Contacts of the helix formed by residues 16 - 32 (chain A) in PDB entry 1DXO
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 SER 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A HIS* 3.2 42.5 + - - +
13A GLU* 2.6 22.4 + - - +
14A ARG 4.7 0.2 - - - +
15A THR* 1.3 85.4 + - - +
17A PHE* 1.3 64.4 + - - +
18A ASN 3.9 0.4 - - - -
19A TYR* 3.3 16.1 + - - +
20A ALA 3.3 14.0 + - - -
301A FAD 3.5 24.2 + - - -
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Residues in contact with PHE 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A SER* 1.3 71.2 - - - +
18A ASN* 1.3 54.3 + - - +
20A ALA* 2.9 6.6 + - + +
21A MET* 2.6 66.5 + - + +
147A THR* 4.1 9.9 - - + -
189A THR* 4.5 2.9 - - - -
192A ILE* 3.8 25.6 - - + -
200A ARG* 3.6 29.8 - - + -
203A ILE* 3.5 33.7 - - + -
204A LEU* 3.7 23.6 - - + -
301A FAD 2.8 60.4 + + - +
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Residues in contact with ASN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.0 6.3 - - + -
11A HIS* 3.4 17.3 - - + -
16A SER* 3.8 8.5 - - - +
17A PHE* 1.3 76.8 - - - +
19A TYR* 1.3 57.8 + - - +
21A MET* 3.0 5.5 + - - +
22A LYS* 2.8 25.6 + - - +
100A GLN* 2.6 39.6 + - - +
101A PHE* 3.1 18.8 + - - +
102A PRO* 3.6 11.8 - - - +
147A THR* 3.2 18.3 + - - +
301A FAD 2.8 36.6 + - - -
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Residues in contact with TYR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.9 19.4 - - + +
11A HIS 6.0 0.4 - - - -
13A GLU 3.7 7.9 - - - +
14A ARG* 3.3 67.2 + - + +
16A SER* 3.3 20.1 + - - +
17A PHE 3.3 0.4 - - - -
18A ASN* 1.3 79.0 - - - +
20A ALA* 1.3 58.2 + - - +
22A LYS* 3.1 33.8 + - - +
23A GLU* 2.9 52.0 + - + +
40A ASP* 4.1 11.4 - - - -
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A SER 3.3 2.8 + - - +
17A PHE* 2.9 11.1 + - + +
19A TYR* 1.3 80.8 - - - +
21A MET* 1.3 58.1 + - - +
23A GLU* 3.2 7.6 + - - +
24A ALA* 2.8 30.0 + - - +
204A LEU* 3.8 11.9 - - + +
301A FAD 3.3 47.8 - - + +
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Residues in contact with MET 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 2.6 49.1 + - + +
18A ASN 3.3 6.1 - - - +
20A ALA* 1.3 74.2 - - - +
22A LYS* 1.3 54.7 + - - +
24A ALA* 3.5 1.5 + - - +
25A ALA* 3.1 22.3 + - - +
100A GLN* 3.0 27.1 - - - +
145A SER* 3.3 26.0 - - - +
147A THR* 5.1 1.6 - - + -
187A GLN* 4.4 3.8 - - + -
189A THR* 3.8 25.4 - - + -
203A ILE* 4.2 6.3 - - + -
204A LEU* 3.9 13.5 - - + -
207A TRP* 3.4 41.1 + - + -
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.7 27.9 - - + +
9A LEU* 4.0 27.8 - - + -
18A ASN 2.8 12.4 + - - +
19A TYR* 3.1 38.4 + - - +
21A MET* 1.3 75.7 - - - +
23A GLU* 1.3 92.9 + - - +
25A ALA* 3.4 6.2 + - - +
26A ALA* 3.1 21.1 + - - +
38A GLU* 3.2 35.8 + - + +
40A ASP* 4.7 5.8 + - - -
100A GLN* 4.5 4.9 + - + -
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 2.9 43.2 + - + +
