Contacts of the helix formed by residues 23 - 36 (chain W) in PDB entry 6P59
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 23 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22W SER* 1.3 82.9 + - - +
24W VAL* 1.3 61.1 + - - +
25W PHE* 3.2 6.7 + - + +
26W GLU* 3.5 27.6 - - + +
27W LEU* 3.6 11.4 + - - +
53W ASP 2.6 27.9 + - - -
54W GLY* 3.9 11.2 + - - -
55W LYS 3.6 6.1 - - - -
56W THR* 4.2 4.2 - - - +
57W LEU* 4.1 5.3 - - - +
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Residues in contact with VAL 24 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23W THR* 1.3 73.9 + - - +
25W PHE* 1.3 67.5 + - - +
27W LEU* 3.0 15.6 + - + +
28W LYS* 3.2 17.7 + - - +
44W LEU* 4.2 19.1 - - + -
51W LEU* 4.0 26.7 - - + +
52W ASP 3.3 24.5 - - - +
53W ASP* 4.2 6.1 - - - +
55W LYS 3.0 18.3 + - - +
57W LEU* 4.1 16.6 - - + -
60W CYS* 3.8 21.3 - - - -
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Residues in contact with PHE 25 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23W THR* 3.2 6.0 + - + +
24W VAL* 1.3 78.3 - - - +
26W GLU* 1.3 66.8 + - + +
28W LYS* 3.1 22.5 + - + +
29W ARG* 3.3 49.1 + - + +
39W PRO* 3.9 21.8 - - + -
40W ASP* 5.0 8.3 - - - -
53W ASP* 3.0 46.9 + - + +
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Residues in contact with GLU 26 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18W ALA* 4.7 11.6 - - - +
22W SER* 3.1 21.0 + - - +
23W THR* 3.5 25.8 + - + +
24W VAL 3.2 0.8 - - - -
25W PHE* 1.3 80.4 - - + +
27W LEU* 1.3 70.5 + - - +
29W ARG* 3.0 27.5 + - + +
30W ILE* 3.3 20.8 + - - +
57W LEU* 5.5 0.7 - - - +
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Residues in contact with LEU 27 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5W LEU* 4.1 30.3 - - + -
7W ILE* 4.3 22.7 - - + -
16W THR* 4.8 6.5 - - + -
17W ASP 5.7 0.2 - - - +
18W ALA* 4.7 15.3 - - + -
23W THR 3.6 6.5 + - - +
24W VAL* 3.0 16.4 + - + +
26W GLU* 1.3 86.2 + - - +
28W LYS* 1.3 60.8 + - - +
30W ILE* 3.0 24.6 + - + +
31W VAL* 3.1 12.5 + - - +
44W LEU* 3.7 20.0 - - + -
51W LEU* 6.3 1.3 - - + -
57W LEU* 4.5 14.8 - - + -
62W PHE* 6.4 0.9 - - + -
75W VAL* 4.4 13.7 - - + -
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Residues in contact with LYS 28 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24W VAL* 3.2 11.0 + - - +
25W PHE* 3.1 16.0 + - + +
27W LEU* 1.3 75.8 - - - +
29W ARG* 1.3 56.5 + - - +
31W VAL* 3.2 5.4 + - - +
32W GLU* 2.8 24.9 + - - +
39W PRO* 3.7 33.2 + - + +
42W GLN* 3.0 47.4 + - + +
43W ARG* 4.5 4.0 - - - +
44W LEU* 3.5 36.5 - - + +
50W LEU* 6.4 0.4 - - - +
51W LEU 5.4 2.9 + - - -
53W ASP* 2.8 32.5 + - - +
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Residues in contact with ARG 29 (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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25W PHE* 3.3 41.8 + - + +
26W GLU* 3.0 21.6 + - + +
28W LYS* 1.3 74.9 - - - +
30W ILE* 1.3 63.5 + - + +
32W GLU* 2.7 42.7 + - - +
33W GLY* 3.1 18.5 + - - -
39W PRO* 3.9 17.4 - - - +
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Residues in contact with ILE 30 (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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7W ILE* 5.2 4.7 - - + -
16W THR* 4.2 27.1 - - + +
17W ASP 5.7 4.7 - - - +
26W GLU* 3.3 23.3 + - - +
27W LEU* 3.0 19.1 + - + +
29W ARG* 1.3 76.5 - - + +
31W VAL* 1.3 63.1 + - - +
33W GLY* 3.4 9.7 + - - +
34W ILE* 3.4 32.7 - - + +
18Z TYR* 4.6 9.9 - - + +
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Residues in contact with VAL 31 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7W ILE* 3.8 35.0 - - + -
14W ILE* 4.9 5.6 - - + -
27W LEU 3.1 13.1 + - - +
28W LYS* 3.4 4.3 - - - +
29W ARG 3.2 0.2 - - - -
30W ILE* 1.3 75.0 - - - +
32W GLU* 1.3 59.9 + - - +
34W ILE* 3.2 4.3 + - - -
35W LEU* 2.9 36.7 + - + +
37W ARG 4.9 0.2 + - - -
42W GLN* 3.2 32.5 - - - +
44W LEU* 4.7 5.4 - - + -
77W LEU* 3.7 21.1 - - + -
79W PHE* 4.2 11.0 - - + -
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Residues in contact with GLU 32 (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 LYS 2.8 12.9 + - - +
29W ARG* 2.7 45.5 + - - +
31W VAL* 1.3 78.9 - - - +
33W GLY* 1.3 57.1 + - - +
36W LYS* 3.1 29.7 + - - +
37W ARG 3.3 29.8 - - - +
38W PRO* 4.0 11.6 - - - +
39W PRO* 3.4 12.5 - - + +
42W GLN* 4.1 0.2 - - - +
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Residues in contact with GLY 33 (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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29W ARG 3.1 12.6 + - - -
30W ILE* 3.4 4.2 + - - -
31W VAL 3.2 0.6 - - - -
32W GLU* 1.3 76.3 - - - +
34W ILE* 1.3 60.8 + - - +
36W LYS* 3.1 20.0 + - - -
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Residues in contact with ILE 34 (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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14W ILE* 3.9 29.8 - - + -
30W ILE* 3.4 25.1 - - + +
31W VAL 3.2 2.7 + - - +
33W GLY* 1.3 82.2 - - - +
35W LEU* 1.3 81.7 + - + +
36W LYS* 3.4 15.4 + - - +
18Z TYR* 3.8 47.3 - - + -
30Z ILE* 4.0 23.8 - - + -
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Residues in contact with LEU 35 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9W ARG* 5.9 0.7 - - + -
12W THR* 4.2 17.9 - - + -
14W ILE* 3.8 19.1 - - + -
31W VAL* 2.9 14.8 + - + +
34W ILE* 1.3 93.2 - - + +
36W LYS* 1.3 71.2 + - - +
37W ARG* 3.3 11.5 + - - +
77W LEU* 4.2 9.2 - - + -
79W PHE* 3.5 39.8 - - + -
30Z ILE* 3.9 17.5 - - + -
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Residues in contact with LYS 36 (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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31W VAL 3.9 0.4 + - - -
32W GLU* 3.1 20.9 + - - +
33W GLY* 3.1 23.2 + - - -
34W ILE* 3.4 13.9 + - - +
35W LEU* 1.3 79.3 - - - +
37W ARG* 1.3 68.4 + - - +
38W PRO* 4.6 2.1 - - - +
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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