Contacts of the helix formed by residues 44 - 49 (chain E) in PDB entry 6AHU
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 PHE 44 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E THR* 1.3 80.6 + - - +
45E GLY* 1.3 61.5 + - - +
47E ALA* 4.1 0.2 - - - -
48E ALA* 3.0 29.4 + - + +
73E PHE* 4.2 28.3 - + - -
76E LEU* 4.7 6.1 - - + -
51H LEU* 3.2 21.4 + - + +
52H PHE* 4.5 17.3 - + + -
170J ILE* 3.6 31.0 - - + +
174J LEU* 4.4 4.7 - - + -
209J LEU* 3.6 43.1 - - + -
3L THR* 5.5 1.1 - - - -
4L LEU* 4.2 9.6 - - + -
7L LEU* 3.8 26.7 - - + -
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Residues in contact with GLY 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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37E ILE* 3.4 20.7 - - - +
41E HIS* 4.8 9.6 - - - +
42E GLY 3.9 4.0 + - - -
44E PHE* 1.3 79.6 - - - +
46E ALA* 1.3 63.8 + - - +
47E ALA 3.2 0.4 - - - -
48E ALA* 3.9 3.6 - - - -
49E CYS* 3.3 22.7 + - - +
76E LEU* 4.1 24.5 - - - -
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Residues in contact with ALA 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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34E ARG* 4.8 11.9 - - - +
37E ILE* 3.9 9.6 - - - +
38E ALA* 4.1 20.4 - - + +
42E GLY 3.4 20.2 + - - +
43E THR* 4.1 3.6 - - - -
44E PHE 3.2 1.0 - - - -
45E GLY* 1.3 77.5 - - - +
47E ALA* 1.3 58.3 + - - +
49E CYS 4.5 1.7 - - - +
50E SER* 3.3 17.4 + - - -
167J ARG* 4.0 27.9 + - - +
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Residues in contact with ALA 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 THR 3.8 1.2 + - - +
44E PHE 3.4 1.8 + - - -
46E ALA* 1.3 79.8 - - - +
48E ALA* 1.3 62.3 + - - +
49E CYS 3.2 1.6 - - - -
50E SER* 3.4 14.6 + - - -
51E ILE* 3.7 21.0 + - - +
167J ARG* 3.3 42.0 - - + +
170J ILE* 3.7 13.2 - - + -
171J SER* 3.9 11.1 - - - -
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Residues in contact with ALA 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 PHE* 3.0 22.2 + - + +
45E GLY* 4.3 5.8 - - - -
47E ALA* 1.3 77.1 - - - +
49E CYS* 1.3 57.6 + - - +
50E SER 3.4 1.6 + - - -
51E ILE* 4.0 16.4 - - - +
52E GLY 5.5 0.2 + - - -
70E ARG* 5.2 2.3 - - - +
73E PHE* 3.7 46.6 - - + +
170J ILE* 4.9 1.0 - - - +
171J SER* 5.7 0.2 - - - +
174J LEU* 3.7 23.3 - - + -
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Residues in contact with CYS 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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34E ARG* 5.1 2.9 - - - +
37E ILE* 4.3 12.3 - - + +
45E GLY 3.3 18.6 + - - +
46E ALA 4.5 1.4 - - - +
47E ALA 3.2 0.2 - - - -
48E ALA* 1.3 75.4 - - - +
50E SER* 1.3 57.6 + - - +
51E ILE 3.9 0.7 - - - +
52E GLY 5.1 0.7 - - - +
53E PHE* 3.3 24.8 - - + +
69E CYS* 5.9 1.1 - - + -
73E PHE* 3.4 35.0 - - - -
76E LEU* 3.7 28.3 - - - -
77E VAL* 3.7 21.1 - - + -
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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