Contacts of the helix formed by residues 47 - 58 (chain Q) in PDB entry 5L4K
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 GLU 47 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Q LYS* 1.3 76.1 - - - +
48Q GLN* 1.3 68.6 + - - +
49Q SER 3.7 0.2 - - - -
50Q ILE* 3.9 14.2 - - + +
51Q LEU* 3.3 17.8 + - - +
84Q LYS* 3.4 37.1 + - - +
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Residues in contact with GLN 48 (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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5Q ALA* 3.5 24.2 + - + +
6Q VAL* 4.2 13.6 - - + +
9Q PHE* 3.5 43.2 - - - +
46Q LYS* 3.1 26.7 - - + +
47Q GLU* 1.3 94.5 - - - +
49Q SER* 1.3 61.9 + - - +
50Q ILE 3.1 1.3 - - - -
51Q LEU* 3.3 19.8 - - - +
52Q GLU* 3.2 32.1 + - - +
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Residues in contact with SER 49 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q ALA* 3.8 6.8 - - - +
30Q ILE* 5.1 3.7 - - - +
31Q VAL* 5.2 5.9 - - - +
36Q GLN* 3.1 33.4 + - - +
43Q VAL* 3.9 14.9 - - - +
44Q GLN* 3.3 35.0 + - - -
46Q LYS 3.5 5.1 + - - -
48Q GLN* 1.3 76.3 - - - +
50Q ILE* 1.3 61.1 + - - +
52Q GLU* 4.3 9.6 - - - +
53Q LEU* 3.7 15.4 + - - +
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Residues in contact with ILE 50 (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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44Q GLN* 3.8 28.5 - - + +
46Q LYS 3.7 16.5 + - - +
47Q GLU* 4.2 13.5 - - + +
48Q GLN 3.1 0.4 - - - -
49Q SER* 1.3 76.1 - - - +
51Q LEU* 1.3 64.7 + - - +
52Q GLU 3.2 2.5 + - - -
53Q LEU* 3.6 8.9 + - - +
54Q GLY* 3.9 8.5 + - - -
80Q ILE* 4.3 17.0 - - + -
84Q LYS* 3.8 47.6 - - + +
87Q ARG* 5.6 7.3 + - - +
88Q LEU* 5.3 13.4 - - + +
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Residues in contact with LEU 51 (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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9Q PHE* 3.7 31.9 - - + -
47Q GLU 3.3 18.2 + - - +
48Q GLN* 3.3 26.6 + - - +
50Q ILE* 1.3 80.3 - - - +
52Q GLU* 1.3 57.6 + - + +
55Q SER* 3.0 35.4 + - - +
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Residues in contact with GLU 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q ALA* 3.9 11.1 - - - +
8Q GLU* 3.1 31.5 - - - +
9Q PHE* 4.6 9.5 + - + +
12Q ALA* 5.7 1.1 - - + +
27Q LEU* 3.8 9.0 - - + +
30Q ILE* 3.3 30.0 - - - +
31Q VAL* 4.5 6.1 - - + +
48Q GLN 3.2 19.7 + - - +
49Q SER* 4.3 10.0 - - - +
51Q LEU* 1.3 79.4 - - + +
53Q LEU* 1.3 71.8 + - - +
54Q GLY 3.5 0.4 - - - -
55Q SER* 4.6 1.3 - - - -
56Q LEU* 2.9 45.7 + - + +
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Residues in contact with LEU 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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27Q LEU* 4.2 9.0 - - + -
31Q VAL* 4.5 19.5 - - + -
44Q GLN* 3.3 25.4 - - - +
49Q SER 3.7 11.6 + - - +
50Q ILE* 3.6 6.3 + - - +
52Q GLU* 1.3 85.4 - - - +
54Q GLY* 1.3 59.2 + - - +
57Q LEU* 3.0 41.6 + - + +
72Q TYR* 4.2 15.3 - - + +
76Q PHE* 3.7 25.8 - - + -
88Q LEU* 4.1 13.5 - - + -
92Q LEU* 4.1 26.2 - - + -
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Residues in contact with GLY 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 ILE 3.9 6.0 + - - -
52Q GLU 3.5 0.2 - - - -
53Q LEU* 1.3 80.7 - - - +
55Q SER* 1.3 60.8 + - - +
58Q ALA* 3.4 24.3 - - - +
87Q ARG* 5.1 6.3 - - - -
88Q LEU* 3.7 23.6 - - - +
91Q SER* 4.3 13.2 + - - -
92Q LEU* 4.0 8.6 - - - +
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Residues in contact with SER 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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51Q LEU* 3.0 28.9 + - - +
52Q GLU* 3.6 2.8 + - - -
53Q LEU 3.3 0.4 - - - -
54Q GLY* 1.3 75.7 - - - +
56Q LEU* 1.3 67.3 + - - +
58Q ALA 3.5 16.2 - - - +
59Q LYS* 3.8 7.3 - - - +
87Q ARG* 5.2 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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8Q GLU* 4.9 4.0 - - - +
12Q ALA* 4.4 16.6 - - + +
16Q LEU* 4.8 9.9 - - + -
23Q SER* 3.5 35.9 - - - +
27Q LEU* 3.9 22.4 - - + -
52Q GLU* 2.9 35.4 + - + +
55Q SER* 1.3 76.5 - - - +
57Q LEU* 1.3 67.7 + - - +
58Q ALA 3.0 3.4 + - - -
59Q LYS* 3.2 49.3 + - + +
65Q GLU* 4.3 1.8 - - - -
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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
----------------------------------------------------------
27Q LEU* 3.8 14.3 - - + +
28Q HIS* 3.6 28.5 - - + +
53Q LEU* 3.0 21.8 + - + +
56Q LEU* 1.3 76.9 - - - +
58Q ALA* 1.3 56.0 + - - +
65Q GLU* 2.9 46.4 - - + +
68Q GLY* 3.4 25.1 - - - +
69Q LEU* 3.6 22.9 - - + -
72Q TYR* 3.9 22.4 - - + -
92Q LEU* 4.2 11.7 - - + -
95Q LEU* 3.2 12.7 - - - +
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Residues in contact with ALA 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 GLY 3.4 18.1 + - - +
55Q SER 3.5 11.1 - - - +
56Q LEU 3.0 0.8 - - - -
57Q LEU* 1.3 76.0 - - - +
59Q LYS* 1.3 62.9 + - - +
91Q SER* 4.0 20.6 - - - +
92Q LEU* 4.0 11.9 - - + -
94Q ASP* 5.8 0.9 - - + -
95Q LEU* 3.9 23.3 - - + -
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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