Contacts of the helix formed by residues 30 - 43 (chain N) in PDB entry 5FLX
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 30 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28N LEU 4.2 0.7 - - - -
29N THR* 1.3 79.3 - - - +
31N ASP* 1.3 86.1 + - - +
32N ASP 3.4 1.4 + - - -
33N VAL* 3.6 17.7 + - - +
34N LYS* 4.1 8.3 + - - +
66N VAL* 6.4 1.6 - - - -
67N THR* 4.7 12.9 + - - +
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Residues in contact with ASP 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N THR* 3.8 2.4 + - - +
30N SER* 1.3 89.3 + - - +
32N ASP* 1.3 58.6 + - - +
34N LYS* 2.3 52.7 + - + +
35N GLU* 2.9 23.4 + - + +
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Residues in contact with ASP 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N LEU* 3.3 25.8 - - + +
29N THR* 3.1 35.6 + - - +
31N ASP* 1.3 78.8 - - - +
33N VAL* 1.3 56.4 + - - +
35N GLU* 2.9 30.6 + - - +
36N GLN* 2.9 37.1 + - + +
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Residues in contact with VAL 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N LEU* 4.3 26.9 - - + +
30N SER 3.6 12.1 + - - +
31N ASP 2.7 4.0 + - - -
32N ASP* 1.3 73.9 - - - +
34N LYS* 1.3 62.2 + - + +
36N GLN* 3.1 12.1 + - - +
37N ILE* 3.0 21.2 + - + +
54N LEU* 4.1 18.9 - - + +
60N VAL* 4.9 17.3 - - + -
63N VAL* 4.3 15.0 - - + -
66N VAL* 4.9 15.0 - - + -
67N THR* 3.9 19.7 - - - +
74N ILE* 6.5 0.2 - - + -
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Residues in contact with LYS 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30N SER* 4.5 6.5 - - - +
31N ASP* 2.3 43.4 + - + +
33N VAL* 1.3 71.1 - - + +
35N GLU* 1.3 62.6 + - + +
37N ILE* 2.9 10.4 + - - +
38N TYR* 2.9 51.2 + - + -
67N THR* 5.0 12.3 - - + +
74N ILE* 3.2 44.6 + - + +
77N SER* 5.6 3.0 + - - -
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Residues in contact with GLU 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N ASP* 2.9 22.9 + - + +
32N ASP* 2.9 34.6 - - - +
34N LYS* 1.3 75.0 - - + +
36N GLN* 1.3 62.2 + - + +
38N TYR* 3.3 9.2 + - - +
39N LYS* 2.9 42.2 + - + +
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Residues in contact with GLN 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N LEU* 5.8 2.9 - - + -
32N ASP* 2.9 23.9 + - + +
33N VAL* 3.1 11.2 + - - +
35N GLU* 1.3 81.2 + - - +
37N ILE* 1.3 57.9 + - - +
39N LYS* 3.2 12.6 + - - +
40N LEU* 2.9 39.1 + - + +
54N LEU* 4.4 15.0 - - + -
58N HIS* 3.2 39.9 + - + +
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Residues in contact with ILE 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N VAL* 3.0 8.2 + - + +
34N LYS* 2.9 31.5 + - - +
36N GLN* 1.3 76.8 - - - +
38N TYR* 1.3 64.5 + - + +
40N LEU* 4.5 0.8 - - - +
41N ALA* 2.8 29.7 + - + +
47N PRO* 6.4 0.4 - - + -
50N ILE* 3.6 33.9 - - + +
54N LEU* 4.1 17.5 - - + +
63N VAL* 6.3 0.2 - - + -
71N ILE* 3.8 42.6 - - + +
74N ILE* 4.5 17.5 - - + -
75N LEU* 6.1 4.5 - - + -
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Residues in contact with TYR 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N LYS* 2.9 67.6 + - + +
35N GLU* 3.8 7.9 - - + +
37N ILE* 1.3 83.2 - - + +
39N LYS* 1.3 66.4 + - + +
40N LEU 3.3 0.2 - - - -
41N ALA* 3.5 4.1 - - + +
42N LYS* 2.9 23.9 + - - +
74N ILE* 3.6 19.4 + - + -
75N LEU* 5.7 6.5 - - + -
77N SER* 4.7 2.1 - - - -
78N LYS* 3.1 41.4 - - + +
80N LEU* 3.8 26.0 - - + +
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Residues in contact with LYS 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N GLU* 2.9 29.6 + - + +
36N GLN* 3.6 16.2 - - - +
38N TYR* 1.3 79.6 - - + +
40N LEU* 1.3 65.0 + - + +
42N LYS* 3.3 20.2 + - + +
43N LYS* 3.5 17.2 - - - +
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Residues in contact with LEU 40 (chain N).
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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36N GLN* 2.9 21.8 + - - +
37N ILE* 4.5 2.0 - - - +
39N LYS* 1.3 76.7 - - + +
41N ALA* 1.3 63.8 + - - +
42N LYS 3.2 0.7 - - - -
43N LYS* 3.2 30.4 + - + +
45N LEU* 3.5 37.4 + - + +
50N ILE* 4.8 9.2 - - + -
53N ILE* 3.5 33.4 - - + -
54N LEU* 3.5 26.7 - - + +
58N HIS* 6.0 2.2 - - - +
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Residues in contact with ALA 41 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N ILE* 2.8 23.7 + - + +
38N TYR* 3.1 11.0 + - + +
40N LEU* 1.3 77.4 - - - +
42N LYS* 1.3 61.5 + - - +
44N GLY* 3.3 12.9 + - - +
45N LEU 5.0 2.2 - - - +
50N ILE* 4.5 12.3 - - + +
75N LEU* 4.9 13.5 - - + -
80N LEU* 4.0 20.9 - - + +
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Residues in contact with LYS 42 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N TYR 2.9 11.5 + - - +
39N LYS* 3.5 15.7 - - + +
40N LEU 3.2 0.2 - - - -
41N ALA* 1.3 77.2 - - - +
43N LYS* 1.3 66.9 + - + +
44N GLY* 3.1 3.9 + - - -
80N LEU* 5.2 3.5 - - + +
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Residues in contact with LYS 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39N LYS* 3.5 17.3 - - - +
40N LEU* 3.2 24.3 + - + +
42N LYS* 1.3 84.7 - - + +
44N GLY* 1.3 60.2 + - - +
45N LEU* 3.4 14.9 - - + +
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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