Contacts of the helix formed by residues 49 - 58 (chain A) in PDB entry 1Y62
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 ARG 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ILE* 4.2 3.1 - - - -
47A PHE* 3.6 7.2 - - - +
48A ARG* 1.3 101.8 - - - +
50A THR* 1.3 66.0 + - - +
51A TYR* 3.3 5.8 - - + +
52A ASP* 3.2 36.5 + - - +
53A CYS 3.4 7.8 + - - -
22F ARG* 5.7 2.2 - - - +
48F ARG* 4.3 30.3 + - - +
49F ARG* 4.7 27.3 - - - +
104F SO4 4.8 2.8 + - - -
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Residues in contact with THR 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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23A ILE* 3.6 30.8 - - + +
32A CYS* 4.2 23.3 - - + +
49A ARG* 1.3 69.3 - - - +
51A TYR* 1.3 61.3 + - - +
53A CYS* 3.0 4.5 + - - +
54A GLN* 2.9 39.2 + - + +
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Residues in contact with TYR 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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49A ARG* 3.3 4.8 - - + +
50A THR* 1.3 79.4 - - - +
52A ASP* 1.3 63.3 + - - +
54A GLN* 3.2 22.8 + - + +
55A ARG* 2.9 67.9 + - + +
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Residues in contact with ASP 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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47A PHE* 3.7 16.1 - - + -
49A ARG* 3.2 33.2 + - - +
50A THR 3.2 0.4 - - - -
51A TYR* 1.3 81.0 - - - +
53A CYS* 1.3 64.6 + - - +
55A ARG* 3.5 18.0 + - - +
56A THR* 2.7 32.9 + - - -
19F ALA 4.1 4.0 - - - +
20F GLU* 3.6 34.3 - - - +
21F LYS* 4.6 6.2 + - - +
22F ARG* 4.9 3.5 + - - -
104F SO4 5.1 1.6 + - - -
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Residues in contact with CYS 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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23A ILE* 3.6 19.3 - - + -
24A TYR 3.9 0.4 - - - -
25A TYR* 3.7 29.2 - - - -
32A CYS* 2.0 45.5 - - - -
47A PHE* 3.8 25.2 - - + -
49A ARG 3.4 2.7 + - - +
50A THR 3.0 8.6 + - - +
52A ASP* 1.3 79.8 - - - +
54A GLN* 1.3 50.9 + - - +
56A THR* 3.4 0.5 + - - -
57A CYS* 2.7 34.3 + - - +
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Residues in contact with GLN 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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32A CYS* 3.9 17.8 + - - +
50A THR* 2.9 33.5 + - + +
51A TYR* 3.6 24.9 - - + +
53A CYS* 1.3 73.2 - - - +
55A ARG* 1.3 60.6 + - - +
56A THR 3.1 4.9 - - - -
58A LEU* 2.8 59.6 + - + +
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Residues in contact with ARG 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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51A TYR* 2.9 56.2 + - + +
52A ASP* 3.5 10.3 - - - +
54A GLN* 1.3 73.3 - - - +
56A THR* 1.3 57.7 + - - +
58A LEU 5.2 2.2 - - - +
19F ALA* 3.2 52.4 + - - +
20F GLU 4.4 1.4 + - - -
21F LYS* 3.3 38.9 - - - +
36F ASP* 3.9 19.0 + - - -
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Residues in contact with THR 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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3A ARG* 4.7 2.3 - - - -
4A PRO* 3.4 31.5 - - + +
6A LEU* 4.5 4.0 - - + -
7A CYS* 4.1 4.5 - - - -
47A PHE* 3.7 24.7 - - + -
52A ASP 2.7 21.8 + - - -
53A CYS 3.8 2.0 - - - -
54A GLN 3.1 0.8 - - - -
55A ARG* 1.3 81.3 - - - +
57A CYS* 1.3 66.7 + - - +
58A LEU 5.5 0.2 - - - -
17F THR 4.2 0.4 - - - +
18F LYS* 4.0 16.2 - - - -
19F ALA* 2.9 27.2 + - - +
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Residues in contact with CYS 57 (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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3A ARG* 5.4 7.5 - - - +
4A PRO* 5.4 0.2 - - - -
6A LEU* 4.2 6.3 - - - -
7A CYS* 2.0 49.4 - - - +
25A TYR* 3.2 48.1 + - + -
47A PHE* 4.4 7.0 - - - -
53A CYS 2.7 18.3 + - - +
56A THR* 1.3 84.7 - - - +
58A LEU* 1.3 60.9 + - - +
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Residues in contact with LEU 58 (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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25A TYR* 4.0 20.1 - - + +
30A LYS* 3.6 26.2 - - + +
31A GLN* 5.1 4.7 - - + -
32A CYS* 5.2 2.5 - - - +
53A CYS 3.9 0.4 + - - -
54A GLN* 2.8 59.2 + - + +
55A ARG* 5.2 2.4 - - - +
56A THR 5.5 0.2 - - - -
57A CYS* 1.3 75.5 - - - +
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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