Contacts of the helix formed by residues 47 - 60 (chain A) in PDB entry 6PAX
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 ASN 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 5.4 0.6 - - - +
36A PRO* 4.0 6.8 - - - +
37A CYS* 3.6 29.9 + - - +
40A SER* 3.4 23.9 + - - -
45A VAL 3.4 2.0 + - - -
46A SER* 1.3 71.1 - - - +
48A GLY* 1.3 56.7 + - - +
50A VAL* 3.2 4.5 + - - +
51A SER* 2.9 29.6 + - - -
1007B T 4.1 23.9 + - + +
1008B T 4.2 19.2 - - + +
2019C G 5.7 0.4 + - - -
2020C A 5.4 2.0 - - - +
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Residues in contact with GLY 48 (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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46A SER* 3.2 2.8 + - - -
47A ASN* 1.3 78.6 - - - +
49A CYS* 1.3 58.1 + - - +
51A SER* 3.5 7.0 + - - -
52A LYS* 3.1 27.0 + - - +
1009B T 3.4 29.9 + - - +
1010B C 4.4 2.7 + - - -
2018C T 3.7 7.0 - - - +
2019C G 3.8 14.1 + - - -
2020C A 4.5 3.4 - - - +
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Residues in contact with CYS 49 (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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18A LEU* 3.2 34.5 - - - -
45A VAL* 3.7 3.1 - - + -
46A SER* 2.9 25.4 + - - +
48A GLY* 1.3 75.5 - - - +
50A VAL* 1.3 65.2 + - - +
52A LYS* 3.1 6.0 + - - +
53A ILE* 3.0 36.4 + - - +
2017C G 3.9 23.1 - - + -
2018C T 3.4 17.8 - - + +
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Residues in contact with VAL 50 (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 ILE* 4.4 17.6 - - + +
36A PRO* 3.8 33.0 - - + +
39A ILE* 4.0 20.0 - - + -
40A SER* 3.9 25.8 - - - +
45A VAL* 3.9 17.5 - - + -
46A SER 3.0 14.2 + - - +
47A ASN* 3.5 7.0 - - - +
49A CYS* 1.3 74.8 - - - +
51A SER* 1.3 59.2 + - - +
53A ILE* 3.4 0.9 + - - +
54A LEU* 2.9 35.8 + - + +
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Residues in contact with SER 51 (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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36A PRO* 5.6 7.4 - - - +
47A ASN 2.9 16.6 + - - -
48A GLY* 3.5 6.5 - - - -
50A VAL* 1.3 79.4 - - - +
52A LYS* 1.3 57.6 + - - +
54A LEU* 4.0 3.2 - - - +
55A GLY* 2.9 28.1 + - - -
1008B T 4.0 25.4 + - - +
1009B T 3.8 21.7 - - - +
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Residues in contact with LYS 52 (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 ARG* 5.0 4.0 - - - +
48A GLY 3.1 17.2 + - - +
49A CYS* 3.1 6.5 + - - +
51A SER* 1.3 74.7 + - - +
53A ILE* 1.3 61.4 + - - +
55A GLY* 3.3 0.9 + - - -
56A ARG* 2.9 56.7 + - + +
1009B T 5.6 0.4 - - + +
2016C C 3.5 30.5 + - - +
2017C G 2.4 42.5 + - - -
2018C T 6.3 0.9 - - - -
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Residues in contact with ILE 53 (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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18A LEU* 4.1 5.4 - - + -
23A ARG* 4.0 57.0 - - + +
26A ILE* 3.9 31.6 - - + -
27A VAL* 6.2 1.1 - - + -
49A CYS* 3.0 39.9 + - - +
50A VAL 4.0 1.8 - - - +
52A LYS* 1.3 80.5 - - + +
54A LEU* 1.3 65.8 + - + +
56A ARG* 3.3 4.3 + - - +
57A TYR* 2.9 24.5 + - + +
62A SER 5.0 0.9 - - - +
63A ILE* 5.2 8.5 - - + +
2017C G 4.0 6.5 - - - +
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Residues in contact with LEU 54 (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 ILE* 3.8 21.3 - - + -
27A VAL* 4.2 13.7 - - + -
30A ALA* 3.7 33.0 - - + -
34A ALA 5.7 0.2 - - - +
36A PRO* 4.3 20.9 - - + -
39A ILE* 4.1 12.8 - - + -
50A VAL* 2.9 21.7 + - + +
51A SER* 4.0 3.6 - - - +
53A ILE* 1.3 76.8 - - + +
55A GLY* 1.3 63.5 + - - +
57A TYR* 3.0 8.2 + - + +
58A TYR* 2.9 51.8 + - + +
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Residues in contact with GLY 55 (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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51A SER 2.9 18.8 + - - -
52A LYS* 3.7 1.1 - - - -
54A LEU* 1.3 76.7 - - - +
56A ARG* 1.3 61.7 + - - +
58A TYR* 3.2 10.1 + - - +
59A ALA* 3.1 22.6 + - - +
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Residues in contact with ARG 56 (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 ARG* 4.6 5.9 - - - +
52A LYS* 2.9 37.8 + - + +
53A ILE* 4.0 4.5 - - - +
55A GLY* 1.3 75.7 - - - +
57A TYR* 1.3 56.6 - - - +
59A ALA* 3.2 5.0 + - + -
60A THR* 2.8 53.7 + - + +
62A SER* 4.3 6.7 - - - +
64A ARG 4.4 11.3 + - - -
65A PRO* 4.4 1.4 - - - +
66A ARG* 3.3 58.0 - - - +
2016C C 2.8 45.3 + - - -
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Residues in contact with TYR 57 (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 VAL* 3.5 36.3 - - + +
53A ILE* 2.9 15.7 + - + +
54A LEU* 3.4 10.8 - - + +
56A ARG* 1.3 77.4 - - - +
58A TYR* 1.3 88.1 + + - +
61A GLY* 2.6 60.4 + - - +
62A SER 3.5 15.6 + - - +
63A ILE* 4.1 18.4 - - + -
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Residues in contact with TYR 58 (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 VAL* 6.0 0.3 - - - +
30A ALA* 3.5 28.4 - - - +
31A HIS* 5.0 0.9 + - - -
54A LEU* 2.9 44.8 + - + +
55A GLY* 3.2 7.6 + - - +
57A TYR* 1.3 102.4 - + - +
59A ALA* 1.3 60.5 + - - +
61A GLY 4.8 0.3 + - - -
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Residues in contact with ALA 59 (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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55A GLY 3.1 15.5 + - - +
56A ARG* 3.8 6.1 - - - +
58A TYR* 1.3 79.0 - - - +
60A THR* 1.3 68.0 + - + +
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Residues in contact with THR 60 (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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56A ARG* 2.8 38.2 + - + +
59A ALA* 1.3 84.7 - - + +
61A GLY* 1.3 63.7 + - - +
62A SER* 3.1 24.3 + - - -
66A ARG* 6.0 2.9 - - - +
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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