Contacts of the helix formed by residues 30 - 42 (chain E) in PDB entry 1XK4
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 TYR 30 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E LYS* 3.4 44.6 - - + +
24E GLY* 3.8 7.5 - - - -
25E ASN* 2.9 23.6 + - - +
28E ALA* 3.8 7.4 - - + -
29E VAL* 1.3 73.9 - - - +
31E ARG* 1.3 67.4 + - - +
32E ASP 3.4 1.1 - - - -
33E ASP* 3.0 24.8 + - - +
34E LEU* 2.9 21.3 + - - +
55E PHE* 3.6 7.4 - - - -
64E GLY 3.5 17.9 - - - +
65E ALA* 4.0 13.7 - - + -
1512E CA 3.6 7.2 - - - -
68H THR 2.6 31.1 + - - -
69H ASN* 4.8 4.4 - - + -
70H ALA* 5.3 0.3 - - - +
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Residues in contact with ARG 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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30E TYR* 1.3 76.5 - - - +
32E ASP* 1.3 63.2 + - - +
34E LEU* 3.5 3.5 + - - +
35E LYS* 3.1 20.8 + - - +
51E ALA* 5.1 4.3 - - + +
52E ASP* 3.9 27.1 + - - +
55E PHE* 3.6 54.3 - - + +
56E LYS* 5.9 1.4 - - - +
64E GLY* 4.9 9.7 + - - -
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Residues in contact with ASP 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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23E LYS* 4.0 19.5 + - - +
30E TYR* 3.4 1.0 - - - +
31E ARG* 1.3 77.4 - - - +
33E ASP* 1.3 62.0 + - - +
35E LYS* 3.3 21.9 + - - +
36E LYS* 2.9 57.2 + - - +
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Residues in contact with ASP 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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19E TYR* 3.8 25.2 - - + +
22E ILE* 3.6 29.6 - - + +
23E LYS* 3.5 24.2 + - - +
28E ALA 4.3 1.2 - - - +
29E VAL* 3.7 12.8 - - + -
30E TYR* 3.0 41.4 + - - +
32E ASP* 1.3 79.0 - - - +
34E LEU* 1.3 58.8 + - - +
36E LYS* 3.3 5.6 + - - +
37E LEU* 2.9 27.5 + - - +
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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 VAL* 3.6 17.2 - - + +
30E TYR 2.9 15.8 + - - +
31E ARG 3.8 4.5 - - - +
33E ASP* 1.3 74.3 - - - +
35E LYS* 1.3 58.7 + - - +
37E LEU* 3.1 12.8 + - + +
38E LEU* 2.8 38.7 + - + +
51E ALA 4.0 6.7 - - - +
54E TRP* 4.1 5.2 - - + -
55E PHE* 3.5 48.7 - - + +
58E LEU* 4.0 26.9 - - + -
66E VAL* 4.6 6.1 - - + -
71E PHE* 5.6 1.6 - - + -
74E LEU* 4.5 14.6 - - + -
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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 ARG 3.1 13.6 + - - +
32E ASP* 3.4 24.5 - - - +
33E ASP 3.3 0.2 - - - -
34E LEU* 1.3 77.6 - - - +
36E LYS* 1.3 55.6 + - + +
38E LEU* 3.3 2.1 + - - +
39E GLU* 3.0 58.7 + - + +
51E ALA* 3.8 28.6 - - + +
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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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19E TYR* 3.8 13.0 - - + -
22E ILE* 4.5 19.7 - - + -
32E ASP* 2.9 42.8 + - - +
33E ASP* 3.6 9.2 - - - +
35E LYS* 1.3 77.6 - - + +
37E LEU* 1.3 62.0 + - - +
39E GLU* 3.5 9.2 + - - +
40E THR* 2.9 32.8 + - - +
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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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15E VAL* 4.8 4.3 - - + +
16E TYR* 5.1 2.7 - - + -
19E TYR* 3.6 42.8 - - + -
29E VAL* 5.1 7.4 - - + -
33E ASP 2.9 14.1 + - - +
34E LEU* 3.1 17.2 + - + +
36E LYS* 1.3 77.9 - - - +
38E LEU* 1.3 64.1 + - + +
41E GLU* 2.7 48.7 + - + +
42E SER* 5.7 1.1 - - - -
71E PHE* 3.6 31.9 - - + -
74E LEU* 4.0 24.5 - - + -
8G LEU* 4.6 5.4 - - + -
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Residues in contact with LEU 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 33.7 + - + +
35E LYS* 3.8 3.8 - - - +
37E LEU* 1.3 72.7 - - + +
39E GLU* 1.3 62.7 + - + +
42E SER* 2.6 44.1 + - - +
46E ILE* 4.0 18.6 - - + -
47E ARG* 3.2 17.7 - - + +
50E GLY 5.0 0.2 - - - -
51E ALA* 3.8 32.5 - - + +
54E TRP* 3.9 27.6 - - + -
74E LEU* 4.1 22.9 - - + -
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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 LYS* 3.0 58.2 + - + +
36E LYS* 3.8 9.9 - - - +
38E LEU* 1.3 80.8 - - + +
40E THR* 1.3 59.4 + - - +
42E SER 4.5 1.0 - - - +
47E ARG* 3.6 25.2 + - - +
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Residues in contact with THR 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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19E TYR* 3.1 27.3 + - - +
36E LYS* 2.9 15.0 + - - +
39E GLU* 1.3 82.4 - - - +
41E GLU* 1.3 65.2 + - - +
42E SER 3.7 0.9 - - - -
6G SER* 3.4 15.1 - - - -
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Residues in contact with GLU 41 (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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15E VAL* 3.9 15.0 - - + -
18E LYS* 2.8 32.7 + - - -
19E TYR* 3.6 26.7 + - + +
37E LEU* 2.7 25.9 + - + +
40E THR* 1.3 81.5 - - - +
42E SER* 1.3 59.0 + - - +
78E MET* 4.0 2.4 - - - +
6G SER* 3.0 28.2 + - - -
7G GLN* 3.5 3.0 + - - +
8G LEU* 3.1 46.8 + - + +
9G GLU* 3.5 11.6 - - - +
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Residues in contact with SER 42 (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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37E LEU* 4.9 1.3 - - - -
38E LEU* 2.6 31.2 + - - +
39E GLU 4.5 1.4 - - - +
40E THR 3.7 0.5 - - - -
41E GLU* 1.3 79.9 - - - +
43E PRO* 1.3 69.6 + - - +
46E ILE* 3.7 21.0 - - - +
47E ARG* 2.8 40.5 + - - +
78E MET* 3.9 12.1 - - - -
9G GLU* 3.3 6.1 - - - +
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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