Contacts of the helix formed by residues 46 - 54 (chain C) in PDB entry 3E4U
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 HIS 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C LEU* 4.5 3.4 - - + -
25C LEU* 4.0 8.6 - - + +
26C ARG* 3.9 15.5 + - + -
30C ILE 3.0 28.5 + - - -
31C LEU 3.4 15.2 + - - -
32C THR* 3.5 18.0 - - + +
33C ASP* 3.1 7.8 + - - +
34C VAL* 4.5 0.4 - - - -
45C ALA* 1.3 74.5 - - - +
47C LYS* 1.3 65.6 + - - +
48C THR* 3.2 15.8 + - - +
49C VAL* 3.2 17.5 + - + +
50C LEU* 3.3 15.6 + - - +
91C TYR* 2.8 39.5 + + - +
48D THR* 3.4 25.9 - - + +
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Residues in contact with LYS 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR* 5.6 6.3 - - - -
33C ASP* 2.6 47.5 + - - +
34C VAL* 3.4 19.1 - - + +
45C ALA 4.1 0.6 + - - -
46C HIS* 1.3 71.4 - - - +
48C THR* 1.3 56.8 + - - +
50C LEU* 3.3 6.8 + - - +
51C MET* 2.9 34.0 + - - +
61C PHE* 4.0 32.8 - - + -
68C ASN* 5.4 6.3 - - - -
69C LEU 2.7 37.0 + - - +
31D LEU* 3.4 33.9 - - + -
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Residues in contact with THR 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ASP* 5.0 3.1 + - - +
46C HIS* 4.0 9.9 - - - +
47C LYS* 1.3 79.7 - - - +
49C VAL* 1.3 60.6 + - - +
51C MET* 3.4 2.5 + - - +
52C ALA* 2.9 29.6 + - - +
22D LEU* 3.7 18.5 - - - +
25D LEU* 3.9 16.0 - - + +
31D LEU* 3.8 32.5 - - + +
46D HIS* 3.9 22.4 - - + +
48D THR* 3.9 17.8 + - - +
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Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 4.9 5.8 - - + -
22C LEU* 4.3 24.9 - - + -
46C HIS* 3.2 10.7 + - + +
48C THR* 1.3 76.9 + - - +
50C LEU* 1.3 69.0 + - - +
52C ALA* 3.0 15.1 + - - +
53C CYS* 3.1 34.9 + - - -
90C MET* 4.3 11.9 - - + +
91C TYR* 3.6 54.7 - - + +
18D VAL* 5.4 2.0 - - + -
22D LEU* 5.1 5.6 - - + -
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL* 3.6 30.5 - - + -
36C ILE* 4.1 19.5 - - + -
45C ALA* 4.2 6.5 - - + -
46C HIS 3.3 10.7 + - - +
47C LYS* 3.5 5.8 - - - +
49C VAL* 1.3 79.5 - - + +
51C MET* 1.3 58.7 + - - +
53C CYS* 3.8 0.3 - - - +
54C SER* 3.0 35.3 + - - -
57C PHE* 3.8 31.0 - - + -
61C PHE* 4.2 11.0 - - + -
83C PHE* 4.8 1.6 - - + -
87C LEU* 3.6 18.8 - - + -
90C MET* 3.6 29.2 - - + -
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Residues in contact with MET 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C LYS 2.9 15.2 + - - +
48C THR* 3.7 5.4 - - - +
50C LEU* 1.3 76.8 - - - +
52C ALA* 1.3 62.2 + - - +
53C CYS 3.5 0.5 + - - -
54C SER 3.5 12.3 + - - +
58C TYR* 3.4 45.5 - - + +
61C PHE* 3.5 27.4 - - + -
62C THR* 3.5 20.2 - - + -
21D ASN* 4.6 3.5 + - - -
25D LEU* 3.4 31.4 - - + -
30D ILE* 4.1 7.9 - - + -
31D LEU* 3.2 33.9 - - - -
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C THR 2.9 17.7 + - - +
49C VAL* 3.0 6.9 + - - +
51C MET* 1.3 76.7 - - - +
53C CYS* 1.3 59.2 + - - +
17D ASP 4.7 3.5 - - - +
18D VAL* 3.7 37.9 - - + +
21D ASN* 2.7 38.5 + - + +
22D LEU* 4.2 9.2 - - + +
25D LEU* 5.1 2.2 - - + -
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Residues in contact with CYS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C VAL* 3.1 22.5 + - - +
50C LEU 4.3 1.3 - - - +
52C ALA* 1.3 79.5 - - - +
54C SER* 1.3 58.4 + - - +
90C MET* 3.9 38.4 - - + -
113C GLN 5.2 0.7 - - - +
114C MET* 3.5 23.2 - - + +
14D HIS* 4.1 11.9 - - - +
18D VAL* 3.7 28.3 - - - -
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Residues in contact with SER 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU 3.0 14.2 + - - +
51C MET 3.5 4.9 + - - +
52C ALA 3.7 1.4 - - - -
53C CYS* 1.3 82.0 - - - +
55C GLY* 1.3 63.3 + - - +
56C LEU 3.9 3.3 + - - -
57C PHE* 3.7 17.4 - - - -
58C TYR* 3.2 22.2 + - - +
90C MET* 4.9 3.1 - - - -
112C LEU* 2.6 44.7 + - - +
114C MET* 4.7 5.2 - - - -
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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