Contacts of the helix formed by residues 44 - 50 (chain E) in PDB entry 3HYW
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 ALA 44 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E PHE* 2.9 16.9 + - + +
43E PRO* 1.3 76.7 - - - +
45E PHE* 1.3 61.8 + - - +
46E PRO 3.5 1.6 - - - -
47E HIS* 3.4 13.5 + - - +
48E LEU* 3.0 26.2 + - - +
53E ARG* 4.2 3.7 - - - +
58E ILE* 3.6 27.1 - - + +
386E GLU* 3.4 24.7 - - - +
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Residues in contact with PHE 45 (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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38E TYR* 5.3 2.2 - + - -
40E GLY* 4.1 17.0 - - - -
41E PHE 3.7 20.0 - - - -
42E THR* 3.0 36.4 + - + +
44E ALA* 1.3 75.6 - - - +
46E PRO* 1.4 63.2 - - + +
48E LEU* 4.1 4.0 - - + -
49E ALA* 2.9 25.1 + - - +
55E PHE* 5.8 0.9 - + - -
58E ILE* 3.8 18.8 - - + -
123E ILE 3.3 17.7 - - - +
124E CYS 3.6 24.5 - - - -
125E THR* 3.7 8.1 - - - -
126E ALA* 3.6 37.2 - - + -
129E ALA* 3.5 12.0 - - + +
441E FAD 4.2 0.9 - - + -
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Residues in contact with PRO 46 (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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42E THR 3.8 4.7 - - - +
43E PRO 3.7 11.2 - - - +
44E ALA 3.6 2.7 - - - -
45E PHE* 1.4 92.7 - - + +
47E HIS* 1.3 55.5 + - - +
49E ALA* 3.3 6.4 + - + +
50E MET* 2.9 31.5 + - - +
123E ILE* 3.9 27.8 - - + -
159E PRO* 4.2 11.0 - - + +
162E GLU* 3.7 23.8 - - + +
163E PHE* 4.4 4.5 - - + -
166E MET* 4.0 24.0 - - + -
441E FAD 4.1 5.6 - - + -
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Residues in contact with HIS 47 (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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43E PRO 3.4 17.2 + - - -
44E ALA* 3.5 21.2 - - + +
45E PHE 3.3 0.2 - - - -
46E PRO* 1.3 72.3 - - + +
48E LEU* 1.3 60.9 + - - +
50E MET* 3.1 7.6 + - - -
51E GLY 3.1 4.7 + - - -
52E TRP* 2.7 44.9 + + + +
53E ARG* 3.6 46.8 + - + +
162E GLU* 4.5 1.1 - - - -
166E MET* 3.3 25.2 - - + +
350E ASP* 2.7 29.0 + - - -
382E LYS* 3.9 15.6 - - + +
386E GLU* 5.1 1.3 - - - -
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Residues in contact with LEU 48 (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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44E ALA 3.0 14.8 + - - +
45E PHE* 3.5 9.6 - - + +
46E PRO 3.3 0.2 - - - -
47E HIS* 1.3 75.4 - - - +
49E ALA* 1.3 58.4 + - - +
51E GLY* 2.9 19.4 + - - -
53E ARG* 3.4 28.5 - - + +
54E LYS 3.9 1.8 - - - -
55E PHE* 3.6 28.9 - - + +
58E ILE* 4.0 15.7 - - + -
126E ALA* 3.7 42.6 - - + +
129E ALA* 4.0 7.0 - - + +
130E LEU* 3.8 25.6 - - + +
133E GLN* 4.2 6.6 - - - +
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Residues in contact with ALA 49 (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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45E PHE 2.9 9.2 + - - +
46E PRO 3.4 9.6 - - - +
48E LEU* 1.3 76.6 - - - +
50E MET* 1.3 56.8 + - - +
51E GLY 3.1 0.4 - - - -
123E ILE* 3.4 31.6 - - + -
129E ALA* 3.2 22.3 - - + +
132E THR* 4.0 4.3 - - - -
133E GLN* 3.0 29.5 - - - +
136E LEU* 3.3 8.2 - - - +
163E PHE* 3.9 8.5 - - + -
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Residues in contact with MET 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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46E PRO 2.9 16.6 + - - +
47E HIS 3.1 8.9 + - - +
49E ALA* 1.3 76.0 - - - +
51E GLY* 1.3 59.9 + - - +
52E TRP* 3.3 33.6 + - + -
133E GLN* 3.3 8.7 + - - +
136E LEU* 3.7 9.9 - - - -
140E TYR* 3.8 15.9 + - - +
163E PHE* 3.7 25.1 - - + -
166E MET* 3.6 32.5 - - + +
167E LEU* 3.8 17.7 - - - -
170E GLU* 3.5 34.9 - - + +
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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