Contacts of the helix formed by residues 36 - 49 (chain Y) 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 PRO 36 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5691 A 5.6 4.0 - - - +
5701 C 3.6 26.5 - - - +
34Y THR 3.8 3.8 - - - +
35Y VAL* 1.3 99.3 - - + +
37Y LYS* 1.3 67.8 + - - +
38Y THR* 3.1 7.7 + - - +
39Y GLU* 3.3 21.3 + - + +
40Y ILE* 3.6 9.7 + - - +
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Residues in contact with LYS 37 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5701 C 3.9 0.2 + - - -
5711 U 3.2 24.7 + - - +
35Y VAL 4.6 0.2 - - - -
36Y PRO* 1.3 73.5 - - - +
38Y THR* 1.3 65.0 + - - +
40Y ILE* 4.2 2.4 + - - +
41Y ARG* 3.3 47.5 + - - +
56Y PHE* 4.9 3.4 - - - +
57Y VAL* 3.2 47.7 + - + +
60Y PHE* 5.0 12.6 - - + -
93Y ARG* 5.6 18.6 - - - +
94Y HIS* 5.3 6.5 + - - -
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Residues in contact with THR 38 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Y PRO* 3.2 4.7 - - - +
37Y LYS* 1.3 80.1 - - - +
39Y GLU* 1.3 60.7 + - - +
41Y ARG* 3.3 13.6 + - + +
42Y GLU* 2.9 53.4 + - + +
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Residues in contact with GLU 39 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Y THR* 6.1 0.7 - - - +
5Y VAL* 4.7 11.2 - - + +
35Y VAL* 3.3 28.7 - - + +
36Y PRO* 3.3 14.9 + - + +
38Y THR* 1.3 77.8 - - - +
40Y ILE* 1.3 66.2 + - - +
42Y GLU* 3.2 10.9 + - - +
43Y LYS* 2.9 57.4 + - + +
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Residues in contact with ILE 40 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y VAL* 6.3 2.0 - - + -
7Y ILE* 3.7 25.6 - - + +
25Y ILE* 5.5 6.5 - - + -
27Y VAL* 4.6 18.8 - - + -
29Y HIS* 4.9 8.1 - - + +
34Y THR* 5.0 1.6 - - + -
35Y VAL* 3.6 46.2 - - + +
36Y PRO 3.6 5.0 + - - +
37Y LYS* 4.7 2.2 - - - +
38Y THR 3.5 0.2 - - - -
39Y GLU* 1.3 76.4 - - - +
41Y ARG* 1.3 58.4 + - - +
43Y LYS* 3.2 2.5 + - - -
44Y LEU* 2.9 31.3 + - + +
57Y VAL* 5.4 12.3 - - + -
60Y PHE* 4.1 27.8 - - + -
69Y THR* 5.6 1.1 - - - +
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Residues in contact with ARG 41 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Y LYS* 3.3 40.3 + - - +
38Y THR* 3.3 13.4 + - - +
39Y GLU 3.2 0.6 - - - -
40Y ILE* 1.3 80.7 - - - +
42Y GLU* 1.3 57.9 + - + +
44Y LEU* 3.5 6.1 + - - +
45Y ALA* 2.9 26.9 + - - +
52Y PRO* 2.9 40.0 + - + +
53Y ASP* 3.1 26.1 + - - +
55Y ILE* 2.7 32.8 + - + +
56Y PHE* 4.2 0.4 - - - +
57Y VAL* 5.1 7.8 - - + +
94Y HIS* 3.2 36.5 + - - -
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Residues in contact with GLU 42 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Y THR* 2.9 41.1 + - + +
39Y GLU* 3.2 9.0 + - - +
41Y ARG* 1.3 75.3 - - + +
43Y LYS* 1.3 68.6 + - - +
45Y ALA* 3.1 9.7 + - - +
46Y LYS* 2.9 44.7 + - - +
52Y PRO* 4.6 16.8 - - + +
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Residues in contact with LYS 43 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y VAL* 4.2 24.7 - - + -
7Y ILE* 3.7 18.4 - - + -
39Y GLU* 2.9 50.5 + - + +
40Y ILE* 4.6 1.3 - - - -
42Y GLU* 1.3 82.6 + - - +
44Y LEU* 1.3 61.9 + - - +
46Y LYS* 3.3 32.9 + - + +
47Y MET* 3.2 31.3 + - + +
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Residues in contact with LEU 44 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8371 A 5.6 5.4 - - - +
7Y ILE* 4.1 17.4 - - + +
9Y THR* 6.5 0.2 - - - -
23Y MET* 4.8 9.0 - - + -
25Y ILE* 3.8 30.3 - - + -
40Y ILE* 2.9 20.2 + - + +
41Y ARG* 3.8 5.4 - - - +
43Y LYS* 1.3 75.7 - - - +
45Y ALA* 1.3 59.1 + - - +
47Y MET* 3.4 11.6 + - + -
48Y TYR* 2.9 35.4 + - + +
55Y ILE* 3.8 25.6 - - + -
56Y PHE 5.4 0.2 - - - +
57Y VAL* 5.9 2.7 - - + -
73Y GLY* 5.4 2.7 - - - -
75Y ILE* 3.8 24.2 - - + -
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Residues in contact with ALA 45 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Y ARG 2.9 16.0 + - - +
42Y GLU* 3.1 8.9 + - - +
44Y LEU* 1.3 76.5 - - - +
46Y LYS* 1.3 58.2 + - + +
48Y TYR* 4.8 0.4 - - - -
49Y LYS* 2.9 21.5 + - - -
50Y THR 3.2 26.2 + - - +
52Y PRO* 3.7 28.0 - - + -
55Y ILE* 3.6 14.5 - - + +
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Residues in contact with LYS 46 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42Y GLU* 2.9 28.8 + - - +
43Y LYS* 3.6 36.2 - - + +
44Y LEU 3.2 0.2 - - - -
45Y ALA* 1.3 77.9 - - + +
47Y MET* 1.3 64.8 + - + +
49Y LYS* 3.4 20.2 + - - +
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Residues in contact with MET 47 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8371 A 3.0 77.3 + - + +
7Y ILE* 3.6 43.7 - - + +
43Y LYS* 3.2 26.2 + - + +
44Y LEU* 4.2 9.9 - - + +
46Y LYS* 1.3 80.8 - - + +
48Y TYR* 1.3 60.3 + - - +
49Y LYS* 3.6 4.7 + - - +
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Residues in contact with TYR 48 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8371 A 5.8 4.3 - - - +
12Y PHE* 6.1 0.9 - + - -
21Y LYS* 2.4 42.4 + - - -
23Y MET* 5.3 7.2 - - + -
44Y LEU* 2.9 22.8 + - + +
45Y ALA* 4.5 1.3 - - - +
47Y MET* 1.3 75.0 - - - +
49Y LYS* 1.3 71.2 + - - +
50Y THR* 3.1 37.4 - - + +
55Y ILE* 4.7 0.4 - - + -
75Y ILE* 3.6 42.3 - - + +
76Y TYR 5.5 0.7 - - - -
77Y ASP* 3.5 14.2 + - - -
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Residues in contact with LYS 49 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8371 A 4.5 22.6 + - + -
45Y ALA 2.9 10.8 + - - -
46Y LYS* 3.6 14.4 - - - +
47Y MET 3.3 4.2 - - - +
48Y TYR* 1.3 81.3 - - - +
50Y THR* 1.3 64.2 + - - +
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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