Contacts of the helix formed by residues 20 - 31 (chain E) in PDB entry 1KXT
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 ARG 20 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E TRP* 1.3 74.2 - - - +
21E TRP* 1.3 66.5 + - - +
22E VAL* 3.5 34.7 - - + +
23E ASP* 3.3 27.6 + - - +
24E ILE* 3.1 23.9 + - - +
72E ARG 4.2 9.5 + - - +
73E SER* 3.4 12.3 + - - +
78E GLU* 5.6 3.2 + - - -
367E ILE* 3.7 45.6 + - + +
368E LYS 3.8 6.5 - - - +
369E GLU* 4.0 17.8 - - - +
382E TRP* 5.9 0.2 - - - -
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Residues in contact with TRP 21 (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 TRP 3.5 14.4 - - - -
20E ARG* 1.3 74.6 - - - +
22E VAL* 1.3 57.5 + - - +
24E ILE* 3.4 13.2 + - + +
25E ALA* 3.0 28.6 + - - +
42E VAL* 3.9 15.9 - - + -
43E SER 3.7 23.3 - - - -
45E PRO* 3.7 29.9 + - + +
61E ARG* 4.1 3.8 - - - -
69E LEU 5.4 1.2 + - - -
71E THR* 4.2 2.3 + - - -
73E SER* 2.7 39.4 + - - +
74E GLY* 3.6 17.7 + - - -
75E ASN 3.6 9.1 + - - -
78E GLU* 3.9 22.0 - - + +
79E PHE* 3.4 38.6 - + - +
82E MET* 3.7 26.1 - - + +
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Residues in contact with VAL 22 (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 ARG* 3.5 44.6 - - + +
21E TRP* 1.3 77.1 - - - +
23E ASP* 1.3 63.3 + - - +
25E ALA* 3.3 8.7 + - - +
26E LEU* 3.1 35.2 + - + +
73E SER 4.7 0.4 + - - -
78E GLU* 4.0 29.6 - - + +
81E ASP* 6.1 0.4 - - - +
85E ARG* 5.1 3.3 + - - +
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Residues in contact with ASP 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E TRP* 4.1 16.2 - - + -
20E ARG* 3.3 38.0 + - - +
22E VAL* 1.3 77.2 - - - +
24E ILE* 1.3 61.3 + - - +
26E LEU* 3.4 13.5 + - - +
27E GLU* 2.8 28.9 + - - +
30E ARG* 3.9 7.1 + - - +
368E LYS 4.0 0.7 - - - +
369E GLU* 3.5 13.7 - - - +
370E VAL* 3.3 38.1 + - + +
382E TRP* 5.7 0.2 - - - -
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Residues in contact with ILE 24 (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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16E LEU* 4.0 22.9 - - + +
19E TRP* 3.6 31.9 - - + +
20E ARG 3.1 13.7 + - - +
21E TRP* 3.9 9.4 - - + -
23E ASP* 1.3 73.6 - - - +
25E ALA* 1.3 66.5 + - - +
27E GLU* 3.7 6.6 - - - +
28E CYS* 2.9 26.8 + - - -
40E VAL* 4.7 9.2 - - + -
42E VAL* 3.7 27.1 - - + -
82E MET* 3.5 29.8 - - + -
86E CYS* 4.1 8.7 - - - -
93E ILE* 5.6 1.1 - - + -
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Residues in contact with ALA 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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21E TRP 3.0 14.8 + - - +
22E VAL* 3.3 12.8 - - - +
23E ASP 3.2 0.2 - - - -
24E ILE* 1.3 79.0 - - - +
26E LEU* 1.3 62.0 + - - +
28E CYS* 3.5 6.2 + - - +
29E GLU* 3.3 21.8 + - - +
81E ASP* 4.7 0.7 - - - +
82E MET* 3.9 18.6 - - - +
85E ARG* 3.5 32.6 + - - +
86E CYS* 4.3 10.5 - - - -
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Residues in contact with LEU 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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22E VAL* 3.1 20.6 + - + +
23E ASP* 3.7 13.0 - - - +
24E ILE 3.2 0.2 - - - -
25E ALA* 1.3 75.6 - - - +
27E GLU* 1.3 65.5 + - - +
29E GLU* 3.1 11.9 + - + +
30E ARG* 2.9 54.1 + - + +
85E ARG* 3.7 19.1 - - - +
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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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16E LEU* 4.6 2.2 - - + -
19E TRP* 3.7 19.3 - - + -
23E ASP 2.8 18.0 + - - +
24E ILE* 3.7 6.5 - - - +
26E LEU* 1.3 77.6 - - - +
28E CYS* 1.3 61.8 + - - +
30E ARG* 2.7 40.7 + - - +
31E TYR* 2.9 25.3 + - - -
32E LEU* 3.0 29.3 + - + -
386E HIS* 2.6 32.3 + - - +
387E ARG* 3.1 24.9 + - - -
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Residues in contact with CYS 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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24E ILE* 2.9 19.3 + - - +
25E ALA 3.6 4.3 - - - +
26E LEU 3.2 0.2 - - - -
27E GLU* 1.3 75.6 - - - +
29E GLU* 1.3 64.4 - - + +
32E LEU* 3.7 16.7 + - - -
33E GLY* 2.9 28.9 + - - -
40E VAL* 4.6 1.3 - - - -
86E CYS* 2.0 59.5 - - - -
89E VAL* 3.7 9.3 - - + +
91E VAL* 3.6 20.6 - - + -
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Residues in contact with GLU 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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25E ALA 3.3 9.7 - - - +
26E LEU* 3.1 13.2 + - + +
28E CYS* 1.3 78.7 - - + +
30E ARG* 1.3 60.1 + - + +
31E TYR 3.6 0.3 + - - -
34E PRO* 3.7 15.4 - - - +
85E ARG* 2.9 66.8 + - + +
89E VAL* 4.4 17.9 - - + +
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Residues in contact with ARG 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E TRP* 4.5 1.8 - - - -
23E ASP* 3.9 14.6 + - - +
26E LEU* 2.9 45.3 + - + +
27E GLU* 2.7 39.0 + - - +
29E GLU* 1.3 74.0 - - + +
31E TYR* 1.3 64.6 + - + +
34E PRO* 4.5 5.1 - - - +
35E LYS* 5.6 2.1 + - - -
370E VAL* 4.0 21.2 + - - +
372E ILE* 3.6 29.9 - - - +
387E ARG* 3.7 10.0 + - - +
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Residues in contact with TYR 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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27E GLU* 2.9 17.8 + - - +
29E GLU 3.4 3.0 + - - -
30E ARG* 1.3 81.5 - - - +
32E LEU* 1.3 74.2 + - + +
33E GLY 3.3 1.3 - - - -
34E PRO* 3.1 6.5 - - - +
35E LYS* 2.8 48.8 + - + +
37E PHE* 3.6 16.8 - + - -
376E THR* 5.8 3.8 - - + -
386E HIS* 2.7 44.0 + + - -
387E ARG* 3.1 47.9 + - + +
392E ARG* 2.7 35.8 - - + +
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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