Contacts of the helix formed by residues 52 - 59 (chain Q) in PDB entry 5OA3
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 LEU 52 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39Q LEU* 3.8 34.8 - - + +
40Q GLU* 5.6 7.6 - - + +
48Q GLN* 3.8 40.4 - - + +
49Q TYR* 3.2 23.1 + - + +
51Q LEU* 1.3 76.5 - - + +
53Q GLU* 1.3 58.4 + - - +
54Q PRO* 3.5 1.3 - - - -
55Q VAL* 3.3 14.4 + - + +
56Q LEU* 2.9 48.0 + - + +
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Residues in contact with GLU 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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48F TYR* 4.0 27.2 + - + +
49Q TYR 3.2 16.3 + - - +
50Q LYS* 3.2 33.3 - - - +
51Q LEU 3.2 0.2 - - - -
52Q LEU* 1.3 77.3 - - - +
54Q PRO* 1.4 72.8 - - + +
56Q LEU* 3.4 5.3 + - - +
57Q LEU* 2.9 30.9 + - + +
85Q ARG* 2.6 33.9 + - - +
115Q TYR* 2.8 33.9 + - + +
119Q LEU* 5.3 2.1 - - + +
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Residues in contact with PRO 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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50Q LYS 4.4 3.1 - - - +
51Q LEU 3.5 15.5 - - - +
53Q GLU* 1.4 95.8 - - + +
55Q VAL* 1.3 63.4 - - + +
57Q LEU* 3.3 0.6 + - + -
58Q LEU* 3.0 39.3 + - + +
63Q PHE* 4.3 0.2 - - - -
85Q ARG* 4.5 12.8 - - + +
88Q ILE* 4.4 19.5 - - + -
89Q SER* 3.4 31.4 - - - +
112Q LEU* 4.0 20.2 - - + -
119Q LEU* 4.9 4.0 - - + -
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Residues in contact with VAL 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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32Q ILE* 5.3 3.4 - - + -
39Q LEU* 4.8 15.9 - - + -
51Q LEU 4.5 4.9 - - - +
52Q LEU* 3.3 26.2 - - + +
53Q GLU 3.2 0.2 - - - -
54Q PRO* 1.3 80.9 - - + +
56Q LEU* 1.3 71.2 + - + +
58Q LEU* 3.9 0.3 - - - +
59Q GLY 3.1 28.3 + - - +
60Q LYS* 5.4 11.4 - - + -
63Q PHE* 3.6 37.0 - - + -
88Q ILE* 5.0 6.1 - - + -
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Residues in contact with LEU 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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16F ASP 5.5 5.2 + - - +
48F TYR* 3.5 45.3 + - + +
49Q TYR* 4.4 11.0 - - + -
52Q LEU* 2.9 41.1 + - + +
53Q GLU 4.1 2.0 - - - +
55Q VAL* 1.3 81.4 - - + +
57Q LEU* 1.3 61.3 + - - +
59Q GLY* 4.1 6.6 + - - +
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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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17F ILE* 5.6 10.3 - - + -
48F TYR* 5.8 8.7 - - + +
53Q GLU* 2.9 22.8 + - + +
54Q PRO 3.7 4.0 - - - +
56Q LEU* 1.3 79.8 - - - +
58Q LEU* 1.3 61.2 + - - +
59Q GLY 3.6 0.3 + - - -
111Q ILE* 3.4 35.8 - - + +
112Q LEU* 4.0 19.5 - - + -
115Q TYR* 3.6 53.6 - - + -
119Q LEU* 4.7 2.2 - - + -
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Residues in contact with LEU 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 PRO* 3.0 24.3 + - + +
57Q LEU* 1.3 76.8 - - - +
59Q GLY* 1.3 59.8 + - - +
62Q ARG* 3.2 40.8 + - - +
63Q PHE* 3.7 17.0 - - + -
89Q SER* 5.8 0.7 - - - -
92Q LEU* 3.6 29.8 - - + -
108Q ILE* 3.7 47.8 - - + +
111Q ILE* 4.2 6.9 - - + +
112Q LEU* 3.9 26.7 - - + -
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Residues in contact with GLY 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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55Q VAL 3.1 12.0 + - - +
56Q LEU* 4.1 6.1 + - - -
57Q LEU 3.4 3.4 - - - -
58Q LEU* 1.3 82.5 - - - +
60Q LYS* 1.3 61.8 + - - -
61Q GLU* 3.2 6.1 + - - -
62Q ARG 4.0 3.5 + - - -
63Q PHE* 3.5 20.8 - - - -
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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