEU* 4.0 2.9 - - + +
35E ALA* 1.3 79.2 - - + +
37E LEU* 1.3 57.7 + - - +
39E GLU* 3.4 19.4 + - + +
40E CYS* 3.1 32.0 + - - +
83E VAL* 4.1 29.6 - - + +
86E GLU* 3.6 34.7 + - + +
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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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1176D MET* 5.2 7.0 - - - -
1179D VAL* 5.6 0.7 - - + -
1180D MET* 5.7 3.1 - - - -
1183D PHE* 3.9 26.9 - - + -
33E LEU* 2.8 32.1 + - + +
34E ARG* 4.0 3.1 - - - +
36E LYS* 1.3 75.1 - - - +
38E ILE* 1.3 62.4 + - + +
40E CYS* 3.6 3.5 - - - -
42E TRP* 2.9 74.7 + - + +
43E LYS* 3.2 4.0 + - + -
79E VAL* 4.5 12.3 - - + -
80E PRO* 4.1 20.4 - - + -
83E VAL* 4.4 15.5 - - + -
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Residues in contact with ILE 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 ARG* 2.9 48.8 + - + +
35E ALA* 3.7 7.4 - - - +
37E LEU* 1.3 78.5 - - + +
39E GLU* 1.3 66.8 + - + +
41E GLY* 3.3 12.5 + - - -
43E LYS* 4.1 31.9 - - + +
44E ASP* 5.1 4.2 - - - +
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Residues in contact with GLU 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 ALA* 3.0 31.6 + - - +
36E LYS* 3.9 27.0 + - - +
37E LEU 3.4 0.2 - - - -
38E ILE* 1.3 83.7 - - + +
40E CYS* 1.3 58.9 + - - +
41E GLY* 3.6 0.5 + - - -
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Residues in contact with CYS 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 LYS 3.1 21.1 + - - +
37E LEU* 3.6 16.6 - - - -
39E GLU* 1.3 77.0 - - - +
41E GLY* 1.3 57.1 + - - +
42E TRP* 3.7 16.2 - - - -
45E GLN* 4.8 5.4 + - - -
80E PRO* 3.8 26.7 - - + -
83E VAL* 4.8 4.3 - - + -
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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