Contacts of the helix formed by residues 47 - 58 (chain A) in PDB entry 5X6G
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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45A LYS 3.3 2.6 + - - -
46A LYS* 1.3 71.1 - - - +
48A ALA* 1.3 63.8 + - - +
50A GLU* 3.1 29.2 + - - +
51A GLU* 3.1 24.3 + - - +
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Residues in contact with ALA 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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42A LEU* 3.6 40.8 - - + +
45A LYS* 3.5 18.2 + - + +
46A LYS 3.2 4.6 + - - +
47A GLY* 1.3 79.6 - - - +
49A MET* 1.3 57.7 + - - +
51A GLU* 3.3 6.2 + - - +
52A LEU* 2.8 30.4 + - - +
66A VAL* 4.1 9.5 - - + +
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Residues in contact with MET 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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39A VAL* 3.5 37.2 - - + -
42A LEU* 3.9 26.4 + - + +
43A LYS* 4.2 23.1 - - + +
45A LYS 5.0 0.4 + - - -
48A ALA* 1.3 74.2 - - - +
50A GLU* 1.3 71.1 + - - +
52A LEU* 3.2 10.2 + - + +
53A GLU* 2.8 48.5 + - + +
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Residues in contact with GLU 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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47A GLY* 3.1 27.9 + - - +
48A ALA 3.7 0.2 + - - -
49A MET* 1.3 87.0 + - - +
51A GLU* 1.3 57.9 + - - +
53A GLU* 3.4 12.2 - - - +
54A LYS* 2.8 27.8 + - - +
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Residues in contact with GLU 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 3.1 18.8 + - - +
48A ALA* 3.5 6.1 - - - +
50A GLU* 1.3 75.1 - - - +
52A LEU* 1.3 66.1 + - - +
54A LYS* 2.9 33.9 + - - +
55A ALA* 3.0 13.2 + - - +
63A SER* 3.5 9.5 - - - -
64A LYS* 2.7 53.1 + - + +
65A CYS 4.6 2.5 - - - +
66A VAL* 3.7 19.5 - - + -
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Residues in contact with LEU 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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35A VAL* 6.3 0.2 - - + -
38A LEU* 3.8 26.7 - - + -
39A VAL* 6.0 3.1 - - + -
42A LEU* 3.8 11.2 - - + -
48A ALA 2.8 21.0 + - - +
49A MET* 3.8 10.5 - - + +
51A GLU* 1.3 73.6 - - - +
53A GLU* 1.3 64.0 + - - +
55A ALA* 3.2 12.7 + - + +
56A LEU* 3.3 27.2 + - + +
66A VAL* 3.8 25.0 - - + +
93A TRP* 4.0 15.5 - - + -
123A ILE* 4.5 9.2 - - + -
124A ASN* 5.1 0.7 - - - -
125A PRO* 4.5 22.0 - - + -
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Residues in contact with GLU 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 MET* 2.8 34.3 + - + +
50A GLU* 3.4 10.0 - - - +
52A LEU* 1.3 79.3 - - - +
54A LYS* 1.3 53.2 + - - +
56A LEU* 4.2 5.9 - - - +
57A SER* 2.6 39.0 + - - +
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Residues in contact with LYS 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 GLU 2.8 16.2 + - - +
51A GLU* 2.9 38.9 + - - +
53A GLU* 1.3 74.1 - - - +
55A ALA* 1.3 66.0 + - - +
57A SER* 3.2 5.1 + - - -
58A SER* 2.9 32.9 + - - +
61A GLN* 4.4 18.2 + - - +
62A PRO 2.9 27.6 + - - -
63A SER* 4.3 3.3 - - - +
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Residues in contact with ALA 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 GLU 3.0 9.8 + - - +
52A LEU* 3.2 10.7 + - + +
54A LYS* 1.3 78.6 - - - +
56A LEU* 1.3 65.2 + - + +
58A SER 3.4 18.2 - - - +
59A PRO* 3.7 7.8 - - - +
63A SER* 3.2 31.4 - - - +
66A VAL* 6.0 0.2 - - + -
124A ASN* 3.7 23.1 - - - +
126A TYR* 3.9 14.2 - - + -
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Residues in contact with LEU 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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52A LEU* 3.3 28.8 + - + +
53A GLU* 4.3 4.5 - - - +
55A ALA* 1.3 79.1 - - + +
57A SER* 1.3 62.1 + - - +
59A PRO* 3.9 11.8 - - - +
93A TRP* 3.6 65.1 - - + +
125A PRO* 3.8 20.6 - - + -
126A TYR* 3.9 17.2 + - + -
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Residues in contact with SER 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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53A GLU* 2.6 27.3 + - - +
54A LYS* 3.2 8.7 + - - -
56A LEU* 1.3 79.1 - - - +
58A SER* 1.3 66.1 + - - +
59A PRO* 3.3 9.2 - - - +
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Residues in contact with SER 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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54A LYS* 2.9 19.1 + - - +
55A ALA* 3.4 8.9 - - - +
57A SER* 1.3 82.7 + - - +
59A PRO* 1.3 67.0 - - - +
60A GLY 3.5 2.6 + - - -
61A GLN* 3.4 43.5 + - - +
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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