Contacts of the helix formed by residues 38 - 50 (chain E) in PDB entry 3KDO
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 THR 38 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E PRO* 3.9 1.7 - - - +
37E TYR* 1.3 76.6 - - - +
39E ILE* 1.3 63.3 + - - +
40E GLU* 3.4 17.6 + - - +
41E GLN* 3.0 39.6 + - - +
42E ALA* 3.2 21.7 + - - +
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Residues in contact with ILE 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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31E VAL* 3.9 31.4 - - + +
33E PRO* 4.3 8.5 - - + +
38E THR* 1.3 70.9 - - - +
40E GLU* 1.3 78.7 + - - +
42E ALA* 3.2 1.1 + - - +
43E ALA* 2.7 38.1 + - + +
77E PHE* 3.7 24.0 - - + -
85E TRP* 3.5 67.3 - - + +
87E VAL* 4.0 6.1 - - + -
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Residues in contact with GLU 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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10E ASP* 5.1 3.1 - - - +
13E VAL* 3.5 22.6 - - + +
15E LYS* 2.8 40.0 + - - +
38E THR* 3.4 18.9 + - - +
39E ILE* 1.3 96.4 - - - +
41E GLN* 1.3 57.7 + - + +
44E GLY* 2.8 26.0 + - - -
77E PHE* 4.3 9.5 - - + -
85E TRP* 5.9 0.3 - - - -
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Residues in contact with GLN 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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9E TYR* 4.6 0.7 - - - +
10E ASP* 4.8 12.6 - - - +
36E GLY 4.1 2.6 - - - +
37E TYR* 3.4 23.4 - - + -
38E THR* 3.0 41.9 + - - +
40E GLU* 1.3 79.3 - - + +
42E ALA* 1.3 59.3 + - - +
44E GLY* 3.7 1.1 + - - -
45E ALA 3.3 13.2 + - - -
117E ARG* 3.0 41.4 + - - +
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Residues in contact with ALA 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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31E VAL* 3.9 17.5 - - + -
33E PRO* 3.9 20.6 - - + -
37E TYR* 5.3 1.1 - - + +
38E THR 3.2 13.3 + - - +
39E ILE* 3.8 2.7 - - - +
41E GLN* 1.3 76.3 - - - +
43E ALA* 1.3 68.2 + - - +
45E ALA* 3.2 4.0 + - - +
46E VAL* 3.0 28.5 + - - +
117E ARG* 4.1 23.1 - - + +
118E VAL* 4.3 4.6 - - + +
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Residues in contact with ALA 43 (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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13E VAL* 4.6 1.3 - - + -
31E VAL* 5.3 3.6 - - - -
39E ILE* 2.7 23.0 + - - +
40E GLU 3.9 1.6 - - - +
42E ALA* 1.3 73.0 - - - +
44E GLY* 1.3 62.6 + - - +
46E VAL* 3.3 8.7 + - - +
47E ALA* 3.0 24.8 + - - +
74E ALA* 4.2 6.2 - - + +
77E PHE* 3.5 30.5 - - + -
87E VAL* 4.0 20.9 - - + -
89E ILE* 4.5 1.7 - - - +
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Residues in contact with GLY 44 (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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9E TYR* 3.3 28.2 - - - +
12E TYR* 3.7 4.3 - - - +
13E VAL* 3.7 10.5 - - - +
40E GLU 2.8 18.9 + - - -
41E GLN 4.1 1.6 - - - -
43E ALA* 1.3 77.3 - - - +
45E ALA* 1.3 56.3 + - - +
47E ALA* 3.3 2.5 + - - +
48E ALA* 2.9 30.5 + - - +
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Residues in contact with ALA 45 (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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9E TYR* 3.5 28.7 - - + +
41E GLN 3.3 13.1 + - - +
42E ALA 3.2 8.4 + - - +
44E GLY* 1.3 76.4 - - - +
46E VAL* 1.3 54.4 + - + +
49E GLU* 2.7 39.2 + - - +
115E MET* 3.7 27.6 - - + -
117E ARG* 4.0 10.8 - - + +
118E VAL* 6.2 0.7 - - + -
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Residues in contact with VAL 46 (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 PHE* 4.0 23.3 - - + -
31E VAL* 4.8 5.4 - - + -
42E ALA 3.0 19.4 + - - +
43E ALA* 3.3 10.3 + - - +
45E ALA* 1.3 76.9 - - + +
47E ALA* 1.3 53.2 + - - +
50E SER* 2.6 37.2 + - - -
89E ILE* 3.5 22.2 - - + -
112E ILE* 3.7 17.0 - - + +
115E MET* 4.9 4.5 - - - -
118E VAL* 4.1 20.6 - - + -
121E LEU* 4.2 22.7 - - + -
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Residues in contact with ALA 47 (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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12E TYR* 3.6 30.3 - - + +
43E ALA 3.0 17.6 + - - +
46E VAL* 1.3 76.5 - - - +
48E ALA* 1.3 57.4 + - - +
50E SER* 3.1 15.2 + - - -
51E SER* 2.8 26.7 + - - -
72E ALA* 4.1 4.8 - - - +
74E ALA* 4.4 3.1 - - + +
89E ILE* 4.0 26.7 - - + -
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Residues in contact with ALA 48 (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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9E TYR* 3.5 24.0 - - + -
12E TYR* 3.4 37.4 - - + -
44E GLY 2.9 17.0 + - - +
45E ALA 3.8 0.2 - - - +
47E ALA* 1.3 72.9 - - - +
49E GLU* 1.3 59.0 + - - +
50E SER 3.0 10.4 + - - -
51E SER 3.0 8.8 + - - -
52E THR 3.4 0.5 + - - -
53E GLY* 3.0 28.7 + - - +
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Residues in contact with GLU 49 (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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9E TYR* 2.8 22.8 + - + +
45E ALA 2.7 23.3 + - - +
48E ALA* 1.3 73.1 - - - +
50E SER* 1.3 56.6 + - - +
51E SER 3.5 0.2 - - - -
53E GLY 3.8 13.5 - - - +
54E THR* 3.7 9.3 - - - -
107E SER* 4.7 1.0 - - - +
111E ASN* 5.2 9.6 + - + +
112E ILE* 4.0 14.8 - - + +
115E MET* 3.4 29.8 - - + -
163I LYS* 5.7 0.2 + - - -
165I LYS* 3.4 22.3 + - - +
192I GLU* 4.8 1.7 - - - +
322I LYS* 2.9 34.6 + - - -
600I CAP 3.6 10.2 - - - +
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Residues in contact with SER 50 (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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46E VAL 2.6 22.8 + - - -
47E ALA* 3.1 8.5 + - - -
48E ALA 3.0 0.2 - - - -
49E GLU* 1.3 78.9 - - - +
51E SER* 1.3 55.1 + - - +
91E TYR* 2.8 35.6 + - - -
107E SER* 2.4 49.2 + - - +
108E ILE* 4.6 0.4 - - - -
112E ILE* 3.9 14.4 - - - -
193I ASN* 4.6 1.8 - - - -
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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