Contacts of the helix formed by residues 42 - 54 (chain A) in PDB entry 5Y7G
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 ASP 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LEU* 1.3 74.9 - - - +
43A ASP* 1.3 84.3 + - - +
44A GLN* 4.1 11.7 + - - +
45A GLU* 2.7 34.5 + - - +
46A ARG* 2.9 35.5 + - - -
215A ARG* 3.9 16.3 + - - +
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Residues in contact with ASP 43 (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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42A ASP* 1.3 88.7 + - - +
44A GLN* 1.3 67.1 + - + +
45A GLU 3.1 0.7 + - - -
46A ARG* 4.3 11.5 + - - +
47A ALA* 3.2 21.5 + - - +
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Residues in contact with GLN 44 (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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42A ASP* 4.1 9.8 + - - +
43A ASP* 1.3 79.8 - - + +
45A GLU* 1.3 65.3 + - + +
47A ALA* 3.4 7.4 - - - +
48A PHE* 3.3 16.8 + - - +
171A LEU* 4.7 3.1 - - + +
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Residues in contact with GLU 45 (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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41A LEU* 3.5 18.3 - - + +
42A ASP* 2.7 41.4 + - - +
43A ASP 3.1 1.0 - - - -
44A GLN* 1.3 75.6 - - + +
46A ARG* 1.3 59.3 + - - +
47A ALA 3.0 1.8 - - - -
48A PHE* 2.6 31.2 + - - +
49A ILE* 3.3 9.6 + - + +
171A LEU* 3.3 34.6 - - + +
174A ARG* 4.0 14.2 + - - -
175A LEU* 5.5 3.8 - - + -
178A MET* 5.4 0.3 - - - +
215A ARG* 2.4 40.4 + - - -
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Residues in contact with ARG 46 (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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38A ALA* 4.0 10.9 + - - +
39A ASP 5.3 0.8 + - - -
41A LEU* 2.8 59.4 + - + +
42A ASP 2.9 22.8 + - - +
43A ASP* 4.3 12.0 + - - +
45A GLU* 1.3 74.3 - - - +
47A ALA* 1.3 59.7 + - - +
49A ILE* 3.5 10.6 + - + +
50A ALA* 3.2 21.5 + - - +
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Residues in contact with ALA 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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43A ASP 3.2 13.4 + - - +
44A GLN* 3.4 13.2 - - - +
45A GLU 3.0 0.4 - - - -
46A ARG* 1.3 75.2 - - - +
48A PHE* 1.3 59.6 + - - +
50A ALA* 3.8 6.0 - - - +
51A ALA* 3.0 29.3 + - - +
99A TRP* 5.7 0.2 - - - -
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Residues in contact with PHE 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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26A PHE* 4.9 10.8 - + - -
30A LEU* 5.1 2.7 - - + -
44A GLN 3.3 5.9 + - - +
45A GLU 2.6 18.9 + - - +
47A ALA* 1.3 70.8 - - - +
49A ILE* 1.3 59.4 + - + -
51A ALA* 3.0 2.1 + - - +
52A PHE* 2.7 54.1 + + + +
63A LEU* 4.7 8.3 - - + -
99A TRP* 3.2 58.6 - + + -
168A CYS* 4.8 14.4 - - + -
171A LEU* 3.5 29.8 - - + -
172A CYS* 4.8 16.2 - - - -
175A LEU* 4.4 21.1 - - + -
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Residues in contact with ILE 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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30A LEU* 4.2 53.6 - - + +
33A ILE* 4.7 7.9 - - + -
34A GLY* 5.0 4.3 - - - +
41A LEU* 4.0 33.7 - - + -
45A GLU* 3.3 9.7 + - + +
46A ARG* 3.5 8.3 + - + +
48A PHE* 1.3 83.6 - - + +
50A ALA* 1.3 63.1 + - - +
52A PHE* 3.6 5.9 + - - +
53A ALA* 3.4 19.8 + - - +
175A LEU* 4.9 7.9 - - + -
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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 ARG 3.2 14.4 + - - +
47A ALA* 3.8 7.4 - - - +
48A PHE 3.2 0.4 - - - -
49A ILE* 1.3 77.0 - - - +
51A ALA* 1.3 67.7 + - - +
53A ALA* 3.2 16.0 + - - +
54A GLU* 3.7 13.7 + - - +
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Residues in contact with ALA 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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47A ALA 3.0 19.2 + - - +
48A PHE 3.0 0.2 + - - -
50A ALA* 1.3 77.5 - - - +
52A PHE* 1.3 63.5 + - - +
54A GLU* 3.2 20.8 + - - +
55A LEU* 3.9 7.1 + - - +
97A LEU* 4.5 14.0 - - + +
99A TRP* 3.6 25.4 - - + -
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.7 15.3 - - + -
26A PHE* 3.6 29.8 - + - -
27A ARG* 4.3 9.2 - - + -
30A LEU* 3.4 29.4 - - + -
48A PHE* 2.7 32.5 + + + +
49A ILE 3.8 5.2 - - - +
50A ALA 3.2 0.2 - - - -
51A ALA* 1.3 72.9 - - - +
53A ALA* 1.3 63.0 + - + +
54A GLU 3.0 1.4 + - - -
55A LEU* 3.1 14.6 + - + +
60A GLN* 2.9 60.4 + - + +
63A LEU* 3.7 32.8 - - + -
64A VAL* 4.8 0.2 - - + -
99A TRP* 4.1 7.7 - + + -
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Residues in contact with ALA 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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27A ARG* 6.3 2.0 - - - +
49A ILE 3.4 9.2 + - - +
50A ALA* 3.2 10.9 + - - +
52A PHE* 1.3 82.6 - - + +
54A GLU* 1.3 64.2 + - - +
55A LEU 4.1 1.9 - - - +
60A GLN* 3.3 17.8 + - - +
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Residues in contact with GLU 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 3.9 13.1 - - - +
51A ALA* 3.2 11.4 + - - +
52A PHE 3.0 1.2 + - - -
53A ALA* 1.3 79.7 - - - +
55A LEU* 1.3 64.0 + - - +
56A PRO* 3.8 2.8 - - - +
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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