Contacts of the helix formed by residues 43 - 54 (chain A) in PDB entry 2GO0
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 SER 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A TYR* 4.4 6.5 + - - -
41A VAL 3.5 1.0 - - - -
42A LEU* 1.3 83.7 - - - +
44A GLY* 1.3 65.4 + - - +
45A ALA* 3.0 19.3 + - - +
46A GLU* 3.1 24.2 + - - -
47A GLY 3.1 10.7 + - - -
92A TYR* 3.8 12.7 - - - +
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Residues in contact with GLY 44 (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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43A SER* 1.3 74.9 + - - +
45A ALA* 1.3 60.6 + - - +
47A GLY 4.1 0.8 - - - -
48A SER* 3.6 19.1 + - - -
92A TYR* 3.5 32.4 + - - -
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Residues in contact with ALA 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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9A TYR* 3.3 19.2 - - + +
43A SER* 3.0 8.8 + - - +
44A GLY* 1.3 79.1 - - - +
46A GLU* 1.3 59.4 + - - +
48A SER* 3.3 5.5 + - - -
49A PHE* 2.8 29.3 + - - +
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Residues in contact with GLU 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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9A TYR* 3.6 32.7 + - + -
14A TYR* 3.5 20.9 + - + -
40A SER* 2.6 41.3 + - - +
41A VAL* 3.6 3.1 - - + -
42A LEU* 3.2 19.1 + - - +
43A SER* 3.1 15.6 + - - +
45A ALA* 1.3 78.3 - - - +
47A GLY* 1.3 61.0 + - - +
49A PHE* 3.9 7.0 - - + -
50A VAL* 2.8 42.8 + - + +
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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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41A VAL* 3.3 22.1 - - - +
43A SER 3.1 13.8 + - - -
44A GLY 4.5 1.3 - - - -
46A GLU* 1.3 77.0 - - - +
48A SER* 1.3 59.8 + - - +
50A VAL* 4.3 2.1 - - - +
51A SER* 3.4 20.6 + - - -
92A TYR* 4.9 8.3 - - - -
111A LEU* 5.2 3.1 - - - +
117A PHE 4.2 4.3 - - - +
118A LEU* 4.1 6.3 - - - +
120A TRP* 5.6 4.3 - - - -
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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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44A GLY 3.6 17.2 + - - -
45A ALA* 3.3 6.0 + - - -
46A GLU 3.1 0.6 - - - -
47A GLY* 1.3 75.9 - - - +
49A PHE* 1.3 65.7 + - - +
51A SER* 3.5 2.4 + - - -
52A SER* 3.2 21.5 + - - -
118A LEU* 4.0 20.6 - - - +
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Residues in contact with PHE 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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7A LYS* 3.6 51.6 + - + -
8A ALA 4.4 9.2 - - - -
9A TYR* 4.1 33.9 - + + -
14A TYR* 6.2 3.4 - + + -
45A ALA 2.8 17.9 + - - +
46A GLU* 3.0 9.8 + - + +
48A SER* 1.3 76.0 - - - +
50A VAL* 1.3 69.1 + - + +
52A SER* 3.2 8.1 + - - -
53A LEU* 3.0 20.9 + - + +
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Residues in contact with VAL 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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14A TYR* 5.2 6.7 - - + -
39A VAL* 3.5 35.4 - - + -
40A SER 4.2 1.8 - - - +
41A VAL* 4.7 3.8 - - + -
46A GLU* 2.8 37.6 + - + +
47A GLY* 4.3 3.8 - - - +
49A PHE* 1.3 76.8 - - + +
51A SER* 1.3 63.5 + - - +
53A LEU* 3.0 19.8 + - + +
54A VAL* 3.1 13.6 + - + +
66A ILE* 5.3 0.9 - - + -
111A LEU* 4.4 21.3 - - + -
132A VAL* 4.3 20.0 - - + -
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Residues in contact with SER 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 GLY 3.4 13.5 + - - -
48A SER 3.6 6.0 + - - -
49A PHE 3.2 0.6 - - - -
50A VAL* 1.3 79.7 - - - +
52A SER* 1.3 59.0 + - - +
54A VAL* 3.2 4.4 + - - +
55A LYS* 2.8 36.4 + - - +
111A LEU* 5.1 1.3 - - - +
116A ALA 2.8 22.2 + - - -
117A PHE* 3.4 33.1 - - - +
118A LEU* 3.7 10.7 - - - +
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Residues in contact with SER 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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7A LYS* 4.5 9.4 + - - -
48A SER 3.2 9.6 + - - -
49A PHE* 3.2 12.1 + - - -
51A SER* 1.3 80.5 + - - +
53A LEU* 1.3 61.6 + - - +
55A LYS* 3.7 28.4 + - - +
56A SER* 4.5 6.6 + - - -
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Residues in contact with LEU 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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5A GLY 3.9 19.1 - - - +
7A LYS* 3.7 33.0 - - + +
14A TYR* 4.3 15.3 - - + +
15A ALA 4.9 0.4 - - - +
16A LEU* 3.8 25.4 - - + +
49A PHE* 3.0 15.2 + - + +
50A VAL* 3.0 16.0 + - + +
52A SER* 1.3 77.9 - - - +
54A VAL* 1.3 65.9 + - + +
56A SER* 4.5 7.2 + - - -
132A VAL* 3.5 36.8 - - + -
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Residues in contact with VAL 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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16A LEU* 3.9 19.7 - - + -
50A VAL* 3.2 16.6 - - + +
51A SER* 3.6 10.8 - - - +
53A LEU* 1.3 87.6 - - + +
55A LYS* 1.3 56.8 + - - +
56A SER 3.2 6.2 + - - +
57A ILE* 3.5 20.1 - - + +
64A VAL* 4.2 19.3 - - + -
111A LEU* 4.4 8.5 - - + -
117A PHE* 3.7 24.7 - - + -
132A VAL* 3.2 35.0 - - + -
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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