Contacts of the helix formed by residues 46 - 56 (chain A) in PDB entry 4MYF
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 LYS 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLY* 2.9 16.4 + - - +
45A LYS* 1.3 104.5 - - + +
47A GLY* 1.3 63.1 + - - +
48A PRO* 3.4 1.8 - - - -
49A ALA* 3.4 13.3 + - + +
50A ALA* 3.2 17.0 + - - +
276A PRO* 3.5 20.2 - - + +
277A LEU* 4.2 29.8 - - + +
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Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA 2.8 13.8 + - - -
46A LYS* 1.3 77.4 - - - +
48A PRO* 1.3 61.4 - - - +
50A ALA 3.2 0.2 + - - -
51A PHE* 2.8 33.5 + - - +
111A GLY 3.6 11.0 - - - -
274A LEU* 3.7 21.1 - - - +
276A PRO* 3.7 9.7 - - - +
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Residues in contact with PRO 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE 3.9 0.7 - - - +
30A PRO* 3.9 23.3 - - + -
45A LYS 3.5 13.5 - - - +
46A LYS 3.6 0.4 - - - -
47A GLY* 1.3 89.4 - - - +
49A ALA* 1.3 55.0 + - - +
51A PHE* 3.7 1.7 - - - +
52A ARG* 3.0 52.4 + - - +
80A ASP* 3.9 11.2 - - - +
110A ILE* 3.5 39.4 - - + +
111A GLY 3.3 13.5 - - - +
112A GLY 3.7 1.3 - - - +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS 5.3 0.6 + - - +
46A LYS* 3.4 15.5 + - + +
47A GLY 3.3 0.6 - - - -
48A PRO* 1.3 79.5 - - - +
50A ALA* 1.3 58.7 + - - +
52A ARG* 3.3 10.9 + - - +
53A PHE* 3.0 26.9 + - - +
80A ASP* 5.8 0.2 + - - -
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LYS 3.2 4.1 + - - +
47A GLY 3.2 2.7 + - - +
49A ALA* 1.3 75.7 - - - +
51A PHE* 1.3 67.1 + - - +
53A PHE* 3.2 16.5 + - - +
54A PHE* 3.4 19.0 + - + -
274A LEU* 4.7 0.9 - - + -
276A PRO* 3.5 33.9 - - + -
280A GLU 5.1 2.0 - - - +
284A PRO* 3.8 23.1 - - + -
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Residues in contact with PHE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 4.7 6.7 - - + -
47A GLY 2.8 17.3 + - - +
48A PRO 3.7 4.3 - - - +
50A ALA* 1.3 76.5 - - - +
52A ARG* 1.3 63.7 + - + +
54A PHE 3.3 0.9 + - - -
55A LEU* 2.9 49.9 + - + +
108A PHE* 3.7 26.2 - + - -
110A ILE* 3.7 34.1 - - + -
271A MET* 4.3 0.9 - - - -
274A LEU* 4.4 6.1 - - + +
284A PRO* 4.9 1.8 - - - -
287A ALA* 3.6 33.2 - - + -
288A VAL* 3.3 28.1 - - + +
291A PHE* 3.7 28.7 - + + -
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Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 4.8 5.0 - - + +
27A ILE 4.7 0.8 - - - -
28A GLY* 3.8 9.6 - - - +
48A PRO* 3.0 36.1 + - - +
49A ALA* 3.6 9.2 - - - +
50A ALA 3.2 0.2 - - - -
51A PHE* 1.3 79.3 - - + +
53A PHE* 1.3 64.6 + - - +
55A LEU* 3.1 23.8 + - + +
56A GLN* 3.2 20.5 + - + +
77A ASP* 2.7 43.1 + - - +
79A GLY* 3.2 21.1 + - - -
80A ASP* 2.7 36.5 + - - -
110A ILE* 5.3 2.7 - - + -
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Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA 3.0 14.1 + - - +
50A ALA* 3.2 12.3 + - - +
52A ARG* 1.3 78.5 - - - +
54A PHE* 1.3 92.4 + + + +
56A GLN* 3.5 7.0 + - - +
57A ARG* 2.7 72.4 + - - +
281A TYR* 5.2 5.2 - + - -
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Residues in contact with PHE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA* 3.4 14.7 + - + -
51A PHE 3.3 2.2 + - - -
53A PHE* 1.3 98.1 - + - +
55A LEU* 1.3 60.5 + - - +
56A GLN 3.1 1.6 - - - -
57A ARG* 2.9 25.4 + - - +
58A LEU* 3.0 35.1 + - + +
280A GLU 4.1 8.3 - - - -
281A TYR* 3.5 50.7 - + - -
284A PRO* 3.6 24.9 - - + +
285A ARG* 3.6 34.8 - - + -
288A VAL* 3.8 14.6 - - + -
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.1 19.6 - - + +
11A LEU* 4.0 16.2 + - - +
14A PHE* 3.7 34.3 - - + -
26A ILE* 3.9 13.9 - - + -
51A PHE* 2.9 30.3 + - + +
52A ARG* 3.3 17.7 - - + +
54A PHE* 1.3 76.2 - - - +
56A GLN* 1.3 66.7 + - - +
57A ARG 3.1 1.3 + - - -
58A LEU 4.2 2.3 + - - +
77A ASP* 4.6 11.9 - - + +
288A VAL* 3.7 8.4 - - + +
291A PHE* 4.0 28.5 - - + -
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Residues in contact with GLN 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ARG* 5.9 0.3 - - - +
11A LEU* 3.6 58.1 - - - +
14A PHE* 6.0 0.9 - - - -
52A ARG* 3.2 16.1 + - + +
53A PHE* 3.5 11.4 - - - +
54A PHE 3.1 0.8 - - - -
55A LEU* 1.3 83.1 - - - +
57A ARG* 1.3 71.9 + - + +
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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