20A ALA* 3.6 7.2 - - - +
22A LYS* 1.3 107.0 + - - +
24A ALA* 1.3 65.7 + - - +
26A ALA* 3.5 6.1 + - - +
27A ALA* 3.0 25.6 + - - +
38A GLU* 4.6 3.7 - - - +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 2.8 17.2 + - - +
21A MET* 3.5 6.5 - - - +
23A GLU* 1.3 77.1 - - - +
25A ALA* 1.3 56.6 + - - +
27A ALA* 3.3 4.8 + - - +
28A ALA* 2.8 31.9 + - - +
204A LEU* 4.0 22.7 - - + +
207A TRP* 4.3 4.5 - - + -
208A LYS* 3.7 27.4 - - + +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.1 15.7 - - + -
21A MET 3.1 17.5 + - - +
22A LYS* 3.6 7.4 - - - +
23A GLU 3.3 0.2 - - - -
24A ALA* 1.3 76.0 - - - +
26A ALA* 1.3 58.3 + - - +
28A ALA* 3.7 0.7 - - - +
29A LEU* 2.9 36.2 + - - +
98A ILE* 4.3 12.3 - - + -
207A TRP* 3.8 13.0 - - + +
211A LEU* 3.6 20.1 - - + +
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.9 12.5 - - + +
22A LYS 3.1 15.6 + - - +
23A GLU* 3.8 9.4 - - - +
24A ALA 3.4 0.2 - - - -
25A ALA* 1.3 78.5 - - - +
27A ALA* 1.3 57.6 + - - +
30A LYS* 2.9 47.2 + - - +
36A VAL* 4.0 11.1 - - + +
38A GLU* 3.9 20.2 - - - +
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU 3.0 19.5 + - - +
24A ALA* 3.6 4.9 - - - +
26A ALA* 1.3 75.0 - - - +
28A ALA* 1.3 64.9 + - - +
30A LYS* 3.9 5.2 - - - +
31A LYS* 3.1 35.5 + - + +
208A LYS* 4.3 14.6 - - - +
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ALA 2.8 17.8 + - - +
25A ALA 3.7 2.9 - - - +
27A ALA* 1.3 78.3 - - - +
29A LEU* 1.3 63.2 + - - +
31A LYS* 3.3 16.8 + - - +
32A LYS* 3.2 24.8 + - - +
208A LYS* 3.6 39.2 - - + +
211A LEU* 4.3 10.8 - - + -
212A GLU* 5.7 2.1 - - + +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ALA* 3.6 28.3 - - + -
7A ILE* 5.1 1.6 - - + -
25A ALA 2.9 21.8 + - - +
28A ALA* 1.3 68.6 - - - +
30A LYS* 1.3 67.5 + - - +
32A LYS* 3.1 9.5 + - - +
33A GLY 3.3 0.3 + - - -
34A TRP* 3.0 50.3 + - + +
36A VAL* 3.6 17.7 - - + -
96A LEU* 4.2 7.0 - - + -
98A ILE* 4.2 20.2 - - + -
211A LEU* 3.5 46.7 - - + +
214A ILE* 4.8 0.4 - - + -
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Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA* 2.9 38.0 + - - +
27A ALA* 3.9 5.4 - - - +
29A LEU* 1.3 76.7 - - - +
31A LYS* 1.3 55.9 + - + +
33A GLY* 2.7 26.5 + - - -
34A TRP 3.7 14.2 - - - +
36A VAL* 3.8 40.1 + - + +
38A GLU* 4.7 5.7 + - - -
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 3.1 30.4 + - + +
28A ALA* 3.4 15.9 - - - +
30A LYS* 1.3 76.9 - - + +
32A LYS* 1.3 61.3 + - + +
33A GLY* 3.0 4.4 + - - -
208A LYS* 2.7 34.7 - - - +
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA 3.2 10.4 + - - +
29A LEU* 3.1 11.2 + - - +
31A LYS* 1.3 81.9 - - + +
33A GLY* 1.3 57.3 + - - +
34A TRP* 3.5 17.8 + - + +
211A LEU 4.9 2.0 - - - +
212A GLU* 3.7 60.2 + - + +
213A ASN* 5.7 1.1 + - - -
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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