Contacts of the helix formed by residues 47 - 58 (chain W) in PDB entry 5IY6
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 GLY 47 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43W PRO* 4.3 4.3 - - - -
45W GLY 3.3 0.6 + - - -
46W THR* 1.3 74.9 - - - +
48W LYS* 1.3 62.5 + - - +
49W THR 3.5 2.2 - - - -
50W VAL* 4.0 18.1 - - - +
51W SER* 3.0 31.8 + - - -
86W GLU* 5.4 6.8 + - - -
671W LYS* 6.5 0.4 - - - -
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Residues in contact with LYS 48 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42W MET* 3.8 37.9 - - + +
43W PRO* 3.6 32.2 - - + +
44W SER 4.7 0.4 - - - -
45W GLY* 3.0 30.3 + - - +
46W THR 3.3 2.6 + - - -
47W GLY* 1.3 71.3 - - - +
49W THR* 1.3 70.8 + - - +
52W LEU* 3.3 19.9 + - - +
234W ASP* 2.8 39.2 + - - +
235W GLU* 3.7 19.9 + - - -
457W THR* 4.2 9.0 - - + +
459W GLY 4.0 11.4 - - - +
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Residues in contact with THR 49 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45W GLY 4.6 1.0 + - - -
47W GLY 3.5 0.2 - - - -
48W LYS* 1.3 91.1 + - - +
50W VAL* 1.4 63.0 + - - +
52W LEU* 3.3 8.0 + - - +
53W LEU* 3.3 19.8 + - - +
72W TYR* 4.7 20.0 + - + -
83W VAL* 4.3 34.9 - - + +
86W GLU* 4.4 11.8 + - + +
234W ASP* 4.3 12.4 + - + -
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Residues in contact with VAL 50 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18W TYR* 3.6 25.3 + - + +
47W GLY* 3.6 22.2 - - - +
49W THR* 1.4 73.5 - - - +
51W SER* 1.3 67.0 + - - +
53W LEU* 3.0 12.0 + - + +
54W ALA* 2.9 25.5 + - - +
86W GLU* 3.8 44.4 + - + +
90W LEU* 4.3 15.6 - - + +
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Residues in contact with SER 51 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18W TYR* 4.1 14.8 - - - -
20W GLU* 3.8 20.1 + - - -
42W MET* 4.9 9.0 - - - -
43W PRO* 6.4 0.4 - - - -
47W GLY* 3.0 23.1 + - - -
48W LYS* 4.0 4.3 - - - -
50W VAL* 1.3 77.8 - - - +
52W LEU* 1.3 58.4 + - - +
54W ALA* 3.4 8.6 - - - +
55W LEU* 2.8 41.5 + - - +
480W THR 5.8 0.4 - - - -
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Residues in contact with LEU 52 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28W LEU* 5.7 2.9 - - + -
40W LEU* 4.0 26.9 - - + -
42W MET* 4.2 12.0 - - + +
48W LYS 3.3 15.5 + - - +
49W THR* 3.5 11.9 - - - +
50W VAL 3.2 1.0 - - - -
51W SER* 1.3 75.5 - - - +
53W LEU* 1.4 51.6 + - - +
55W LEU* 3.1 9.8 + - + +
56W ILE* 2.7 42.9 + - + +
70W LEU* 5.1 0.7 - - + -
72W TYR* 2.6 43.1 - - + +
232W VAL* 3.7 19.7 - - + -
455W ILE* 4.6 10.3 - - + -
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Residues in contact with LEU 53 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49W THR 3.3 8.9 + - - +
50W VAL* 3.0 11.9 + - + +
52W LEU* 1.4 77.5 - - - +
54W ALA* 1.3 56.4 + - - +
56W ILE* 3.4 7.5 + - + -
57W MET* 3.1 24.9 + - - +
70W LEU* 4.2 23.3 - - + -
72W TYR* 4.3 4.6 + - + +
87W LEU* 3.7 50.5 - - + -
90W LEU* 3.5 25.5 - - + +
91W LEU* 4.0 9.4 - - + -
102W LEU* 3.8 16.1 - - + +
104W PHE* 5.4 0.9 - - + -
204W VAL* 4.7 8.1 - - + -
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Residues in contact with ALA 54 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17W ILE* 3.8 19.3 - - + -
18W TYR* 3.5 33.9 - - + +
21W GLN* 3.0 25.9 + - + -
50W VAL 2.9 7.7 + - - +
51W SER* 3.4 9.2 - - - +
53W LEU* 1.3 77.0 - - - +
55W LEU* 1.4 58.4 + - - +
57W MET* 3.3 20.4 - - - +
90W LEU* 4.0 6.9 - - + +
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Residues in contact with LEU 55 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21W GLN* 3.9 26.9 - - + +
24W TYR* 3.3 31.9 - - + +
25W MET* 4.0 8.1 - - + -
28W LEU* 3.9 31.7 - - + +
42W MET* 4.5 7.9 - - + -
51W SER* 2.8 30.7 + - - +
52W LEU* 3.8 8.1 - - + +
54W ALA* 1.4 73.8 - - - +
56W ILE* 1.4 60.7 + - - +
58W ALA* 3.6 18.4 - - - +
59W TYR* 4.6 1.4 + - - +
480W THR* 3.7 33.4 - - + +
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Residues in contact with ILE 56 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28W LEU* 5.3 5.6 - - + -
32W LEU* 4.4 24.7 - - + -
52W LEU* 2.7 34.3 + - + +
53W LEU* 3.4 9.6 + - + +
55W LEU* 1.4 71.0 - - - +
57W MET* 1.3 62.3 + - - +
58W ALA 3.2 2.9 - - - -
59W TYR* 2.9 19.6 + - + +
60W GLN* 3.1 12.0 + - - +
70W LEU* 4.4 37.9 - - + -
72W TYR* 4.6 0.2 - - - +
102W LEU* 5.9 0.9 - - + -
104W PHE* 5.1 14.1 - - + -
230W VAL* 5.9 4.7 - - + -
455W ILE* 5.1 11.4 - - + -
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Residues in contact with MET 57 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17W ILE* 3.9 24.7 - - + -
21W GLN* 3.8 22.2 - - - +
25W MET* 6.2 0.2 - - - -
53W LEU 3.1 12.6 + - - +
54W ALA* 3.3 15.0 - - - +
55W LEU 3.4 0.2 - - - -
56W ILE* 1.3 74.6 - - - +
58W ALA* 1.4 56.5 + - - +
59W TYR 3.1 5.2 + - - -
60W GLN* 2.9 31.3 + - - +
90W LEU* 5.7 1.1 - - + -
101W LYS* 3.3 65.7 - - + +
102W LEU* 4.3 11.9 - - + +
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Residues in contact with ALA 58 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21W GLN* 4.5 3.0 - - - +
25W MET* 3.3 44.0 - - + +
28W LEU* 6.3 0.4 - - + -
29W LYS* 5.0 12.7 - - + +
54W ALA 4.1 1.2 + - - -
55W LEU 3.6 13.4 + - - +
56W ILE 3.2 0.2 - - - -
57W MET* 1.4 74.7 - - - +
59W TYR* 1.3 65.6 + - + +
60W GLN* 5.6 0.2 - - - -
62W ALA* 5.7 0.2 - - - -
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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