Contacts of the helix formed by residues 49 - 58 (chain E) in PDB entry 5NC5
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 THR 49 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19E LEU* 3.8 1.3 - - - -
40E VAL 4.7 1.3 - - - -
41E ASN* 3.9 31.2 - - + +
42E ALA 3.2 3.6 - - - +
43E ALA* 4.7 3.6 - - + -
47E GLY 4.5 5.2 - - - +
48E TRP* 1.3 76.6 - - - +
50E PRO* 1.3 74.7 - - - +
51E LEU* 3.5 9.6 + - - +
52E HIS* 3.0 33.4 + - - +
53E LEU* 3.1 14.2 + - - +
72E ASP 5.1 0.3 + - - -
75E ALA* 3.8 26.0 - - + +
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Residues in contact with PRO 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E LEU* 3.8 29.8 - - + -
19E LEU* 3.5 17.9 - - + -
22E ALA* 4.0 19.9 - - + +
40E VAL 3.8 13.9 - - - +
42E ALA* 3.0 18.6 - - + +
49E THR* 1.3 87.6 - - - +
51E LEU* 1.3 55.8 + - - +
53E LEU* 3.7 3.8 - - + +
54E ALA* 2.9 30.0 + - - +
66E LEU* 3.4 24.1 - - + +
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Residues in contact with LEU 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E VAL 5.3 1.0 + - - +
49E THR* 3.1 9.3 + - - +
50E PRO* 1.3 78.2 - - - +
52E HIS* 1.3 63.9 + - - +
54E ALA* 4.5 1.1 - - - +
55E ALA* 2.9 26.6 + - + +
63E VAL* 3.6 43.3 - - + +
66E LEU* 3.4 13.1 - - + +
67E LEU* 4.0 17.0 - - + -
71E ALA* 4.2 10.1 - - + -
72E ASP 3.5 25.4 - - - +
73E VAL* 3.9 14.4 - - - -
83E PRO* 3.9 17.4 - - + +
99E LEU* 4.4 6.5 - - + -
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Residues in contact with HIS 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E GLY 3.8 15.7 - - - -
48E TRP* 3.7 24.9 - + + -
49E THR* 3.0 38.0 + - - +
51E LEU* 1.3 78.9 - - - +
53E LEU* 1.3 57.4 + - - +
55E ALA* 3.1 1.6 + - - +
56E TYR* 2.8 26.0 + - - +
75E ALA* 3.4 36.3 + - + -
76E TYR 4.1 0.4 - - - -
77E ASP* 4.1 2.9 + - - +
81E SER* 3.1 24.1 + - - -
82E THR 3.7 4.8 - - - -
83E PRO* 3.8 16.9 - - + +
86E LEU* 3.4 30.6 - - + +
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Residues in contact with LEU 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811A TYR* 3.6 27.1 - - + +
19E LEU* 3.1 53.2 - - + +
22E ALA* 4.8 1.8 - - + -
23E ARG* 4.2 22.4 - - + +
44E ASP* 4.8 3.4 - - - +
48E TRP* 3.7 23.1 - - + -
49E THR 3.1 8.7 + - - +
50E PRO* 3.7 7.2 - - + +
51E LEU 3.3 0.4 - - - -
52E HIS* 1.3 79.0 - - - +
54E ALA* 1.3 63.8 + - - +
56E TYR* 3.2 3.4 + - - -
57E TRP* 3.0 39.5 + - - +
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Residues in contact with ALA 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ALA 4.4 10.0 + - - +
50E PRO 2.9 18.0 + - - +
51E LEU* 4.2 3.1 - - - +
53E LEU* 1.3 76.2 - - - +
55E ALA* 1.3 62.0 + - - +
58E GLY* 3.1 5.2 + - - -
59E HIS* 3.0 35.5 + - + +
62E ILE* 3.9 24.2 - - + -
63E VAL* 3.7 22.0 - - + +
66E LEU* 4.7 0.2 - - + -
95E ILE* 4.0 2.3 - - - +
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Residues in contact with ALA 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E LEU* 2.9 22.3 + - + +
52E HIS 3.1 4.2 + - - +
54E ALA* 1.3 79.5 - - - +
56E TYR* 1.3 60.7 + - - +
58E GLY* 4.1 0.4 - - - -
63E VAL* 4.2 7.3 - - + +
83E PRO* 3.7 31.2 - - + +
86E LEU* 4.3 3.7 - - + -
87E ALA* 3.9 12.2 + - - +
92E HIS* 3.3 19.6 + - - -
95E ILE* 4.6 15.6 - - + +
99E LEU* 4.9 1.1 - - + -
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Residues in contact with TYR 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809A TRP 5.5 0.4 - - - -
810A GLU* 4.0 8.3 - - + +
811A TYR* 3.1 44.0 + + + +
48E TRP* 3.8 29.4 - + + -
52E HIS 2.8 18.8 + - - +
53E LEU 3.2 4.5 + - - +
55E ALA* 1.3 74.3 - - - +
57E TRP* 1.3 100.4 + + + +
58E GLY 3.2 0.9 - - - -
86E LEU* 4.1 14.9 - - + +
90E PHE* 3.1 56.4 - + - -
92E HIS* 3.2 19.8 - - - -
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Residues in contact with TRP 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693A GLU* 5.9 11.0 - - + -
696A THR* 5.9 8.7 - - + -
697A GLN* 6.1 4.5 - - + -
723A ASP* 4.3 19.1 - - + -
811A TYR* 3.8 31.8 - + + -
23E ARG* 3.8 44.1 - - + +
53E LEU* 3.0 29.0 + - + +
56E TYR* 1.3 109.4 - + + +
58E GLY* 1.3 61.3 + - - +
59E HIS* 3.5 34.7 + - + +
92E HIS* 4.3 2.1 + - - -
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Residues in contact with GLY 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ALA 3.1 6.4 + - - -
55E ALA 4.1 0.2 + - - -
56E TYR 3.2 5.1 + - - -
57E TRP* 1.3 80.3 - - - +
59E HIS* 1.3 63.4 + - - +
60E LEU* 3.4 7.1 + - - +
92E HIS* 3.5 25.7 - - - -
95E ILE* 3.8 12.0 - - - +
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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