Contacts of the helix formed by residues 47 - 55 (chain A) in PDB entry 2Q24
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 GLY 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ALA* 3.8 1.8 - - - +
46A VAL* 1.3 83.6 - - - +
48A SER* 1.3 61.0 + - - -
49A GLY 3.3 3.1 - - - -
50A THR* 3.3 12.1 + - - -
51A LEU 3.1 20.8 + - - -
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Residues in contact with SER 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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37A LEU 6.0 0.2 - - - -
38A GLU* 5.1 14.6 - - - -
41A ALA* 4.2 15.0 - - - +
46A VAL 4.1 0.2 + - - -
47A GLY* 1.3 69.7 - - - -
49A GLY* 1.3 60.9 + - - +
51A LEU* 3.7 5.3 - - - +
52A TYR* 3.0 29.6 + - - +
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Residues in contact with GLY 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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47A GLY* 3.3 1.0 - - - -
48A SER* 1.3 78.3 + - - +
50A THR* 1.3 57.7 + - - +
52A TYR* 3.3 7.6 + - - +
53A ARG* 2.8 46.2 + - - +
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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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20A ILE* 4.9 3.4 - - + -
46A VAL* 3.8 24.1 - - + +
47A GLY* 3.3 20.6 + - - -
48A SER 3.3 0.2 - - - -
49A GLY* 1.3 73.9 - - - +
51A LEU* 1.3 64.5 - - - +
53A ARG* 3.2 30.3 + - - +
54A ASN* 2.7 40.7 + - - +
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Residues in contact with LEU 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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20A ILE* 3.5 38.1 - - + -
37A LEU* 3.3 39.3 - - + +
40A ILE* 4.3 7.4 - - + -
41A ALA* 3.7 21.1 - - + +
46A VAL* 4.2 4.2 - - + +
47A GLY 3.1 13.5 + - - +
48A SER* 3.7 9.9 - - - +
49A GLY 3.3 0.2 - - - -
50A THR* 1.3 74.6 - - - +
52A TYR* 1.3 54.7 + - - +
54A ASN* 3.1 4.0 + - - +
55A PHE* 2.8 48.3 + - + +
61A LEU* 4.2 13.9 - - + -
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Residues in contact with TYR 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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48A SER 3.0 19.1 + - - +
49A GLY* 3.7 7.4 - - - +
51A LEU* 1.3 76.3 - - - +
53A ARG* 1.3 72.2 + - + +
55A PHE 3.8 5.4 - - - -
56A PRO* 3.2 59.8 - - + +
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Residues in contact with ARG 53 (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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49A GLY* 2.8 36.1 + - - +
50A THR* 3.2 34.6 + - - +
52A TYR* 1.3 81.9 - - + +
54A ASN* 1.3 67.0 + - - +
56A PRO* 4.8 3.3 - - - +
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Residues in contact with ASN 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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17A ARG* 6.3 1.3 - - + -
20A ILE* 4.7 5.9 - - + +
50A THR* 2.7 34.0 + - - +
51A LEU* 3.1 1.8 + - - -
53A ARG* 1.3 86.5 + - - +
55A PHE* 1.3 91.7 + - + +
56A PRO* 3.8 5.9 - - - +
120B ASP* 5.7 5.7 - - - +
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Residues in contact with PHE 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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17A ARG* 3.8 33.7 - - + -
20A ILE* 3.8 22.9 - - + -
21A LEU* 3.7 14.6 - - + -
51A LEU* 2.8 31.2 + - + +
52A TYR* 3.5 7.1 - - - +
54A ASN* 1.3 98.8 - - + +
56A PRO* 1.3 67.3 - - - +
57A THR 3.3 7.0 + - - +
60A ALA* 4.5 6.5 - - + -
61A LEU* 3.7 37.0 - - + +
64A ALA* 3.4 30.3 - - + -
120B ASP* 4.9 8.1 - - + -
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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