Contacts of the helix formed by residues 53 - 63 (chain Q) in PDB entry 2X86
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 LYS 53 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30Q VAL* 3.7 8.5 - - - -
31Q ASP 2.7 13.0 + - - +
32Q ASN* 3.7 22.9 - - + +
51Q MET 3.8 0.2 + - - -
52Q ASP* 1.3 77.1 - - - +
54Q GLU* 1.3 64.0 + - + +
56Q PHE 3.5 0.2 + - - -
57Q LEU* 3.0 17.5 + - - +
88Q TYR* 3.0 13.9 + - - -
92Q ASN* 2.7 25.2 + - - +
96Q TYR* 2.7 36.0 + - + +
400Q NAP 2.5 66.5 + - + +
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Residues in contact with GLU 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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87P LYS* 5.4 5.6 - - - +
52Q ASP* 2.9 15.8 + - - +
53Q LYS* 1.3 84.0 - - + +
55Q ASP* 1.3 64.8 + - - +
57Q LEU* 3.4 18.9 + - - +
58Q ILE* 3.1 41.6 + - + +
96Q TYR* 5.4 1.5 - - - -
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Residues in contact with ASP 55 (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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87P LYS* 5.5 1.1 + - - -
91P ASP* 4.3 14.6 - - - +
95P GLN* 5.9 1.9 - - - +
51Q MET* 4.0 15.4 - - + +
52Q ASP* 3.1 26.9 + - - +
54Q GLU* 1.3 75.6 - - - +
56Q PHE* 1.3 68.4 + - - +
58Q ILE* 3.2 14.3 + - - +
59Q GLN* 3.0 34.0 + - - +
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Residues in contact with PHE 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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3Q ILE* 4.1 29.6 - - + -
5Q THR* 4.2 11.4 - - + -
28Q LEU* 4.4 2.5 - - + -
30Q VAL* 3.6 35.2 - - + -
51Q MET* 4.0 16.5 - - + +
52Q ASP 3.0 15.3 + - - +
53Q LYS 3.6 3.8 - - - +
55Q ASP* 1.3 78.3 - - - +
57Q LEU* 1.3 58.2 + - - +
59Q GLN* 3.1 4.7 + - - +
60Q ILE* 2.8 46.9 + - + +
66Q PHE* 3.6 31.9 - + - -
72Q ILE* 4.7 5.6 - - + -
96Q TYR* 3.5 16.6 - + - -
100Q LEU* 3.7 25.1 - - + -
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Residues in contact with LEU 57 (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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53Q LYS 3.0 17.4 + - - +
54Q GLU* 3.7 20.6 - - - +
55Q ASP 3.2 0.2 - - - -
56Q PHE* 1.3 76.4 - - - +
58Q ILE* 1.3 63.2 + - - +
60Q ILE* 3.2 9.6 + - + +
61Q MET* 2.9 47.8 + - + +
91Q ASP 6.2 0.2 - - - +
96Q TYR* 3.6 43.4 + - + -
99Q GLU* 4.0 31.6 - - + -
100Q LEU* 5.2 0.9 - - + -
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Residues in contact with ILE 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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54Q GLU* 3.1 38.3 + - + +
55Q ASP* 3.2 16.4 + - - +
57Q LEU* 1.3 79.2 - - + +
59Q GLN* 1.3 62.5 + - + +
61Q MET* 3.3 13.5 + - + +
62Q ALA* 3.0 29.4 + - + +
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Residues in contact with GLN 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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51Q MET* 4.1 20.8 - - - +
55Q ASP* 3.0 21.0 + - - +
56Q PHE* 3.6 7.2 - - - +
58Q ILE* 1.3 79.4 - - + +
60Q ILE* 1.3 66.1 + - - +
62Q ALA* 3.2 2.6 + - - -
63Q GLY 3.0 4.3 + - - -
64Q GLU* 3.0 54.0 + - + +
66Q PHE* 3.4 28.6 - - + -
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Residues in contact with ILE 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 PHE* 2.8 45.8 + - + +
57Q LEU* 3.4 11.2 - - + +
59Q GLN* 1.3 76.0 - - - +
61Q MET* 1.3 65.3 + - + +
63Q GLY* 3.0 19.1 + - - -
66Q PHE* 3.7 20.0 - - + -
72Q ILE* 5.4 0.7 - - + -
99Q GLU* 3.9 17.3 - - + +
100Q LEU* 3.9 15.5 - - + -
103Q TYR* 3.5 55.6 - - + -
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Residues in contact with MET 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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57Q LEU* 2.9 45.7 + - + +
58Q ILE* 3.8 11.4 - - + +
60Q ILE* 1.3 76.8 - - - +
62Q ALA* 1.3 59.4 + - - +
63Q GLY 3.2 1.0 + - - -
99Q GLU* 3.4 44.2 - - + +
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Residues in contact with ALA 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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58Q ILE* 3.0 20.0 + - + +
59Q GLN* 3.7 6.3 - - - +
60Q ILE 3.2 0.2 - - - -
61Q MET* 1.3 77.0 - - - +
63Q GLY* 1.3 61.9 + - - +
64Q GLU* 3.7 17.9 + - - +
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Residues in contact with GLY 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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60Q ILE 3.0 16.4 + - - -
61Q MET 3.2 1.6 + - - -
62Q ALA* 1.3 80.6 - - - +
64Q GLU* 1.3 66.5 + - - +
65Q GLU* 3.6 6.8 + - - +
103Q TYR* 4.3 0.9 - - - -
107Q ARG* 3.5 25.9 + - - -
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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