Contacts of the helix formed by residues 50 - 58 (chain A) in PDB entry 1X0X
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 LEU 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A SER* 5.8 0.4 - - - +
40A VAL* 4.1 17.5 - - + -
41A PHE 4.7 0.7 - - - +
42A GLU* 2.9 8.6 + - - +
43A GLU* 3.0 47.6 + - + +
45A ILE* 4.2 17.5 - - + +
48A LYS 3.7 0.6 + - - -
49A LYS* 1.3 71.2 - - - +
51A THR* 1.3 63.7 + - - +
53A ILE* 3.1 18.6 + - + +
54A ILE* 3.1 37.4 + - + +
60A ASN* 3.7 30.5 - - - +
62A LYS* 5.3 4.9 - - + +
63A TYR* 4.3 7.6 - - + -
2001A NAD 6.1 0.4 - - - +
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Residues in contact with THR 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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40A VAL* 3.8 28.5 - - + +
42A GLU* 2.4 43.2 + - - +
49A LYS* 3.9 5.9 - - - +
50A LEU* 1.3 78.2 - - - +
52A GLU* 1.3 63.4 + - - +
54A ILE* 4.7 0.9 - - - -
55A ASN* 2.9 34.9 + - - -
75A ALA* 3.6 13.2 - - + +
77A PRO* 3.6 32.5 - - + +
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Residues in contact with GLU 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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48A LYS* 5.6 3.0 - - + +
49A LYS* 3.0 49.0 + - + +
51A THR* 1.3 80.1 + - - +
53A ILE* 1.3 66.9 + - + +
55A ASN* 3.5 4.6 + - - +
56A THR* 3.0 32.5 + - - +
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Residues in contact with ILE 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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45A ILE* 5.0 14.6 - - + -
48A LYS* 3.2 44.4 - - + -
49A LYS 3.2 14.0 + - - +
50A LEU* 3.1 21.7 + - + +
52A GLU* 1.3 75.3 - - + +
54A ILE* 1.3 55.4 + - - +
56A THR* 3.1 3.8 + - - -
57A GLN* 2.6 59.5 + - + +
59A GLU* 4.3 13.2 - - + +
61A VAL* 5.8 6.7 - - + -
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Residues in contact with ILE 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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38A MET* 4.2 11.0 - - + -
40A VAL* 3.9 26.9 - - + -
50A LEU* 3.1 32.6 + - + +
53A ILE* 1.3 79.0 - - - +
55A ASN* 1.3 59.7 + - - +
58A HIS* 2.6 36.6 + - - +
59A GLU 3.9 20.0 - - - +
60A ASN* 3.9 24.5 - - + +
69A LEU* 4.1 21.5 - - + -
73A VAL 5.1 5.8 - - - +
75A ALA* 3.7 20.0 - - + +
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Residues in contact with ASN 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 THR* 2.9 23.9 + - - +
52A GLU* 4.2 5.0 - - - +
53A ILE 3.4 0.2 - - - -
54A ILE* 1.3 76.3 - - - +
56A THR* 1.3 58.9 + - - +
58A HIS* 3.3 24.1 + - + -
73A VAL 4.1 3.1 - - - +
74A VAL* 3.6 13.1 - - - +
75A ALA* 2.6 48.5 + - - +
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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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52A GLU* 3.0 20.5 + - - +
53A ILE* 3.6 2.2 - - - -
55A ASN* 1.3 80.5 - - - +
57A GLN* 1.3 79.1 + - + +
58A HIS* 3.3 12.5 + - - -
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Residues in contact with GLN 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 ILE* 2.6 38.8 + - + +
56A THR* 1.3 88.5 - - + +
58A HIS* 1.3 72.0 + - - +
59A GLU* 3.3 26.9 + - + +
68A LYS* 3.2 22.7 + - - +
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Residues in contact with HIS 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 ILE* 2.6 28.9 + - - +
55A ASN* 3.3 27.9 + - + -
56A THR 3.8 11.3 + - - -
57A GLN* 1.3 76.2 - - - +
59A GLU* 1.3 55.4 + - - +
68A LYS* 3.3 10.5 - - - +
69A LEU* 2.7 47.2 + - - +
70A PRO 4.6 2.0 + - - -
71A PRO* 3.6 47.1 + - + +
73A VAL 4.8 6.2 + - - -
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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