Contacts of the helix formed by residues 52 - 64 (chain Q) in PDB entry 2DYS
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 52 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50Q SER 3.9 1.4 + - - -
51Q LEU* 1.3 75.5 - - - +
53Q ILE* 1.3 66.9 + - - +
54Q ASP* 3.5 10.3 + - - +
55Q GLU* 2.8 39.5 + - - +
56Q LYS* 2.8 24.0 + - - +
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Residues in contact with ILE 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Q LEU 4.1 0.2 + - - -
52Q SER* 1.3 70.9 - - - +
54Q ASP* 1.3 69.7 + - - +
56Q LYS* 2.8 25.2 + - + +
57Q VAL* 2.9 28.5 + - + +
99R SER* 4.1 12.6 - - - +
103R GLU* 4.1 18.6 - - + +
104R LEU* 3.9 23.3 - - + +
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Residues in contact with ASP 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Q SER* 3.3 7.8 + - - +
53Q ILE* 1.3 87.6 + - - +
55Q GLU* 1.3 57.5 + - + +
57Q VAL* 3.6 7.0 + - - +
58Q GLU* 3.0 29.4 + - - +
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Residues in contact with GLU 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40Q LEU* 3.6 15.5 - - + +
43Q LYS* 2.8 41.6 + - - +
51Q LEU* 3.6 12.0 - - + -
52Q SER* 2.8 42.5 + - - +
54Q ASP* 1.3 74.9 - - + +
56Q LYS* 1.3 61.5 + - - +
58Q GLU* 4.2 11.9 - - - +
59Q LEU* 3.0 33.5 + - - +
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Residues in contact with LYS 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48Q TRP 3.5 18.9 + - - -
49Q SER* 5.1 1.8 - - - +
51Q LEU* 4.0 19.7 + - + +
52Q SER 2.8 17.1 + - - +
53Q ILE* 3.1 10.7 - - + +
55Q GLU* 1.3 74.3 - - - +
57Q VAL* 1.3 60.1 + - - +
59Q LEU* 3.2 9.1 + - - +
60Q TYR* 3.0 26.6 + - - +
61R PHE* 3.7 36.7 - - + -
97R GLY* 2.5 33.6 + - - -
98R ILE 4.3 0.2 - - - -
99R SER* 2.7 29.8 + - - +
104R LEU* 3.8 13.5 - - + -
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Residues in contact with VAL 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Q ILE* 2.9 25.3 + - + +
54Q ASP* 4.1 6.1 - - - +
56Q LYS* 1.3 73.0 - - - +
58Q GLU* 1.3 65.5 + - - +
60Q TYR* 3.2 6.9 + - - +
61Q ARG* 2.9 41.8 + - + +
104R LEU* 3.4 42.6 - - + +
106R LEU* 4.5 11.4 - - + -
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Residues in contact with GLU 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q SER* 4.6 6.4 + - - +
37Q GLN* 3.6 25.7 - - - +
40Q LEU* 3.3 24.6 - - + +
54Q ASP 3.0 18.7 + - - +
55Q GLU* 3.6 11.4 - - - +
56Q LYS 3.2 0.4 - - - -
57Q VAL* 1.3 76.3 - - - +
59Q LEU* 1.3 59.9 - - - +
61Q ARG* 3.3 6.9 + - - +
62Q LEU* 3.0 36.1 + - + +
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Residues in contact with LEU 59 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Q LEU* 3.8 20.4 - - + -
41Q LYS* 3.8 23.2 + - + +
44Q GLU* 3.1 45.3 - - + +
51Q LEU* 3.3 34.5 - - + -
55Q GLU 3.0 13.2 + - - +
56Q LYS* 3.2 8.7 + - - +
58Q GLU* 1.3 73.9 - - - +
60Q TYR* 1.3 64.6 + - - +
62Q LEU* 3.4 18.1 + - + +
63Q LYS* 3.4 9.2 + - - +
61R PHE* 3.9 13.2 - - + -
62R ALA* 3.7 11.2 - - - +
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Residues in contact with TYR 60 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Q LYS 3.0 13.1 + - - +
57Q VAL* 3.2 11.2 + - - +
59Q LEU* 1.3 77.6 - - - +
61Q ARG* 1.3 72.7 + - - +
63Q LYS* 3.3 3.1 + - - +
64Q PHE* 2.8 62.0 + + + +
67Q SER* 3.2 14.2 - - - -
61R PHE* 5.3 3.1 - - + -
62R ALA* 3.8 22.6 - - + +
65R VAL* 4.1 11.0 - - + -
66R ARG* 3.1 17.5 + - - -
69R GLU* 2.8 35.5 + - - -
104R LEU* 5.8 0.2 - - + -
106R LEU* 3.6 43.1 - - + -
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Residues in contact with ARG 61 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q HIS* 3.5 15.1 - - - -
30Q VAL* 4.0 3.5 - - - +
57Q VAL* 2.9 27.4 + - + +
58Q GLU* 3.3 7.4 + - - +
60Q TYR* 1.3 86.3 - - + +
62Q LEU* 1.3 62.4 + - - +
64Q PHE 3.2 14.1 - - - +
65Q LYS 3.2 25.5 + - - -
66Q GLU* 3.7 1.4 - - - +
67Q SER 3.7 7.7 - - - +
70Q GLU* 2.8 41.6 + - - -
105R GLY 5.5 1.2 + - - -
106R LEU* 3.7 23.2 - - - +
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Residues in contact with LEU 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Q ALA* 4.0 1.4 - - - +
29Q HIS* 3.3 3.6 + - - +
30Q VAL* 2.9 44.3 + - + +
33Q LEU* 4.3 14.1 - - + -
37Q GLN* 3.3 43.3 - - + +
40Q LEU* 4.6 7.6 - - + -
41Q LYS* 4.0 33.2 - - + +
58Q GLU* 3.0 28.0 + - + +
59Q LEU* 3.6 19.1 - - + +
60Q TYR 3.2 0.8 - - - -
61Q ARG* 1.3 79.2 - - - +
63Q LYS* 1.3 57.9 + - - +
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Residues in contact with LYS 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Q TYR* 3.6 9.9 - - - -
27Q VAL 4.5 0.6 - - - +
28Q ALA* 3.7 20.2 - - + +
29Q HIS* 2.9 19.9 + - - +
41Q LYS* 4.9 13.5 - - - +
59Q LEU 3.4 2.0 + - - +
60Q TYR 3.3 1.7 + - - +
62Q LEU* 1.3 81.6 - - - +
64Q PHE* 1.3 84.4 + - + +
60R ASP* 2.8 43.9 + - - -
62R ALA* 3.5 21.8 - - + -
63R SER* 3.7 7.8 + - - +
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Residues in contact with PHE 64 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Q TYR* 3.3 11.0 - - - +
23Q PRO 3.3 11.0 - - - -
24Q LEU* 4.0 9.6 - - + -
25Q PRO* 3.7 13.9 - - + -
29Q HIS* 3.7 4.9 - - - -
60Q TYR* 2.8 42.1 + + + +
61Q ARG* 3.2 27.0 - - - +
63Q LYS* 1.3 102.5 - - + +
65Q LYS* 1.3 66.2 + - - +
66Q GLU 4.1 11.4 - - - +
62R ALA 3.7 15.0 - - - -
63R SER* 4.4 4.0 - - - -
66R ARG* 3.2 60.1 - - + +
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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